HB-0804-010_1108754_UM_IAS_QX_Advanced_1117_WW

November 2017
QIAxcel Advanced
User Manual
For use with QIAxcel ScreenGel Software v1.6
Sample to Insight
Contents
Safety..............................................................................................................1
information
Proper use
......................................................................................................1
Electrical safety
......................................................................................................2
Environment
......................................................................................................3
Chemicals
......................................................................................................4
Waste disposal
......................................................................................................5
Mechanical hazards
......................................................................................................5
Symbols on the QIAxcel Advanced
......................................................................................................6
Introduction
..............................................................................................................7
About......................................................................................................7
this user manual
General information
......................................................................................................8
Intended use of the QIAxcel Advanced
......................................................................................................8
Requirements for QIAxcel Advanced users
.......................................................................................9
General description
..............................................................................................................10
QIAxcel Advanced principle
......................................................................................................10
External features of the QIAxcel Advanced
......................................................................................................11
Gel......................................................................................................12
cartridges
Computer and software
......................................................................................................13
Installation procedures
..............................................................................................................15
Requirements
......................................................................................................15
Site .......................................................................................15
Power.......................................................................................16
requirements
Grounding requirements
.......................................................................................16
Unpacking the QIAxcel Advanced
......................................................................................................17
Installing the QIAxcel Advanced
......................................................................................................18
Releasing the transport lock
.......................................................................................18
QIAxcel Advanced User Manual 11/2017 2

Instrument setup
.......................................................................................18
Installation of AC power cord

.......................................................................................19
Installation of the N2 cylinder
.......................................................................................19
Installation of the QIAxcel ScreenGel Software
.......................................................................................20
First-time installation from a CD
.............................................................................20
Updating the.............................................................................22
QIAxcel ScreenGel Software
Re-installation.............................................................................24
from a CD
Uninstall software
.............................................................................26
Getting started with the QIAxcel ScreenGel Software
.......................................................................................27
Packing the QIAxcel Advanced
......................................................................................................28
Operating procedures
..............................................................................................................29
Unpacking a QIAxcel Kit
......................................................................................................29
Setting up the QIAxcel Advanced
......................................................................................................31
Preparing the buffer tray
.......................................................................................31
Loading the buffer tray
.......................................................................................33
Installing a QIAxcel gel cartridge and smart key
.......................................................................................34
Removing a QIAxcel gel cartridge
.......................................................................................36
Storing.......................................................................................36
a QIAxcel gel cartridge
Operating the QIAxcel Advanced
......................................................................................................37
Things.......................................................................................38
to do before starting
Starting a run
.......................................................................................38

..............................................................................................................50
Concepts
......................................................................................................50
Modes.......................................................................................51
User roles
.......................................................................................52
Environments
.......................................................................................53
Profiles.......................................................................................54
General software usage
.......................................................................................55
Editing data in tables
.............................................................................57

Displaying errors and warnings
.............................................................................58
Displaying modifications
.............................................................................60
Getting help .............................................................................64
User......................................................................................................66
authentication
Process
......................................................................................................70
Running a process with advanced options
.......................................................................................71
Provide sample information
.............................................................................79
Modifying a process profile

.......................................................................................83
Process profile options
.......................................................................................86
Selecting general process options
.............................................................................87
Selecting run .............................................................................90
parameters
Selecting analysis parameters
.............................................................................94
Selecting marker
.............................................................................95
Selecting peak calling instructions
.............................................................................98
Selecting distribution profiles
.............................................................................99
Selecting report/export parameters
.............................................................................102
Run parameters and result structure
.............................................................................104
Creating a new process profile
.......................................................................................107
Viewing method details
.......................................................................................109
Status information panel
.......................................................................................111
Analysis
......................................................................................................114
Introduction into analysis
.......................................................................................115
Handling samples and experiments
.......................................................................................116
Meaning of.............................................................................118
sample icons
Loading sample data
.............................................................................118
Selecting samples
.............................................................................120
Selecting samples for analysis or report
.............................................................................122
Expanding and collapsing
.............................................................................123
Activating an experiment
.............................................................................123
Saving an experiment
.............................................................................124

Closing an experiment
.............................................................................126
Importing BioCalculator Data

.............................................................................126
Revising sample information
.............................................................................127
Handling an.............................................................................128
incomplete experiment
Viewing sample data
.......................................................................................129
Adding samples to views
.............................................................................129
Removing samples from views
.............................................................................133
Exporting view to clipboard

.............................................................................135
Direct printing view
.............................................................................136
Result table .............................................................................137
Gel view .............................................................................145
Electropherogram view
.............................................................................148
Electropherogram overview
.............................................................................155
Electropherogram superposition view
.............................................................................160
Inspecting sample properties
.............................................................................163
Saturated signals
.............................................................................165
Peak.......................................................................................166
detection
Peak detection procedure
.............................................................................167
Modifying an analysis profile
.............................................................................171
Creating a new analysis profile
.............................................................................177
Size .......................................................................................177
and concentration determination
Size and concentration determination
procedure .............................................................................179
Creating a reference marker
.............................................................................182
Creating a new size marker table
.............................................................................186
Peak.......................................................................................188
Calling
Activating peak calling features
.............................................................................191
Modifying a.............................................................................191
peak calling instruction
Creating a new peak calling instruction
.............................................................................194
Peak pattern.............................................................................195
matching

Analysis of DNA samples
.......................................................................................196
Standard DNA analysis

.............................................................................197
Fast Analysis.............................................................................200
DNA analysis
Smear DNA.............................................................................202
analysis
gDNA analysis
.............................................................................205
Distribution analysis
.............................................................................208
Analysis of RNA samples
.......................................................................................218
Standard RNA analysis

.............................................................................219
RNA quality.............................................................................221
control analysis
Manually modifying analysis results
.......................................................................................224
Modifying the threshold
.............................................................................224
Deleting a peak
.............................................................................224
Adding a peak
.............................................................................224
Removing analysis results
.............................................................................225
Checking alignment marker
.............................................................................227
Modifying areas of interest
.............................................................................227
Reusing used analysis parameters
.............................................................................227
Reanalysis of multiple experiments
.......................................................................................229
Customizing experiments
.......................................................................................231
Creating a new experiment
.............................................................................232
Modifying an experiment
.............................................................................233
Report/Export
.......................................................................................236
Generating .............................................................................237
a report
Report options
.............................................................................238
Exporting data
.............................................................................257
Export options
.............................................................................258
Modifying a.............................................................................268
report/export profile
Creating a new report/export profile
.............................................................................269
Service
......................................................................................................270
Calibrating a cartridge
.......................................................................................271

Running the.............................................................................272
calibration wizard
Recalibrating a cartridge
.............................................................................274
System check
.......................................................................................274
Complete check
.............................................................................274
Detector test.............................................................................276
Filter check .............................................................................277
Movement check
.............................................................................278
Leakage test.............................................................................279
Maintenance
.......................................................................................280
Purge .............................................................................280
Long purge .............................................................................281
Empty N2 bottle
.............................................................................282
Setting the instrument ID
.............................................................................283
Troubleshooting folder and log files
.............................................................................283
Configuration
......................................................................................................286
Settings
.......................................................................................286
Profile management
.......................................................................................292
User .......................................................................................293
management
Maintenance procedures
..............................................................................................................295
Cleaning of the QIAxcel Advanced
......................................................................................................295
Minor corrective maintenance
......................................................................................................296
Fuse .......................................................................................296
replacement and cleaning
N2 cylinder replacement
.......................................................................................297
Alternate N2 supply
.......................................................................................297
Blocked purge filter
.......................................................................................298
Troubleshooting
..............................................................................................................300
System setup
......................................................................................................300
Operation
......................................................................................................302
DNA applications
......................................................................................................303

RNA applications
......................................................................................................306
Glossary
..............................................................................................................308
Appendices
..............................................................................................................310
Appendix A
......................................................................................................310
Appendix B
......................................................................................................314
Appendix C
......................................................................................................321
Appendix D
......................................................................................................324
Appendix E
......................................................................................................329
Appendix F
......................................................................................................330
Appendix G
......................................................................................................336
Appendix H
......................................................................................................342

Safety information
Before using the QIAxcel Advanced, it is essential that you read this user manual carefully and pay
particular attention to the safety information. The instructions and safety information in the user manual must
be followed to ensure safe operation of the instrument and to maintain the instrument in a safe condition.
The following types of safety information appear throughout this manual:
WARNING The term WARNING is used to inform you about situations that could result in
personal injury to you or other persons.
Details about these circumstances are given in a box like this one.
CAUTION The term CAUTION is used to inform you about situations that could result in
damage to the instrument or other equipment.
Details about these circumstances are given in a box like this one.
The advice given in this manual is intended to supplement, not supersede, the normal safety requirements
prevailing in the user’s country.
Proper use
WARNING/ Risk of personal injury and material damage [W1]

CAUTION
Improper use of the QIAxcel Advanced may cause personal injuries or damage to
the instrument.
The QIAxcel Advanced must only be operated by qualified personnel who have
been appropriately trained.
Servicing of the QIAxcel Advanced must only be performed by QIAGEN Field

Service Specialists.
Perform the maintenance as described in the Maintenance Procedures section. QIAGEN charges for repairs
that are required due to incorrect maintenance.

CAUTION
The QIAxcel Advanced is too heavy to be lifted by one person. To avoid personal
injury or damage to the instrument, do not lift the instrument alone.
In case of emergency, switch off the QIAxcel Advanced at the power switch at the rear of the instrument
and unplug the power cord from the power outlet.
CAUTION Damage to the instrument [C1]
If the Pressure 1 status is Low, increase system pressure before performing the
unlatch command. Removing the cartridge and unlatching with reduced pressure
may damage the instrument.
Do not use bleach, solvents, or reagents containing acids, alkalis, or abrasives to

clean the QIAxcel Advanced.
Electrical safety
Disconnect the line power cord from the power outlet before servicing.
WARNING Electrical hazard [W3]
Any interruption of the protective conductor (earth/ground lead) inside or outside

the instrument or disconnection of the protective conductor terminal is likely to make
the instrument dangerous.
Intentional interruption is prohibited.
Lethal voltages inside the instrument

When the instrument is connected to line power, terminals may be live, and opening
covers or removing parts is likely to expose live parts.
To ensure satisfactory and safe operation of the QIAxcel Advanced, follow the advice below:
The line power cord must be connected to a line power outlet that has a protective conductor (earth/
ground).

Do not adjust or replace internal parts of the instrument.
Do not operate the instrument with any covers or parts removed.
If liquid has spilled inside the instrument, switch off the instrument, disconnect it from the power outlet,
and contact QIAGEN Technical Services.
When replacing the main fuse, replace only with the type and current rating specified on the rating label.
If the instrument becomes electrically unsafe, prevent other personnel from operating it, and contact
QIAGEN Technical Services. The instrument may be electrically unsafe when:
The line power cord appears to be damaged.
It has been stored under unfavorable conditions for a prolonged period.
It has been subjected to severe transport stresses.
Environment
Operating conditions
WARNING Explosive atmosphere [W4]
The QIAxcel Advanced is not designed for use in an explosive atmosphere.
WARNING Risk of explosion [W5]
The QIAxcel Advanced is intended for use with reagents and substances supplied
with the QIAGEN QIAxcel Kits. Use of other reagents and substances may lead to
fire or explosion.
Direct sunlight may bleach parts of the instrument and cause damage to plastic
parts.
The QIAxcel Advanced must be located out of direct sunlight.

CAUTION Damage to the cartridge [C4]
When in use, the gel cartridge should not be left out of the Wash park position of
the buffer tray for more than 15 minutes. Failure to do so will cause the capillary
tips to dry out, affecting correct function of the cartridge. Dry tips will void the
warranty.
The capillary tips are made of glass and are very fragile. Take care not to knock
the tips on any hard surfaces. Failure to do so will cause the capillary tips to break,
affecting correct function of the cartridge. Broken tips will void the warranty.
If less than 12 samples are processed, fill the empty sample wells with the QX DNA
Dilution Buffer or QX RNA Dilution buffer. Failure to do so may cause damage to
the capillary channels.
Chemicals
WARNING Hazardous chemicals [W6]
Some chemicals used with this instrument may be hazardous or may become
hazardous after completion of the protocol run.
Always wear safety glasses, gloves, and a lab coat.
The responsible body (e.g., laboratory manager) must take the necessary
precautions to ensure that the surrounding workplace is safe and that the instrument
operators are not exposed to hazardous levels of toxic substances (chemical or
biological) as defined in the applicable Safety Data Sheets (SDSs) or OSHA* ,
ACGIH † or COSHH ‡ documents.
Venting for fumes and disposal of wastes must be in accordance with all national,
state, and local health and safety regulations and laws.
* OSHA: Occupational Safety and Health Administration (United States of America).

† ACGIH: American Conference of Government Industrial Hygienists (United States of America).
‡ COSHH: Control of Substances Hazardous to Health (United Kingdom).
WARNING Risk of fire [W7]
When cleaning the QIAxcel Advanced with alcohol-based disinfectant, leave the
QIAxcel Advanced doors open to allow flammable vapors to disperse.

Waste disposal
Used labware and containers may contain hazardous chemicals. Such wastes must be collected and
disposed of properly according to local safety regulations.
For information on how to dispose of the QIAxcel Advanced, see Appendix A.
Mechanical hazards
The cartridge door and sample door of the QIAxcel Advanced must remain closed during operation of the
instrument.
WARNING Moving parts [W8]
To avoid contact with moving parts during operation of the QIAxcel Advanced, the
instrument must be operated with the cartridge door and sample door closed.
If the door sensors are not functioning correctly, contact QIAGEN Technical
Services.

Symbols on the QIAxcel Advanced
Symbol Location Description

Type plate on the back of the CE mark for European Conformity
instrument
Type plate on the back of the CSA listing mark for Canada and the USA
instrument
Type plate on the back of the Legal manufacturer

instrument
Type plate on the back of the Waste Electrical and Electronic Equipment (WEEE)
instrument
Type plate on the back of the FCC mark of the United States Federal Communications
instrument Commission
Type plate on the back of the RCM mark for Australia and New Zealand
instrument

Introduction
Thank you for choosing the QIAxcel Advanced. We are confident it will become an integral part of your
laboratory.
Before using the QIAxcel Advanced, it is essential that you read this user manual carefully and pay
particular attention to the safety information. The instructions and safety information in the user manual must
be followed to ensure safe operation of the instrument and to maintain the instrument in a safe condition.
About this user manual

This user manual provides information about the QIAxcel Advanced in the following sections:
Safety information
Introduction
General description
Troubleshooting
Glossary
Appendices
The appendices include the following:
Technical data
QIAxcel Advanced methods and accessories
Data analysis algorithm descriptions
Warranty liability clause

General information
Technical assistance
At QIAGEN, we pride ourselves on the quality and availability of our technical support. Our Technical
Services Departments are staffed by experienced scientists with extensive practical and theoretical expertise
in sample and assay technologies and the use of QIAGEN products. If you have any questions or
experience any difficulties regarding the QIAxcel Advanced or QIAGEN products in general, do not
hesitate to contact us.
QIAGEN customers are a major source of information regarding advanced or specialized uses of our
products. This information is helpful to other scientists as well as to the researchers at QIAGEN. We
therefore encourage you to contact us if you have any suggestions about product performance or new
applications and techniques.
For technical assistance and more information, please see our Technical Support Center at www.qiagen.
com/goto/TechSupportCenter or call one of the QIAGEN Technical Service Departments or local
distributors (see back cover or visit www.qiagen.com).
For up-to-date information about the QIAxcel Advanced system, visit www.qiagen.com/p/QIAxcel.
Policy statement
It is the policy of QIAGEN to improve products as new techniques and components become available.
QIAGEN reserves the right to change specifications at any time.
In an effort to produce useful and appropriate documentation, we would appreciate your comments on this
user manual. Please contact QIAGEN Technical Services.
Version management
This document is the QIAxcel Adv anced User M anual, version 7.0. Updated versions can be found at
www.qiagen.com/p/QIAxcel.
Intended use of the QIAxcel Advanced

The QIAxcel Advanced is a multicapillary electrophoresis instrument, designed to perform fast and fully
automated DNA fragment analysis, or qualitative and quantitative RNA analysis.
The QIAxcel Advanced instrument is intended to be used only in combination with QIAxcel Kits for
applications described in the respective QIAxcel Kit handbooks.
The QIAxcel Advanced instrument is intended for use by professional users, such as technicians and
physicians trained in molecular biological techniques and the operation of the QIAxcel Advanced
instrument.

Requirements for QIAxcel Advanced users
This table covers the general level of competence and training necessary for transportation, installation,
use, maintenance, and servicing of the QIAxcel Advanced.
Task Personnel Training and experience

Transportation No special requirements No special requirements
Installation Laboratory technicians or Appropriately trained and experienced

equivalent personnel familiar with use of computers and
automation in general
Instrument Laboratory technicians or Appropriately trained and experienced

administration equivalent personnel familiar with use of computers and
Routine use (running Laboratory technicians or Appropriately trained and experienced

profiles) equivalent personnel familiar with use of computers and
Analyzing data Laboratory technicians or Appropriately trained and experienced

Instrument maintenance Laboratory technicians or Appropriately trained and experienced

Servicing QIAGEN Field Service Specialists

only

General description
The QIAxcel Advanced system performs fully automated separation of DNA and RNA fragments according
to their molecular weight and can process up to 96 samples without user intervention. The QIAxcel
Advanced system consists of the QIAxcel Advanced instrument, a QIAxcel Kit (containing a QIAxcel gel
cartridge and reagents), a computer, and QIAxcel ScreenGel Software, which have been optimized to
work together across a wide variety of applications and provide unmatched resolution, speed, and
throughput for DNA fragment and RNA analysis.
The QIAxcel ScreenGel Software supplied with the QIAxcel Advanced provides both electropherograms
and gel images of the nucleic acid separation and can be used to perform the following types of analysis:
Determination of the size and concentration of DNA fragments
Determination of the 28S/18S ratio, concentration, and quality of total RNA, and the quality of cRNA/
cDNA and fragmented RNA/DNA
Note: We do not recommend determining nucleic acid concentration with the QIAxcel DNA Fast Analysis
Kit.
QIAxcel Advanced principle

The QIAxcel Advanced uses capillary electrophoresis to enable high resolution and sensitive separation of
DNA and RNA samples. This 12-channel capillary electrophoresis instrument uses disposable, multiple-use
cartridges for cost-effective analysis of up to 96 samples in as little as 25 minutes.
1. The QIAxcel Advanced is set up with a gel cartridge, running buffer and wash buffer, and calibrated
using intensity markers.
2. The samples for analysis (in a 96-well plate or 12-tube strips) are placed onto the sample plate holder.
3. Required data collection settings are selected and the samples pass through the capillaries of the
QIAxcel gel cartridge.
4. Data is analyzed using the QIAxcel ScreenGel Software.

External features of the QIAxcel Advanced
External features of the QIAxcel Advanced.
1 Sample door 8 N2 door
2 Cartridge door 9 Transport lock and buffer tray location
3 Service door 10 Sample plate holder
4 Power connection for AC 11 Cartridge bay

connection
5 Tube fitting for external N2 12 Slot for smart key

supply
6 RS232 connection 13 Digital pressure display
7 N2 regulator and cylinder 14 Purge filter
Note: If using an external N2 source, the output pressure must not exceed 75 psi. The QIAxcel Advanced is
equipped with an internal regulator that will regulate the pressure provided by the external N2 source to
approximately 40 psi (37–45 psi), which is the instrument’s operating pressure.

Gel cartridges
The QIAxcel Advanced can be operated using any of the QIAxcel Kits listed in the table below. Each kit
contains a gel cartridge that has been specifically developed for particular applications. Each gel cartridge
consists of a gel matrix with a proprietary linear polymer with ethidium bromide intercalating dye.
Kit Application
QIAxcel DNA High Analysis of DNA 15 bp – 10 kb in size. 96 samples can be

Resolution Kit (1200) analyzed in <1.5 hours.
QIAxcel DNA Screening Fast analysis of DNA

Kit (2400) 15 bp – 5 kb in size. 96 samples can be analyzed in just 40
minutes.
QIAxcel DNA Fast Analysis Kit Routine evaluation of DNA fragments in qualitative single or
(3000) multiplex PCR applications. 96 samples can be analyzed in
approximately 25 minutes.
QIAxcel RNA QC Kit v2.0 (1200) Analysis of RNA quality and quantity. 96 samples can be analyzed
in <1.5 hours
Each QIAxcel Kit contains the following additional reagents that are required for use of the QIAxcel
Advanced:
QX Intensity Calibration Marker – calibrates the signal intensity for each new gel cartridge
QX DNA or RNA Separation Buffer (QIAxcel DNA or RNA Kits) – enables separation of DNA or RNA
molecules
QX FA DNA Separation Buffer (QIAxcel DNA Fast Analysis Kit) – enables separation of DNA molecules
(only for use with the QIAxcel DNA Fast Analysis Cartridge)
QX Wash Buffer – for washing the capillary tips to prevent cross-contamination
QX DNA or RNA Dilution Buffer – for optimization of sample concentration
QX Mineral Oil – for covering solutions and/or samples to prevent evaporation
QX Alignment Marker – used in every run to equalize the migration time variation across all channels
(included in the QIAxcel RNA QC Kit v2.0 and QIAxcel Fast Analysis Kit only; for all other kits, see
ordering information, Appendix C)
Note: QIAxcel DNA Size Marker is required for use with QIAxcel DNA Kits only. This enables creation of a
reference marker table allowing DNA size and concentration to be determined (not included in kit; see
ordering information, Appendix C). QIAxcel RNA Size Marker is provided with the QIAxcel RNA QC Kit
v2.0.

Computer and software
The QIAxcel Advanced is shipped with the QIAxcel ScreenGel Software.
A computer with the correct specifications for operation of the QIAxcel Advanced instrument and QIAxcel
ScreenGel Software is supplied as part of the QIAxcel Advanced system. However, if a different computer
is used to operate the QIAxcel Advanced instrument or run the QIAxcel ScreenGel Software, then the
following requirements are necessary:
Computer specifications:
At least 2.3 GHz CPU
Minimum 80 GB free hard drive capacity, NTFS formatted
At least 2 GB RAM (recommended 4 GB RAM)
1024 x 768 screen resolution or higher
9-PIN Serial Port or I/O card (not provided, contact QIAGEN Technical Services for more information).
DVD/CD-ROM
Pointer device (mouse or similar)

®
Windows 7 Professional (32 or 64 bit) with service pack 1 or higher; Windows 10 (64 bit) with
minimum required version 1607
Adobe® Reader® Software 8.2 or higher (for reading PDF reports)
To view reports in PDF format, a PDF reader must be installed on the computer. Adobe Reader can be
downloaded at www.adobe.com.
Additional configuration steps:
Turn off all automatic processes or services, such as indexing or similar, which could produce a high
workload, especially when connecting to the QIAxcel Advanced instrument.
Ensure that energy saving options and hibernation are deactivated during the operation of the QIAxcel
Advanced.
For Windows 10 only – if UEFI Boot is used, the Secure Boot option must be disabled. Otherwise, the
Device Driver Installation of the QIAxcel Advanced device driver will fail during installation of the
QIAxcel ScreenGel Software.
Note: In case of any concern regarding the Windows configuration, please contact your local IT support.
If connecting the computer to a network, be sure to consider the following:

Ensure that update processes are scheduled to download and install only outside the operating times of
the QIAxcel Advanced.
Turn off auto-restart after an installation of Windows security patches to prevent automatic computer
restart during the operating times of the QIAxcel Advanced.
Note: In order to complete a security update installation, perform a manual restart later.
If virus protection software is required, ensure that the following tasks are scheduled to run outside the
operating times of the QIAxcel Advanced:
Scans (also ensure that files that are created by the QIAxcel ScreenGel are not scanned during creation
or on access)
All kind of updates (download and installation)
Note: The QIAxcel ScreenGel is tested by QIAGEN using the original image supplied with your laptop
without connecting the laptop to the Internet. Updates on your operating system might lead to unexpected
behavior of the QIAxcel ScreenGel. In such cases, please contact your local IT support.
Note: The minimal screen resolution can be used in combination with small fonts. However, medium size
fonts can be used in combination with an improved resolution (e.g., the medium font size (125%) setting in
Windows 7 requires a minimum screen resolution of 1400 x 1050). Larger font sizes are not supported.

This section provides instructions on unpacking and installing the QIAxcel Advanced.
Requirements
This section of the QIAxcel Adv anced User M anual specifies the requirements for operating the QIAxcel
Advanced.
Site
The QIAxcel Advanced must be located out of direct sunlight, away from heat sources, and away from
sources of vibration and electrical interference. Refer to Appendix A for the operating conditions
(temperature and humidity). The site of installation should be free of excessive drafts, excessive moisture,
excessive dust, and not subject to large temperature fluctuations.
Use a level workbench that is large enough to accommodate the QIAxcel Advanced and computer. Refer to
Appendix A for the weight and dimensions of the QIAxcel Advanced.
Ensure that the workbench is dry, clean, vibration-proof, and has additional space for accessories.
Approximately 72 cm (28 in.) clearance above the workbench is recommended to allow cartridge loading.
The QIAxcel Advanced must be placed within approximately 1.5 m (4.92 ft.) of a properly grounded
(earthed) AC power outlet. The power line to the instrument should be voltage regulated and surge
protected.
Ensure that the switch and the main power input socket at the rear of the instrument are easily reachable.
Maintain sufficient clearance at the rear to unplug the power line from the main power input socket.
Note: We recommend plugging the instrument directly into its own wall socket and not to share the socket
with other lab equipment. To achieve proper capillary electrophoresis separation, do not place the QIAxcel
Advanced on a vibrating surface or near vibrating objects.
WARNING Explosive atmosphere [W9]
The QIAxcel Advanced is not designed for use in an explosive atmosphere.

WARNING Risk of overheating [W10]
To ensure proper ventilation, maintain a minimum clearance of 10 cm (3.94 in.) at

the sides and rear of the QIAxcel Advanced.
Slits and openings that ensure the ventilation of the QIAxcel Advanced must not be
covered.
Power requirements
The QIAxcel Advanced operates at 100–240 V AC, 50–60 Hz, 360 VA.
Ensure that the voltage rating of the QIAxcel Advanced is compatible with the AC voltage available at the
installation site. Main supply voltage fluctuations are not to exceed 10% of nominal supply voltages.
Grounding requirements
To protect operating personnel, the instrument is equipped with a 3-conductor AC power cord. To preserve
this protection feature, do not operate the instrument from an AC power outlet that has no ground (earth)
connection.
For replacement of the 3-conductor AC power cord, contact QIAGEN Technical Services for an authorized
spare part.

Unpacking the QIAxcel Advanced
Before unpacking the QIAxcel Advanced, move the package to the site of installation and check that the
arrows on the package point upward. In addition, check whether the package is damaged. In case of
damage, contact the transporter of the package.
When lifting up the QIAxcel Advanced, slide your fingers under both sides of the instrument and keep your
back straight.

CAUTION
After unpacking the QIAxcel Advanced, check that the following documents are supplied:
Packing list
Warranty registration form
Quick-start guide
Read the packing list to check that you have received all items. If anything is missing, contact QIAGEN
Technical Services.
The QIAxcel Adv anced User M anual is available on the software CD in PDF format.
Check that the QIAxcel Advanced is not damaged and that there are no loose parts. If anything is
damaged, contact QIAGEN Technical Services. Make sure that the QIAxcel Advanced has equilibrated to
ambient temperature before operating it.
Retain the package in case you need to transport or ship the QIAxcel Advanced in the future. Instructions
for packing the QIAxcel Advanced are given in section Packing the QIAxcel Advanced. Using the original
package minimizes damage during transportation of the QIAxcel Advanced.
Carefully place the QIAxcel Advanced onto the workbench where it will be used. For site requirements,
please refer to section Requirements.

Installing the QIAxcel Advanced
Before operating the QIAxcel Advanced:
The transport lock must be removed
The power cord must be installed
The N2 cylinder or an external N2 supply must be installed
Releasing the transport lock
The QIAxcel Advanced is delivered with a transport lock that secures the tray/transport mechanism during
shipment. This transport lock must be removed before the QIAxcel Advanced can be operated.
Note: Please reinstall the transport lock whenever shipping the instrument.
Remove the transport lock as follows:
1. Open the sample door.
2. Release the transport lock securing the buffer tray/sample plate holder.
3. Keep the transport lock in case you need to transport the QIAxcel Advanced in the future.
Removing the transport lock.
Instrument setup
Set up the QIAxcel Advanced as follows:
1. Set up the computer and monitor as described in the computer installation instructions provided with the
computer.
2. Connect the RS232 serial cable from the instrument to the computer.

Installation of AC power cord
Connect the QIAxcel Advanced to the power outlet as follows:
1. Ensure that the power switch of the QIAxcel Advanced is set to the off position.
2. Check that the voltage rating on the label at the back of the QIAxcel Advanced matches the voltage
available at the installation site.
3. Plug the power cord into the power cord socket at the rear of the instrument.
4. Plug the power cord into a grounded power outlet.
Installation of the N2 cylinder
Important: Use only N2 cylinders provided by QIAGEN (cat. no. 929705).
1. Ensure that the power switch of the QIAxcel Advanced is set to the off position.
2. Open the N2 door and gently pull up on the N2 cylinder port. Do not pull past the detent hole.
3. Screw the N2 cylinder into the port clockwise.
4. Turn until the needle inside the port punctures the N2 cylinder. Do not overtighten; the cylinder should
only be finger tight.
5. Gently push down on the N2 cylinder until it is in its stowed (down) position.
6. Close the N2 door.
Alternatively, use an external N2 supply and attach to the rear of the instrument.

Installation of the QIAxcel ScreenGel Software
The QIAxcel ScreenGel version 1.6 is the first version supporting Windows 10 (64 bit). The QIAxcel
ScreenGel must be installed before the QIAxcel Advanced is connected to the computer for the first time. A
user with Windows administrator privileges is required to install the QIAxcel ScreenGel, but such privileges
are required for software installation only.
For computer system requirements, see section Computer and software.
1. Set up the computer as described in the computer installation instructions provided with the computer.
2. Before installing the QIAxcel ScreenGel, shut down all other software and make sure that the QIAxcel
Advanced is not connected to the computer.
3. If a previous version of the QIAxcel ScreenGel Software is already installed on the computer, refer to
Updating the QIAxcel ScreenGel Software. A dedicated update package is available to update the
software. In this case it is not possible to install the QIAxcel ScreenGel software from a CD. If the
software shall be installed for the first time, follow the instructions in First-time installation from a CD. A
first-time installation is possible from a CD, only. If you have previously installed any version of the
QIAxcel ScreenGel Software and need to install it again from a CD, follow the re-installation
procedure.
Note: Default settings are recommended where appropriate for all installation steps.
We recommend having no other software installed on the computer that controls the QIAxcel Advanced
other than the QIAxcel ScreenGel. In particular, the BioCalculator Software should not be installed.
However, if it is needed to have both software installed on the same computer for a period of time,
consider the following:
Ensure that you open only one software at a time.
If switching between QIAxcel ScreenGel and BioCalculator Software to run the QIAxcel Advanced, close
the open software, turn the QIAxcel Advanced off at the power switch, wait for 20 seconds and then turn
it on again before launching the other software. A computer restart might be necessary if the connection
to the instrument isn't working.
First-time installation from a CD
To install the QIAxcel ScreenGel Software from a CD for the first time, follow the steps below.
If a previous version of the software is already installed on the computer, it is not possible to install the
QIAxcel ScreenGel Software from a CD. Refer to section Installation of the QIAxcel ScreenGel Software.
Things to do before starting:
1. Ensure that the computer meets the minimum requirements (see Computer and software).
2. Use a Windows account with administrator privileges.
Note: Windows administrator privileges are required for software installation only.

3. Close any programs running on the computer and make sure that the QIAxcel Advanced is not connected
to the computer (i.e., unplug the cable from the computer).
To install the software for the first time from CD:
4. Place the CD in the computer’s CD-ROM drive.
5. The setup wizard will automatically start installing the QIAxcel ScreenGel Software and will guide you
through the setup process. Select the language from the drop-down box.
Important: If the setup wizard does not start automatically, double-click on My Computer and double-click
on the CD-ROM drive. Launch the setup.exe program. This will start the QIAxcel ScreenGel Software
installation.
Note: Default settings are recommended where appropriate for all installation steps.
Note: It is possible to switch the language of the installed software later using the File menu.
6. Select the option Install QIAxcel ScreenGel Software to start the actual installation procedure.
Note: Select the option User Manual to read the user manual in the selected language.
7. The Microsoft Visual C++ 2010 x 86 Redistributable will be installed if it is not already present. In this
case, another dialog opens. Accept the license agreement and click Install. Click Finish to complete the
installation of this package. If you cancel or close the dialog before, the QIAxcel ScreenGel will not be
able to operate.
8. The appropriate version of the Microsoft .NET Framework will be installed at the beginning of the
QIAxcel ScreenGel Software setup, if it is not already present. In this case, another dialog opens. Click
Install to install the Microsoft .NET Framework. This may take some time. If you cancel or close the
dialog, the QIAxcel ScreenGel will not be able to operate.
9. A Microsoft .NET Framework software update will be installed, if it is not already present. In this case,
another dialog opens. Click Next to start the installation of this package. Accept the license agreement
and click Next. Click Finish to complete the installation of this package. If you cancel or close the dialog
before, the QIAxcel ScreenGel will not be able to operate.
10.Depending on the installed software packages from steps 8–10, a computer restart might be required
before proceeding with the setup. After the reboot, the installation procedure is resumed automatically.
11.The QIAxcel ScreenGel setup wizard opens. Click Next.
12.Accept the license agreement and click Next.
13.Select the program installation path. The default path is C:\Program

Files\QIAGEN\QIAxcel\ScreenGel. Click Next.
Note: If C:\Program Files\QIAGEN\QIAxcel\ScreenGel is selected on a Windows 64 bit system, the

installation will appear in C:\Program Files\x86\QIAGEN\QIAxcel\ScreenGel.
14.Select the data path for acquired data and all other application data. The default path is C:
\ProgramData\QIAGEN\QIAxcel\ScreenGel. Click Next.
Note: It is not possible to choose C:\Program Files\QIAGEN\QIAxcel\ScreenGel also as the data path. It
is also not possible to choose the system root path (e.g., C:\Windows) as the data path.

Note: All paths in this manual refer to the data path as %DATA_DIR%.
Note: The %DATA_DIR% directory and its subdirectories can be opened in the Windows Explorer directly
from QIAxcel ScreenGel Software using the menu item File/Open Data Directory.
15.Click Install to begin the installation. This may take some time.
16.The QIAGEN QIAxcel Advanced Driver Installer dialog opens, if the driver is not already present on the
computer. Click Next. The driver installs. Click Finish to complete the driver installation.
17.Click Finish to complete the QIAxcel ScreenGel setup wizard.
18.Click Exit to close the installation window.
19.Connect the QIAxcel Advanced to the computer.
20.After the installation, the QIAxcel ScreenGel Software can be started either from the Windows start
menu under QIAGEN/QIAxcel or from the desktop icon. The user manual can be accessed in the
available languages from the Windows start menu.
Updating the QIAxcel ScreenGel Software
To update the QIAxcel ScreenGel Software, a previous version of the software must already be installed on
the computer and an upgrade package must be used. The upgrade package is available under Product
Resources at www.qiagen.com/p/QIAxcel. Before updating, read the information provided on the web
page. Experiments and user settings will be retained.
The upgrade can be done from any previous version of the QIAxcel ScreenGel Software directly to the
latest version. Furthermore, it is possible to upgrade from a previous English version to another available
language version (and vice versa).
Note: The installers for software versions below 1.4 allowed the software to be installed for the current user
or for all users of the computer. If the currently installed version had been installed with an option selected
for the current user, a direct upgrade cannot be performed. In this case, uninstall the software first (all
experiments, reports, user-created profiles are retained). Then re-install any available version of QIAxcel
ScreenGel from a CD, making sure to install this version for all users of the computer. Follow the
instructions in section Re-installation from a CD. After installing the older version from a CD, do not launch
the software. Continue directly with the update procedure below to a higher software version using the
update package. It is not possible to launch the intermediate installation if the software version is below the
one that was initially installed on the computer.

To update the software from web download:
4. Download the update package for the latest version from the QIAGEN website onto your computer. It is
available under Product Resources at www.qiagen.com/p/QIAxcel.
5. Unzip the update package.
6. Launch the setup.exe program. This will start the QIAxcel ScreenGel Software installation.
7. Select the language in which the QIAxcel ScreenGel Software shall be installed from the drop-down box.
8. Select the option Install QIAxcel ScreenGel Software to start the actual installation procedure.
9. The Microsoft Visual C++ 2010 x 86 Redistributable will be installed if it is not already present. In this
case, another dialog opens. Accept the license agreement and click Install. Click Finish to complete the
installation of this package. If you cancel or close the dialog before, the QIAxcel ScreenGel will not be
able to operate.
10.The appropriate version of the Microsoft .NET Framework will be installed at the beginning of the
QIAxcel ScreenGel Software setup, if it is not already present. In this case, another dialog opens. Click
Install to install the Microsoft .NET Framework. This may take some time. If you cancel or close the
dialog, the QIAxcel ScreenGel will not be able to operate.
11.A Microsoft .NET Framework software update will be installed, if it is not already present. In this case,
another dialog opens. Click Next to start the installation of this package. Accept the license agreement
and click Next. Click Finish to complete the installation of this package. If you cancel or close the dialog
before, the QIAxcel ScreenGel will not be able to operate.
12.Depending on the installed software packages from steps 8–10, a computer restart might be required
before proceeding with the setup. After the reboot, launch the setup.exe program again and select Install
QIAxcel ScreenGel Software.
13.The QIAxcel ScreenGel setup wizard opens. Click Next.
14.Accept the license agreement and click Next.

Files\QIAGEN\QIAxcel\ScreenGel. Click Next.
Note: If C:\Program Files\QIAGEN\QIAxcel\ScreenGel is selected on a Windows 64 bit system, the

installation will appear in C:\Program Files\x86\QIAGEN\QIAxcel\ScreenGel.
16.Select the data path for acquired data and all other application data. Use the same data path as the
installed software version. The default path is C:\ProgramData\QIAGEN\QIAxcel\ScreenGel. Click
Next.
from QIAxcel ScreenGel Software using the menu item File/Open Data Directory.
17.Click Install to begin the installation. This may take some time.

Note: Reference markers that were created with versions 1.0.0 or 1.0.2 of the QIAxcel ScreenGel Software
will be removed during installation. If needed, create the reference markers again from the appropriate size
marker runs.
18.The QIAGEN QIAxcel Advanced Driver Installer dialog opens, if the driver is not already present on the
computer. Click Next. The driver installs. Click Finish to complete the driver installation.
19.Click Finish to complete the QIAxcel ScreenGel setup wizard. Click Exit to close the installation
window.
20.Connect the QIAxcel Advanced to the computer.
22.Use one of the previously created user IDs for login.
Note: It is not possible to update from the BioCalculator Software to the QIAxcel ScreenGel Software.
However, run files of the Biocalculator Software can be imported. Refer to section Importing BioCalculator
Data for more information. It is not possible to import the run setup or method files created for the
BioCalculator Software.
Re-installation from a CD
Note: The installers for software versions below 1.4 allow the software to be installed for the current user or
for all users of the computer. Always use the option for all users of the computer.
Note: Downgrading (i.e., replacing a newer version with an older version of the software) the QIAxcel
ScreenGel Software is not recommended. Experiments and profiles created with the newer version cannot
be used with the older version. However, it may be necessary to re-install an older version of the software
from a CD to perform an upgrade. In this case, do not launch the software after re-installing it from a CD.
Continue instead directly with the update procedure described above. It is not possible to launch the
intermediate installation if the software version is below that which was initially installed on the computer.
If you have installed any version of the QIAxcel ScreenGel Software before and need to install the QIAxcel
ScreenGel Software again from a CD, follow the steps below.
To re-install from CD:
4. Ensure that you know the data path of the installed QIAxcel ScreenGel Software. Alternatively, launch
the installed QIAxcel ScreenGel Software and login. Select Open Data Directory in the File menu. Keep
open the launched Windows Explorer and close the software.

5. Uninstall the existing installation of the QIAxcel ScreenGel Software through the Windows Control Panel.
6. If downgrading the QIAxcel ScreenGel Software, rename or move the data directory of the existing
version.
7. Place the CD in the computer’s CD-ROM drive.
8. The setup wizard will automatically start installation of the QIAxcel ScreenGel Software and will guide
you through the setup process. It supports the installation of the QIAxcel ScreenGel Software. Select the
language from the drop-down box.
Important: If the setup wizard does not start automatically, double-click on “My Computer” and double-click
on the CD-ROM drive. Launch the setup.exe program. This will start the QIAxcel ScreenGel Software
installation.
9. QIAxcel ScreenGel uses several software packages provided by Microsoft. If they are not installed on
the system, these software packages are automatically installed at the beginning of the QIAxcel
ScreenGel Software setup. When the respective dialog is displayed, click the Install button to install
these required software packages. Depending on the installed software packages, a reboot of the system
may be required before proceeding with the setup. After the reboot, the installation procedure is resumed
automatically.
10.Select the option Install QIAxcel ScreenGel Software to start the actual installation procedure.
11.The installers for software versions below 1.4 allow the software to be installed for the current user or
for all users of the computer. Always use the option for all users of the computer.
12.Accept the license agreement.

Files\QIAGEN\QIAxcel\ScreenGel.
14.Select the data path for acquired data and all other application data. The default path is:
C:\Documents and Settings\All Users\Application Data\QIAGEN\QIAxcel\ScreenGel for Microsoft

Windows XP Professional
C:\ProgramData\QIAGEN\QIAxcel\ScreenGel for Microsoft Windows 7 Professional
If you re-install an older version of the software from a CD, as a prerequisite for an update to the current
version, select the path, mentioned in step 4.
If downgrading, it is important that the selected data path does not contain any files of the previously
installed version. In particular, do not select the renamed directory from step 6.
Note: Reference markers that were created with versions 1.0.0 or 1.0.2 of the QIAxcel ScreenGel Software
cannot be used with other software versions. If needed, create the reference markers again from the
appropriate size marker runs.

from QIAxcel ScreenGel Software, through the menu item File/Open Data Directory.
15.After the installation finished, click Exit to close the installation window.
16.If you re-installed an older version of the software from a CD, as a prerequisite for an update to the
current version, do not launch the software. Continue directly with the update procedure. In the update
procedure, use the same data path as used in step 14.
Note: When downgrading, error messages may appear indicating that one of the packages from Microsoft
cannot be installed or that the QIAxcel ScreenGel Software cannot be launched after installation. If the
computer is intended to be used only for the QIAxcel ScreenGel Software, access the Windows Control
Panel and uninstall the QIAxcel ScreenGel Software, all items starting with "Microsoft Visual C++ 20xx
Redistributable - ...," and the "Microsoft.NET Framework" items. Then try to install the QIAxcel ScreenGel
Software again. If the problem persists, contact QIAGEN Technical Services. If the computer is not intended
to be used only for the QIAxcel ScreenGel Software, exercise care when uninstalling the listed items. These
may be used by other software running on the computer. Have the installation package(s) of the other
software at hand in case repair is necessary.
Uninstall software
Note: Do not uninstall the software if you want to update the software. Follow the instructions in Updating
the QIAxcel ScreenGel Software.
When uninstalling the QIAxcel ScreenGel Software, all data within the data folder is retained.
If you want to uninstall the QIAxcel ScreenGel Software together with all data (experiments, reports) from
the %DATA_DIR%, ensure that you know the data path of the installed QIAxcel ScreenGel Software.
Alternatively, launch the installed QIAxcel ScreenGel Software and login. Select Open Data Directory in the
File menu. Keep the launched Windows Explorer open.
To uninstall the QIAxcel ScreenGel, follow these steps:
1. Close the QIAxcel ScreenGel Software.
2. Open the Control Panel by clicking on the Windows Start menu and selecting Control Panel.
3. Depending on your layout settings, either click Programs and Features or Add/Uninstall Programs.
4. Select QIAxcel ScreenGel to be uninstalled and click Uninstall.
Note: Depending on the Windows configuration, there may be a pop-up message asking if you want to
allow the program to install. Allow the program to install.
5. The installer window opens. Click Uninstall.
6. Follow the instructions of the installer to uninstall.
7. Finally, click Exit to close the installer window.

If you want to uninstall the QIAxcel ScreenGel Software together with all the data, switch to the Windows
Explorer before uninstalling the software. Delete the data from the data folder.
Getting started with the QIAxcel ScreenGel Software
Before using the software, read the Concepts of QIAxcel ScreenGel. Afterwards, configure the software.
This can only be carried out by a user with the Administrator role.
1. Launch the QIAxcel ScreenGel Software from the Windows start menu in the QIAGEN/QIAxcel folder or
from the desktop icon.
2. Log in as Administrator and click OK (for this first login, no password is required).
3. Provide a valid password for the Administrator account. Leave the field for the old password empty, then
provide a new valid password and enter it again.
Note: The password must contain one upper-case character, one lower-case character, and one digit. The
minimum size of the password is eight characters.
4. The Configuration environment is displayed by default. Select the User Manager tab.
5. Create user accounts for all relevant users. For more information, refer to User management and User
roles.
6. Configure which COM port is to be used for connection to the QIAxcel Advanced system. The default
adjustment is COM1. For more detailed information, refer to Settings.
7. Configure the global settings for the QIAxcel ScreenGel Software. For further details, refer to Settings.

Packing the QIAxcel Advanced

CAUTION
If you need to transport the QIAxcel Advanced, pack the instrument as follows:
1. Switch on the QIAxcel Advanced.
2. Switch on the computer and launch the QIAxcel ScreenGel Software.
3. Click in the Status Information panel to move the buffer tray to the front of the instrument.
4. Open the sample door and remove the buffer tray.
5. Remove the QIAxcel gel cartridge from the QIAxcel Advanced and store in the QX Cartridge Stand as
described in section Unpacking a QIAxcel Kit.
6. Remove the N2 bottle as described in section N2 cylinder replacement.
7. Close the QIAxcel ScreenGel Software and switch off the QIAxcel Advanced.
8. Disconnect the RS232 serial cable from the instrument to the computer and remove the AC power cord.
9. Reinstall the transport lock holding down the sample plate holder (see section Installing the QIAxcel
Advanced).
10.Place the QIAxcel Advanced into the original packaging it was shipped in.

This section describes how to operate the QIAxcel Advanced.
Before proceeding, we recommend that you familiarize yourself with the features of the QIAxcel Advanced
by referring to the section General Description.
The QIAxcel Advanced cartridge door, sample door, and service door must remain closed during
operation of the instrument. Only open the doors when the instrument is not operating or when instructed to
do so by the software.
Note: Opening the cartridge door or sample door during operation of the QIAxcel Advanced will cause the
system to stop the action it is currently performing. Any sample run in progress cannot be recovered.
However, due to the small volume of sample used, a new run can be performed.

CAUTION
Do not attempt to move the QIAxcel Advanced during operation.
WARNING Moving parts [W8]
To avoid contact with moving parts during operation of the QIAxcel Advanced, the
instrument must be operated with the cartridge door and sample door closed.
If the door sensors are not functioning correctly, contact QIAGEN Technical
Services.
Unpacking a QIAxcel Kit

1. Carefully read the handbook supplied with the QIAxcel Kit before starting.
2. Remove all buffer bottles from the kit. Refer to the handbook for a detailed description of the kit contents.
3. Add 10 ml QX Wash Buffer to both reservoirs of the QX Cartridge Stand (provided with the QIAxcel
instrument) reservoir and cover it with 2 ml mineral oil.
4. Remove the QIAxcel gel cartridge from its packaging and carefully wipe off any soft gel debris from the
capillary tips using a soft tissue.
Note: The QIAxcel gel cartridge is provided together with a smart key, which is used for fully automatic
cartridge detection. Do not remove the smart key from the cartridge.
5. Remove the purge cap seal from the back of the QIAxcel gel cartridge and place it in the QX Cartridge
Stand.

Note: A soft tissue should be used to wipe off any gel that may have leaked from the port.
Note: Ensure that the capillary tips are submerged in QX Wash Buffer.
6. Important: New cartridges must be allowed to equilibrate at room temperature for at least 20 minutes
prior to use. Place the gel cartridge in the QX Cartridge Stand, protected from light with the QX
Cartridge Stand Cover, or store the cartridge latched in the instrument in the Park position with wash
buffer in the wash park (WP) position, and allow to stand at room temperature (15–25°C) for at least 20
minutes. Do not equilibrate the gel cartridges inside the kit box or in the black cartridge blister.
Note: Incorrect cartridge handling or shorter equilibration times may cause damage to your QIAxcel
instrument and could result in a loss of warranty.
QIAxcel gel cartridge in the QX Cartridge Stand.

Setting up the QIAxcel Advanced
The steps required for correct setup of the QIAxcel Advanced instrument before each use are described in
this section.
Preparing the buffer tray
Important points before starting

If using pre-aliquoted alignment marker, the 12-tube strip containing QX Alignment Marker should be
equilibrated to room temperature (15–25ºC) and centrifuged briefly before use.
When using QIAxcel DNA Kits, we recommend changing the alignment markers every 50 runs or 3 days,
whichever comes first. Additional markers and buffers may need to be purchased (see Appendix C).
When using the QIAxcel RNA QC Kit v2.0, we recommend changing the alignment markers every 15–20
runs or 3 days, whichever comes first. Additional markers and buffers may need to be purchased (see
Appendix C).
When not in use, store the 12-tube strip with QX Alignment Marker at –20°C.
The volumes of QX Separation Buffer and QX Wash Buffer provided are sufficient for the maximum
number of runs stated on the gel cartridge.
The 12-tube strips should fit loosely in the MARKER1 position. Tightly fitting tube strips or tube strips that
are too loose may cause injection problems and damage the cartridge capillaries.
Allow all reagents to equilibrate to room temperature before use.
Procedure
1. Wash the buffer tray in warm water using a mild detergent and rinse thoroughly with deionized or
reverse-osmosis water.
2. Fill the positions of the buffer tray as listed below:

Buffer tray position
Wash Park Buffer

Cartridge type (WP) Wash Inject (WI) (BUF)
DNA High 8 ml QX Wash 8 ml QX Wash 18 ml QX DNA
Resolution Buffer Buffer Separation Buffer
DNA Screening 8 ml QX Wash 8 ml QX Wash 18 ml QX DNA
Buffer Buffer Separation Buffer
DNA Fast Analysis 8 ml QX Wash 8 ml QX Wash 18 ml QX FA DNA
RNA 8 ml QX Wash 8 ml QX Wash 18 ml QX RNA
3. Add QX Mineral Oil to cover all 3 positions to prevent evaporation. Add 2 ml QX Mineral Oil to
positions WP and WI, and add 4 ml QX Mineral Oil to the position BUF.
4. Load 15 µl QX Alignment Marker into each well of a QX 0.2 ml 12-Tube Strip or use a pre-aliquoted
strip.
5. Add 1 drop of QX Mineral Oil to each well and insert the strip into the M1 position of the buffer tray.
6. If the cartridge is not calibrated yet, load 15 µl QX Intensity Calibration Marker into each well of a QX
Color 0.2 ml 12-Tube Strip. Add a drop of QX Mineral Oil, and insert the strip into the M2 position of
the buffer tray.
Buffer tray.

Loading the buffer tray
If not already carried out:
1. Switch on the QIAxcel Advanced at the power switch.
2. Switch on the computer, launch the QIAxcel ScreenGel Software from the Windows start menu under
QIAGEN/QIAxcel or from the desktop icon.
3. In the QIAxcel ScreenGel software, select a mode (DNA or RNA) and log in (for detailed information,
refer to the User authentication section). The Process environment opens and displays the first screen of
the process profile of the process wizard.
Note: The icon indicates that the connection is being established and the icon shows that the
QIAxcel Advanced is connected. In the case that the instrument could not be connected, a message will be
shown notifying that the instrument is not available. If you didn't switch on the instrument at the moment,
click Instrument not needed. If you need the instrument, click Troubleshoot.
Follow the instructions in the message. For more detailed instructions, refer to the troubleshooting section
System setup. Close the message. To retry to connect to the instrument, click the icon.
Note: The QIAxcel ScreenGel Software comes with an up-to-date instrument software for the QIAxcel
Advanced instruments with serial number 30281 and higher. If the software connects to the instrument for
the first time, it checks if the instrument software on the instrument is up-to-date. If not, it updates the
instrument software. This process takes a few minutes. A message is shown during that time. Let the update
be completed. Do not turn off the instrument or disconnect the cable between the computer and the
instrument, and do not close the QIAxcel ScreenGel Software until the update is complete. After a
successful update, the QIAxcel ScreenGel Software automatically connects to the instrument.
To load the buffer tray proceed as follows:
1. Close the cartridge door and the sample door.
Note: The QIAxcel Advanced cartridge and sample doors must remain closed during operation of the
instrument. Opening either door during operation will cause the system to stop any action it is currently
performing.
2. Click in the Status Information panel at the left to move the buffer tray holder to the front of the
instrument. Wait until the buffer tray holder has reached its stop position.
3. Open the sample door.
4. Carefully place the filled buffer tray into the buffer tray holder. Be careful not to spill any solutions in the
instrument or cause any cross-contamination between buffers loaded on the buffer tray.
Note: The 12-tube strips should be positioned towards the front of the instrument with the buffers towards the
back.
5. Close the sample door and click in the Status Information panel to move the buffer tray holder to
the Wash Park position.
Note: Leave the sample door open if you want to load your samples immediately afterward.

Note: If you close the sample door, the buffer tray automatically moves to the Wash Park position after a
period of 5 minutes.
Installing a QIAxcel gel cartridge and smart key
Note: Read section Unpacking a QIAxcel Kit prior to performing this procedure.
1. Remove the QIAxcel gel cartridge from the QX Cartridge Stand.
2. Open the cartridge door and insert the QIAxcel gel cartridge into the QIAxcel Advanced. The cartridge
description label should be facing toward the front and the purge hole should be toward the rear of the
instrument.
Note: Ensure the purge cap seal has been removed as described in Unpacking a QIAxcel Kit.
3. Insert the smart key into the smart key socket near the cartridge. The smart key can be inserted in either
direction.
Note: The system will not recognize the cartridge and will not operate if the smart key is not inserted.
Note: If the settings option Latch cartridge automatically is selected, the cartridge will be automatically
latched after the smart key is detected. Therefore, it is important to insert the smart key as soon as the
cartridge has been inserted and the cartridge door has been closed. Refer to section Settings for
information about settings.
4. Close the cartridge door. The cartridge ID and cartridge type will be displayed automatically in
Cartridge Status in the Status Information panel.

Cartridge status area.

Removing a QIAxcel gel cartridge
To remove a QIAxcel gel cartridge from the QIAxcel Advanced proceed as follows:
1. Prepare the QX Cartridge Stand as described in section Unpacking a QIAxcel Kit.
2. Open the cartridge door.
3. Remove the smart key.
Note: If the settings option Latch cartridge automatically is selected, the cartridge will be unlatched
automatically after the smart key is removed. Therefore, it is important to remove the smart key first before
trying to remove the cartridge. Refer to section Settings for information about settings.
Note: If the QIAxcel Advanced is switched on and Latch cartridge automatically is unchecked, ensure the
QIAxcel gel cartridge is unlatched. If latched, unlatch it. See section Status Information panel for
information on how to do this.
4. Remove the QIAxcel gel cartridge.
5. Install the purge cap seal to close the purge port.
6. Place the QIAxcel gel cartridge in the QX Cartridge Stand.
Note: Ensure that the capillary tips are submerged in QX Wash Buffer.
Storing a QIAxcel gel cartridge
Storage of QIAxcel DNA gel cartridges after delivery

All components of the QIAxcel DNA High Resolution Kit, and the QIAxcel DNA Screening Kit, except for
the gel cartridge and the QX Intensity Calibration Marker, can be stored dry at room temperature (15–25°
C) and are stable until the expiration date under these conditions.
The QIAxcel gel cartridge and the QX Intensity Calibration Marker should be stored at 2–8°C upon arrival
and are stable until the expiration date under these conditions.
All components of the QIAxcel DNA Fast Analysis Kit can be stored dry at room temperature, except for the
QIAxcel gel cartridge, QX Intensity Calibration Marker, QX DNA Size Marker 50 bp – 1.5 kb, and QX
Alignment Marker 15 bp/3 kb. The QIAxcel gel cartridge and the markers should be stored at 2–8°C upon
arrival. Components are stable until the expiration date under the indicated conditions.
Storage of the QIAxcel RNA gel cartridge after delivery

QX RNA Size Marker 200–6000 nt should be stored at –20° to –80°C, and is stable until the expiration
date under these conditions.
QX RNA Denaturation Buffer should be stored at 2–8°C and is stable until the expiration date under these
conditions.
All other components of the QIAxcel RNA QC Kit v2.0, except for the QIAxcel gel cartridge, can be stored
dry at room temperature (15–25°C) and are stable until the expiration date under these conditions.
The QIAxcel gel cartridge should be stored at at 2–8°C and is stable until the expiration date under these
conditions.

Occasional use
Store QIAxcel DNA and RNA gel cartridges at 2–8°C until the first use. If the QIAxcel gel cartridge is not
being used on a daily basis, close the purge port with the purge port seal, return the gel cartridge to the
blister package, inserting the capillary tips into the soft gel. Store the QIAxcel DNA or RNA gel cartridge
at 2–8°C in an upright position (see orientation label on blister package).
Note: Storing the QIAxcel DNA or RNA gel cartridge below 2°C can severely damage the cartridge.
Prior to use, the QIAxcel gel cartridge should be placed into the QX Cartridge Stand and protected with
the cover whenever exposed to light, and allowed to stand for at least 20 minutes at room temperature.
Daily use
If the QIAxcel gel cartridge is being used on a daily basis, store the cartridge latched in the QIAxcel
Advanced in the “Park Position.”
Note: The QIAxcel Advanced must be left on if the cartridge is stored in the “Park Position” and the
cartridge must be latched. Do not switch the QIAxcel Advanced off.
If more than one QIAxcel gel cartridge is being used on a daily basis, store the second cartridge in the QX
Cartridge Stand in the dark or protected with the cover. Make sure that the cartridge stand reservoir is
filled with wash buffer and covered with mineral oil (refer to Unpacking a QIAxcel Kit). Alternatively, close
the purge port with the purge port seal, return the QIAxcel gel cartridge to the blister package, inserting the
capillary tips into the soft gel, and store the QIAxcel gel cartridge at room temperature in an upright
position (see orientation label on blister package).
The QIAxcel gel cartridge can be stored in this manner until expiration date as indicated on the kit label.
Operating the QIAxcel Advanced

Samples are processed using the Process environment of the QIAxcel ScreenGel Software.
Depending on the role of the user logged in, the environments behave differently. Users with the Routine
User role are guided step by step to start a process. Users with the Advanced User role will not be guided
step by step, they can freely define analysis and process profile parameters when starting a run.
This section describes the operating procedure of the QIAxcel Advanced for the routine user. Advanced
features of the QIAxcel ScreenGel Software, which are not available to the routine user, are described in
the Process section.

Things to do before starting
Carefully read the handbook supplied with the QIAxcel Kit.
Prepare the reagents and QX Alignment Marker to be used. For instructions about how to do this, see
section Setting up the QIAxcel Advanced, or refer to the QIAxcel Kit handbo o k.
Note: Refer to steps 1, 2, 3, 4, 7 and 8 in Running procedure for information about the alignment marker or
size marker. These steps can be skipped later. The alignment marker required is displayed in the software
and can now be prepared.
Prepare your samples. Refer to the handbook supplied with the QIAxcel Kit for instructions about how to
do this. For optimal results, the sample solution should be pH 6–9 and should not have an ionic content
greater than that of a typical PCR buffer.
Note: If you need to run a size marker side by side with the samples, prepare it in the required position on
the sample plate. Refer to the handbook supplied with the QIAxcel Kit for instructions about how to do this.
If less than 12 samples are processed, fill the empty sample wells with the QX DNA
Dilution Buffer or QX RNA Dilution buffer. Failure to do so may cause damage to
the capillary channels.
Starting a run
Routine users can run predefined process profiles using the process wizard of the QIAxcel ScreenGel
Software only (for advanced process options refer to section Running a process with advanced options).
Follow these steps to perform runs as a routine user:

4. Install the QIAxcel gel cartridge to be used as described in Installing a QIAxcel Gel Cartridge and
smart key.
Note: You can inspect the cartridge status in the Status Information panel to the left of the Process
environment. Refer to the Status Information panel section for detailed information.
5. Place the buffer tray containing the QX Alignment Marker onto the buffer tray holder as described in
Loading the buffer tray.
6. Place the sample strips (in position A) or a 96-well plate onto the sample plate holder.
7. Close the sample door.
Note: If the instrument doors are closed, the buffer tray automatically moves to the Wash Park position after
a period of 5 minutes.
8. In QIAxcel ScreenGel Software, select a predefined process profile in the Process Profile screen.

Process Profile screen.
Note: In DNA mode, the Process Profile drop-down list does not display profiles that contain peak calling
and profiles that contain distribution analysis at the same time. If you miss a profile in the list, activate
distribution analysis features for samples containing DNA libraries or genomic DNA and peak calling
features for Fast Analysis or standard DNA analysis. To do so, select Activate Distribution Analysis Features
or Activate Peak Calling Features from the View menu at the top left. This setting is user specific. It may
change automatically, when you open an experiment for review in the Analysis environment, that contained
peak calling or distribution analysis.
9. Click the Next button to proceed to the next screen, Sample Selection.

Sample Selection screen.
10.You can optionally change the directory where the experiment will be saved. This can be a local or a
network directory.
Note: The directory can only be changed if the process profile used allows it (see Selecting general process
options).
11.Optionally, change the plate ID.
Note: The plate ID will be used to name all the results from this process, for the experiment storing the
sample data, as well as for generated report/export files. Therefore, a unique plate ID is required. See Run
parameters and result structure for further information.
Note: For the plate ID, the software allows alpha numeric characters. Special characters such as /&!%$§
'´´ @*+~#=<>|;, etc cannot be used. The software removes blanks at the start and at the end
automatically.
Note: After the process, the plate ID cannot be modified.

Note: If the settings option Generate plate ID is selected, the system automatically generates a plate ID
following the rules specified in the settings. Refer to section Settings for more information. However, the
plate ID may be modified.
12. You can optionally change selection of sample rows to be processed. Use this option if you want to
process less rows than specified in the process profile. Left-click the row to deselect/select.
Note: Changing sample rows is only possible if the process profile used allows it (see Selecting run
parameters).
Note: It is not possible to deselect a row containing the size marker. If you want to do so, proceed to the
next step first and then deselect the row.
Sample row H was deselected. Changing the size marker position to

D1.
13. You can optionally change the position of the size marker on the plate, by right-clicking the new marker
position. Select the option Toggle Analysis Marker from the context menu that appears. This size marker will
be used for automatic analysis during process, if analysis is included in the process profile.
Note: The size marker position can only be changed if the process profile used allows it (see Selecting run
parameters).
Optional: If you have an additional size marker in the sample plate, right-click the position and select the
Set as Additional Marker option from the context menu. A rotated ladder symbol appears. Right-click again
and select the Size Marker Name from the context menu. This information can be used for manual analysis,
but will not be used for automatic analysis during the process.
14. If the No Marker option is selected, select the prepared alignment marker from the Alignment Marker
drop-down box. If you leave the Alignment Marker drop-down box empty, you have to acknowledge a
warning later in the Run Check screen.

15. Optional: Provide lot information of buffers and markers by checking the Show Lot Information box and
editing the lot information in the fields displayed.
Visible lot information fields.

Note: This is available only if either the settings option Enable input fields for Buffer lot IDs or Marker lot IDs
is selected (see Settings).
Note: The last used lot information values can be selected from drop-down lists. Restore the last used
combination of the lot information by clicking on the button Last used.
16. Optional: Check the Provide Sample Information box if you want to provide sample information. If not,
proceed to step 19.
Provide Sample Information box checked.

Note: The Sample Information screen is enabled only if the check box is checked.
17. Click the Next button to proceed to the next screen, Sample Information.

Sample Information screen.
18. Optional: Provide sample information, entered manually or imported from file.
To provide sample information manually, enter the sample information into the grid. Position A1 is
preselected by default. Confirm the information for each position by pressing the Enter or the Tab key; the
next position will be selected automatically for the next input. To provide sample information for a specific
position, click the position and enter the sample information.
To save the provided sample information in rack file format for later reuse, click the Save as button. In the
resulting dialog, navigate to the directory where the sample information should be stored, enter a unique
file name, and click OK.
To import sample information from a file, click the Import button. In the lower part of the dialog that
appears, select the type of file to be imported. The dialog lists all available files of this type. Alternatively,
navigate to the directory where the sample information was stored, select the file and click OK. The
imported data overwrites all sample information previously provided.

To enter sample comments, click Sample Comments. To enter a comment for a specific position, click the
relevant cell in the Sample Comments tab and enter the text.
Note: Sample comments can also be imported from a file along with sample information.
For more details, refer to section Provide Sample Information, or click a position in the grid and press the
F1 key.
Note: The size marker positions are marked by a "ladder" symbol.
Note: Click the Reset button to clear sample information; use the arrow and Tab/Shift+Tab keys to navigate
through the positions.
19. Click the Next button to proceed to the next screen, Run Check.
Run Check screen with "Sample door is open" error.

20. Confirm all check boxes. Resolve the problems indicated by warnings and errors. Use the Back and
Next buttons to navigate.
Note: The process can be started only when all run checks are confirmed and no errors/warnings are
shown.
Note: A handover to an Advanced User may be required.
Note: If the Run button is still deactivated, check the Status Information panel for cartridge and instrument
status or refer to the Troubleshooting section.
Run Check screen with all confirmation boxes checked and all problems resolved.

21. Start the process by clicking the Run button.
The process wizard will be closed and a preview will be shown for each row currently processed. The
actions performed by the instrument are shown in the Instrument Status panel on the left. A progress bar
below the preview shows the progress of the whole process and the estimated remaining process time.
Depending on the report settings the generated report may be displayed.
Note: Opening the cartridge door or sample door during operation of the QIAxcel will cause the system to
stop the action it is currently performing. The process is stopped and cannot be recovered. No sample data
are stored for the row currently processed. Sample data are stored for completed rows only. No analysis,
peak calling or report/export is performed. Thus, the stored sample data contain raw data only.
Process currently running row A.
Actions during process run:

You can switch between the gel and electropherogram preview by clicking on the respective tabs.

Switching from Gel Image to Electropherogram.
Optionally, adjust the separation time. To do so, move the Adjust Separation Time slider below the
preview. Moving it to the extreme left position will shorten the separation time by 120 seconds, moving it
to the extreme right position will extend the separation time by 120 seconds. Moving the slider takes
effect for an actual ongoing separation as well as for all following separations during the process.
Adjust separation time.
Note: When starting the next process by clicking the Run button, the slider is automatically reset to the
middle position and the separation time will be applied as defined in the method.
Optionally, switch the check box Individual Scaling on/off to adapted colors to the overall maximum
signal height of all samples. See Gel view for more information about individual scaling. The check box
Individual Scaling is initially set to off.
The process can be stopped by clicking the STOP button below the preview.
Note: If the instrument motors are currently moving, the process will stop after this movement.
Note: No sample data are stored for the row processed. Sample data are stored for completed rows only.
No analysis, peak calling, or report/export are performed. Thus, the stored sample data contains raw
data only.

Actions after the process has finished:
Process has finished.

The next process can be started by returning to the process wizard by clicking the Back to Wizard button
below the preview.
To inspect the sample data, switch to the Analysis environment. For information on how to do that, refer
to sections Environments, Handling samples and experiments and Viewing sample data, respectively.
Return to the Process environment and click the Back to Wizard button to start the next process.

The user-friendly QIAxcel ScreenGel Software has been specifically developed for use with the QIAxcel
Advanced system. The software offers interactive tools that simplify data analysis, allow fast data
interpretation, and provide flexibility in viewing data and results in both electropherogram and gel image
formats.
The software provides wizard-based run setup and convenient analysis and template profiles for
standardized sample processing, and offers effortless, customizable documentation of results.
The QIAxcel ScreenGel Software is based on a unique algorithm, that has been proven to analyze
separation data more reproducibly and accurately than other chromatographic analysis packages. It
calculates a variety of peak properties, such as peak number, peak height, peak width, and peak area.
Concepts
This section explains fundamental concepts that each user working with QIAxcel ScreenGel Software should
become familiar with:
Modes
User management
Environments
Profiles
User interface

Modes
The QIAxcel ScreenGel Software has two modes – one for DNA and one for RNA analysis. The main
purpose of the modes is to adapt the data analysis algorithms to the properties of the analytes. In addition,
the modes ensure that valid cartridge types are used and that only data of the right type can be loaded
from files.
Mode selection in login dialog box.

User roles
The QIAxcel ScreenGel Software distinguishes four different user roles, which differ in permissions. Each
user is assigned one of these four user roles. This section provides a short overview of the use and
permissions of each user role:
Role Used for Tasks Access

Administrator User management Installation of software Configuration
environment
Software configuration Configuration of global settings
Administration of user accounts
Routine User Routine sample processing Sample processing All environments

and data viewing (restricted access)
Inspecting samples
Basic User Sample processing and Sample processing All environments

analysis of data without (restricted access)
Analysis of samples
the option of modifying
profiles Report/export
Advanced User Sample processing Creating/modifying profiles All environments (full

access)
Analysis of data with full Sample processing
access to analysis
Analysis of samples
parameters
Report/export
Creation and modification
of profiles
Administrator
This role is intended for management of settings and users.
Users assigned this role can change the global settings and perform user management, i.e., management
of user accounts (rights, user role, etc.). Users do not have access to profiles, the Process environment,
the Analysis environment, or the Service environment.
Handover to a user with the user role Administrator is possible.
Advanced User
This role is intended for experienced users.
Users assigned this role have access to the full functionality of the software, except for user management.
Users can create analysis, process, and report profiles and therefore prepare the working base for other
users. They can perform advanced analyses, such as comparison of results from different processes (see
Customizing experiments) and modify profile parameters, if required.
Handover to a user with the user role Advanced is possible.

Basic User
This role ensures the use of predefined profiles, particularly analysis profiles.
Users assigned this role have access to all environments of the software; however, they can not create
new or modify predefined profiles, such as analysis and process profiles. While setting up a new process
using predefined process profiles, they can modify marker settings and rows that need to be processed.
In the analysis environment, they can open existing experiments and perform routine analyses using
predefined analysis profiles, but they cannot modify individual analysis parameters. They can perform
report and export using predefined report/export profiles with the option to modify the report/export
parameters, but without the option to save this changes.
Handover to a user with the user role Basic User or Advanced User role is possible.
Routine User
This role is intended for laboratories that routinely process large numbers of samples. Users are guided
by a wizard for efficient process setup.
Users assigned this role are limited to performing processes using predefined process profiles. In the
analysis environment, they can open existing experiments for viewing purposes only.
Handover to a user with the user role Routine User, Basic User, or Advanced User role is possible.
Note: One person can be assigned several user roles by creating several user accounts with different roles.
Refer to the User management section for information on how to create user accounts.
Environments
The QIAxcel ScreenGel Software is composed of four environments providing different functionality. Only
one environment can be used at a time.
Environment icons with active "Process" environment.
To switch to an environment, click the environment icon. The functionality of the environments is briefly
described in the following table:

Environment enabling runs to be performed on the QIAxcel Advanced system.
Supports data acquisition, allowing integrated data analysis and reporting. For
detailed information, refer to the Process section.
Environment that displays and enables analysis of sample data.
Provides advanced visualization and analysis tools for sample data as well as report
and export functionality. For detailed information, refer to the Analysis section.
Environment for maintenance or service of the QIAxcel Advanced system.
Contains all functions for maintenance and troubleshooting of instrument and

cartridges. For detailed information, refer to the Service section.
Environment for administration of users and system configuration.
Provides access to user management, profile management, and software preferences

(settings). For detailed information, refer to the Configuration section.
Profiles
Data acquisition and analysis in the QIAxcel ScreenGel Software are controlled by Profiles. Profiles
combine settings and parameters and can be conveniently reused for different purposes (see table below).
The standard procedure is to use predefined profiles. The QIAxcel ScreenGel Software will be installed with
a set of predefined profiles that cannot be modified. However, if modifications are necessary, experienced
users can create new profiles or change profile settings as required. See the following table:
Profile Description
Process profile To define settings for data acquisition. Defines all parameters for the
electrophoresis run.
Analysis profile To define the settings for sample data analysis (analysis parameters).
Peak calling instruction To define search criteria for peaks of interest.
Note: In DNA mode, peak calling instructions are available only if peak
calling features are active.
Distribution profile To define criteria for quality assessment of a DNA library, such as the
distribution of the library, including quality checks of the molar ratio or
height, as well as molarity or concentration.
Note: Distribution profiles are available only in DNA mode and only if
distribution analysis features are active.
Report/export profile To define report and export of sample data and analysis results in various
formats.

Note: Process profiles can include an Analysis profile, a Peak Calling Instruction or a Distribution profile, and
a Report/Export profile, which allows fully automated processing including analysis and report.
Note: Analysis, Distribution and Report/Export profiles and Peak Calling Instructions are included in a
process profile by copying the profile name and all profile parameters into the process profile. That means
that modifications to the original profiles are not automatically present in the process profile. This prevents
process profiles from being changed by mistake and ensures process stability. If the modifications should
also be in the process profile, include the modified profile again.
Available profiles and methods are loaded once, upon starting the software.
Profiles created with a previous version of the QIAxcel ScreenGel Software are automatically converted
(migrated) to the newest version.
Note: A profile created or saved with a newer version of the QIAxcel ScreenGel Software cannot be
opened in previous software versions.
Note: The profile names of the predefined profiles which are installed together with the software are
displayed in the selected software language. The profile names of user created profiles are displayed in the
language in which the profiles were created. For information how to change the software language, refer to
the end of section Settings.
General software usage
QIAxcel ScreenGel Software is a modern software with a state-of-the-art graphical user interface. The
controls of the user interface behave in the same way as standard Windows controls. This section explains
frequently used terms and several concepts which are specific for the QIAxcel ScreenGel Software user
interface.
In the following table, user interface-related terms that are used in this manual are explained.
Left-click Press the left button of a computer mouse or touchpad.

Right-click Press the right button of a computer mouse or touchpad.
Double-click Left-click twice, very quickly.

Drag-and-drop Move an object (sample, lane) to another place using a computer mouse or
touchpad. Left-click to pick up the object. Hold the left mouse button pressed while
dragging the object to the new place. Release the mouse button to release the object
in its new position.
If more than one object was selected, the left-click picks up all selected objects.
Ctrl click Press and hold the Ctrl key while pressing the left mouse button.
Ctrl+A Press and hold the Ctrl key while pressing the A key.
Context menu When right-clicking certain controls, a context-sensitive menu is shown. Not all
controls provide a context menu.

Context menu in the Experiment Explorer.
Tool tip When the mouse pointer hovers over a control without clicking it, a small text
window appears. Not all controls provide a tool tip. Usually a tool tip gives useful
information about the functionality of a control, or useful information about possible
problems (errors or warnings).
Drop-down box Drop-down lists allow the selection of one item from a predefined list of items. First,
left-click on the triangle to open the list. Then move the mouse down to the correct
item. Left-click to select the item.
Drop-down box example.

Toggle button Left-click the button to toggle. When the button is pressed, the functionality is on. Left-
click the button again to toggle the functionality off.
Rubber band Span a "rubber band" to define a rectangular region (for zooming into). Left-click to
function define the starting point, hold the mouse button pressed while dragging. While
dragging, a "rubber band" is shown, outlining the rectangular region. Release the
mouse button to define the region. The "rubber band" disappears. The system
performs the (zooming) functionality based on the defined region.
The status bar (the information line at the bottom of the application window) shows the current user logged
in, the date and time, user login name, and application mode (DNA or RNA).
Status bar.
Some areas in the software can be expanded or collapsed; e.g., collapse the Experiment Explorer and
Parameters Panel in the Analysis environment by clicking and expand them again by clicking .
Editing data in tables
The graphical user interface of QIAxcel ScreenGel contains many tables. When the table data is editable,
this can be performed in a special edit area at the bottom of the table. The table cells themselves are not
editable.
An example of an editable table is a Size Marker table in the Process environment.
Special area for editing table contents.
For example, to change the base pair size from 603 to 610:

1. Highlight the required row by left-clicking it.
2. Click on the Size edit field below the table.
3. Enter 610. While editing, only the controls of the edit area are enabled. In this case, the edit fields Size
and Concentration as well as the buttons OK and Cancel are all enabled.
4. To accept the values into the Size and Concentration fields, click OK. To cancel editing and discard the
changes, click Cancel.
Note: The OK and Cancel buttons are only enabled if the values in the editable fields have been changed
and are valid.
Displaying errors and warnings
In QIAxcel ScreenGel, yellow controls indicate an error, a warning, or an inconsistency or incompleteness

in entered data.
Validation during editing

If an incorrect value is entered into an editable field, the background becomes yellow. In addition, a tool
tip will be displayed which explains the problem. The following screenshots show examples of errors and
the corresponding tool tips.
Negative numbers are not allowed.
You must select an item.

1. Duplicate entries are not allowed.
2. Exceeding the range of the Alignment Marker is
not allowed.

Process screens
If a Process wizard screen contains an error or a warning, its screen marker background becomes yellow.
You should check the data in this screen and correct the problem.
Run Parameters screen is incomplete and therefore the process profile is invalid. Additionally, the instrument
is not connected.
Note: The screen marker Run Check remains blue (normal state) even if errors/warnings have been detected.
To start a process, operate as described in the Running procedure section for routine users or the Running a
process with advanced options section.

Message boxes
Most problems in QIAxcel ScreenGel are reported using message boxes.
Error message box.
Displaying modifications
The QIAxcel ScreenGel displays modifications in a Windows compliant way, using an asterisk at the left of
the name of the modified object. This is demonstrated by a few examples.
Analysis environment/modification of an experiment (apply or remove analysis, change the lane order,
etc.). The name of the experiment will be displayed with an asterisk.

Modified experiment.
Note: A changed profile will be shown in the same way.

Process environment/change of any parameter in the Process wizard
The selected process profile will be displayed with an asterisk.
Modified process profile.

Change of parameters in the Peak Calling screen
The selected peak calling instruction in the Peak Calling Instruction drop-down list will also be displayed
with an asterisk.
Modified peak calling instruction.

Note: You can start a process or leave the Process environment without saving your changes. QIAxcel
ScreenGel Software will not remind you to save a process profile as well as the corresponding analysis
profile, report/export profile, or peak calling instruction. If you leave the Process environment, log out, or
exit the application, you should save your changes if they are to be reused.

Getting help
The QIAxcel ScreenGel Software has a context-sensitive help system. After pressing the F1 key, a context-
specific help page is shown. The following image shows the help page corresponding to the login screen:
Help page shown after pressing the F1 key while in the login screen.
Note: The start menu folder under QIAGEN/QIAxcel also contains links to the user manual in PDF and CHM
format.
Alternatively, select Help from the Help menu.
Access help from the Help menu.

Find a description of the software features in the section QIAxcel ScreenGel Software, organized into
sections corresponding to the environments of the software, respectively. Use the content tree on the left-
hand side to navigate through the help system.
Click to expand the content tree.
The help system provides several links to other sections. Use the navigation links or buttons of the help
system to return to the previous topic.
Click to navigate back.

User authentication
To use the QIAxcel ScreenGel Software, the user must first log in. User authentication is required before
working with the instrument.
For details about how to create/add users and modify user settings, refer to the User management section.
Log in
After launching the QIAxcel ScreenGel Software the Log in dialog appears:
Log in dialog.
To log in to the software:
1. Select the application mode (DNA or RNA mode).
2. Enter the User ID.
3. Enter the password.
4. Click Login.
Note: The mode last used is preselected in the Mode drop-down list.
Note: To change the mode, log out and then log back in again, or restart the application.

Note: If 21 CFR Part 11 support is activated in the Settings and Maximum number of failed logins is set, the
number of failed login attempts is limited. If the limit of failed login attempts is exceeded, the user account is
locked. The administrator can unlock the user account in the user manager. If the administrator account is
locked, please contact QIAGEN Technical Services.
Note: Refer to the User management section for information on how to create user accounts.
Note: Refer to the Getting started with the QIAxcel ScreenGel software section for information about the first
login.
Log out
To log out:
1. Select File/Logout from the application menu bar.
2. A dialog appears that asks whether you really want to log out. Click the Yes the button to confirm the
log out.
3. After logging out, the log in dialog appears.
Note: If you want to exit the QIAxcel ScreenGel Software, cancel the log in dialog first.
Hand over
The user can hand over the current session to another user. Hand over is particularly useful as the current
working environment, including all open experiments, can be transferred to a different user with equal or
extended user rights, e.g., for changing a shift, or advanced analysis, or maintenance.
Note: A handover can only be made to users with an equal or higher user role.
To hand over:
1. Select File/Handover from the application menu bar.
2. The Handover dialog appears.
3. Enter the User ID and password and click Login.
Changing the user password

To change your password:
1. Select File/Change Password from the application menu bar.
2. The Change password dialog is displayed.
3. Enter the old password.
4. Enter the new password.
5. Confirm the new password.

6. Click OK.
Dialog box that enables the user password to be changed.
Locking the software

The software can be locked to block user access if the computer is left unattended.
To lock the software:
1. Select File/Lock Application from the application menu bar.
2. When the application is locked, the following dialog is shown:

Dialog box that enables the application to be unlocked.
Automatic software lock

In order to support 21 CFR Part 11 requirements, the software can be automatically locked after a defined
time without user interaction. You can activate 21 CFR Part 11 support and specify the auto-lock time
period in the Settings. For further details, refer to the Settings section.
Unlocking the software

To unlock the software:
1. Click the Unlock button.
2. The Log in dialog is displayed.
3. Enter User ID and password, click Login.
Note: Only a user with an equal or higher user role can unlock the application.

Process
The Process environment provides all functionality required for data acquisition:
Defines process parameters
Starts the sample process
Observes the data acquisition process
Process environment with active Process Profile screen and Status Information panel to the left (Advanced
User view).
The parameters for the process can be stored for re-use in a process profile.
Refer to the Starting a run section for information on how to start data acquisition using a predefined
process profile. This means that all parameters for data acquisition and also for analysis and report are
already defined. The specific sample information has to be entered and the process started. This can be
performed by users with the assigned user roles Routine User, Basic User, or Advanced User.
Refer to the Running a process with advanced options section for detailed information about how to define
process parameters and to start a process. This requires the user roles Basic User or Advanced User;
however, there are some limitations for users with the user role Basic User with respect to analysis
parameters and methods.

To fully automate a process, define a process profile that optionally includes an Analysis profile for
analysis parameters and marker information, as well as a peak calling instruction, and a Report profile for
report/export parameters. Refer to the Creating a new process profile and Modifying a process profile
sections for information on how to prepare and save process profiles for reuse. This requires the user role
Advanced User.
The data acquired during processing will be stored in an experiment. Refer to the Run parameters and result
structure and Handling samples and experiments sections for detailed information.
Running a process with advanced options
Users with the assigned user role Advanced User or Basic User can modify process profiles, if required.
Restrictions apply to users with the role Basic User as they can, for example, start a modified process
profile, but cannot save it. Restrictions are annotated, where they apply.
Note: For information on how to start a process as a user with the assigned role Routine User, refer to
section Starting a run.
Follow these steps to perform runs with advanced options:
4. Install the QIAxcel gel cartridge to be used as described in Installing a QIAxcel Gel Cartridge and
smart key.
Note: You can inspect the cartridge status in the Status Information panel to the left of the Process
environment. Refer to the Status Information panel section for detailed information.
5. Place the buffer tray containing the QX Alignment Marker onto the buffer tray holder as described in
Loading the buffer tray.

6. Place the sample strips (in position A) or a 96-well plate onto the sample plate holder.
7. Close the sample door.
Note: If the instrument doors are closed, the buffer tray automatically moves to the Wash Park position after
a period of 5 minutes.
8. In the Process environment of QIAxcel ScreenGel, select a process profile in the Process Profile screen.
The Process Profile drop-down lists the available process profiles for the current mode and the cartridge
type. The QIAxcel ScreenGel Software comes with a set of predefined process profiles. As a starting
point, select the process profile that fits best to your sample type.
Process Profile screen with Screening profile selected.

Note: In DNA mode, the Process Profile drop-down list does not display profiles that contain peak calling
and distribution analysis in parallel. If you miss a profile in the list, activate distribution analysis features for
samples containing DNA libraries or genomic DNA, and peak calling features for Fast Analysis or standard
DNA analysis. To do so, select Activate Distribution Analysis Features or Activate Peak Calling Features from
the View menu at the top left. This setting is user specific. It may change automatically when you open an
experiment for analysis in the Analysis environment that contained peak calling or distribution analysis.

Note: Select NewProcessProfile to create a process profile from scratch. The system will show
NewProcessProfile after selection. This is only possible for users with the assigned role Advanced User.
However, it may be easier to select a predefined process profile close to your needs and only modify it
slightly.
9. Optional: Modify the process profile options if required, as described in the Process profile options
section; restrictions for Basic Users are described here.
Note: Experiment directory, markers, and sample rows can be adjusted in the Sample Selection screen
below, if the process profile allows it. As these adjustments override the options defined in the process
profile, modify these options in the process profile only if you want to save them for reuse.
10.Optional: Switch to the Sample Selection screen.

11.Optional: Change the plate ID.
Note: The plate ID will be used to name all the results from this process, for the experiment storing the
sample data, as well as for generated report/export files. Therefore, a unique plate ID is required. See Run
parameters and result structure for further information.
Note: For the plate ID, the software allows alpha numeric characters. Special characters such as /&!%$§
'´´ @*+~#=<>|;, etc cannot be used. The software removes blanks at the start and at the end
automatically.
Note: After the process, the plate ID cannot be modified.

Note: If the settings option Generate plate ID is selected, the system automatically generates a plate ID
following the rules specified in the settings. Refer to section Settings for more information. However, the
plate ID may be modified.
12.Optional: Adjust the directory where the experiment will be saved.
Note: This can be a directory on the network. However, during the process, the experiment will be always
saved to a local directory first (refer to Settings), and then copied to the experiment directory defined here,
when the process finished.
Note: Changing the experiment directory here is only possible if the process profile allows it (see Selecting
general process options); however, you can switch to the Process Profile screen to modify this.
13.Optional: Change the selection of sample rows to be processed. Use this option if you want to process
less rows than specified in the Run Parameters screen. Left-click the row to deselect/select.
Optional: Change the position of the size marker on the plate, by right-clicking the new marker position.
Select the option Toggle Analysis Marker from the context menu that appears. This size marker will be used
for automatic analysis during processing, if analysis is included in the process profile.
Sample row H was deselected. Changing the size marker position to

D1.
Note: Changing sample rows or size marker position here is only possible if the process profile allows it
(see Selecting run parameters); however, you can switch to the Run Parameters screen to modify this.
Note: It is not possible to deselect a row containing the size marker.
Optional: If you have an additional size marker in the sample plate, right-click the position and select the
Set As Additional Marker option from the appearing context menu. A rotated ladder symbol appears. Right-
click it again and select the Size Marker Name from the context menu. This information can be used for
manual analysis, but will not be used for automated analysis during processing.
14.Optional: Select the size and alignment marker in the Size Marker and Alignment Marker drop-down lists
as required. This information will be used for automated analysis during the process.
Note: If the No Marker option is selected, select the prepared alignment marker. If you do not select an
alignment marker in the Alignment Marker drop-down list, you will have to acknowledge a warning later in
the Run Check screen.

15.Optional: Provide lot information of buffers and markers by checking the Show Lot Information box.
Up to five last-used lot information are stored separately for each lot type. These lastly used values can be
selected from drop-down list to use them again. Alternatively, the lot numbers can be typed into the edit
field of the combo box. Restore the last used combination of the lot information by clicking on the button
Last used.
Note: This option is available only if either the option Enable input fields for Buffer lot IDs or Marker lot IDs is
selected in the settings (see Settings).
16.Optional: Check the Provide Sample Information box if you want to provide sample information. If not,
proceed to step 18.
Provide Sample Information box checked.

17. Optional: Provide sample information in the Sample Information screen, entered manually or imported
from a file. For detailed information, refer to section Provide Sample Information, or click on one of the
positions in the grid and press the F1 key.
Note: The Provide Sample Information box must be checked in the Sample Selection screen to access this
screen.
18. Switch to the Run Check screen. Confirm all check boxes. Resolve the problems indicated by warnings
and errors.

Run Check screen with error.
Note: The process can be started only when all run checks are confirmed and no errors are shown.
Warnings must be checked as well or removed by eliminating the cause of the warnings.
Note: Advanced Users can acknowledge an uncalibrated cartridge and a red marked reference marker (
Basic Users can acknowledge a yellow one).
Note: If the run button is still deactivated, check the Status Information panel for cartridge and instrument
status.
19. Start the process by clicking the Run button.
The process wizard will be closed and a preview will be shown for each row currently processed. The
actions performed by the instrument are shown in the Instrument Status panel on the left. A progress bar
below the preview shows the progress of the whole process and the estimated remaining process time.
Depending on the report settings the generated report may be displayed.
Note: Opening the cartridge door or sample door during operation of the QIAxcel will cause the system to
stop the action it is currently performing. The process is stopped and cannot be recovered. No sample data
are stored for the row currently processed. Sample data are stored for completed rows only. No analysis,
peak calling or report/export is performed. Thus, the stored sample data contain raw data only.

Actions during process run:
You can switch between the gel and electropherogram preview by clicking on the respective tabs.
Switching from Gel Image to Electropherogram.
Optionally, adjust the separation time. To do so, move the Adjust Separation Time slider below the
preview. Moving it to the extreme left position will shorten the separation time by 120 seconds, moving it
to the extreme right position will extend the separation time by 120 seconds. Moving the slider takes
effect for an actual ongoing separation as well as for all following separations during the process.
Adjust separation time.
Note: When starting the next process by clicking the Run button, the slider is automatically reset to the
middle position and the separation time will be applied as defined in the method.
Optionally, switch the check box Individual Scaling on/off to adapted colors to the overall maximum
signal height of all samples. See Gel view for more information about individual scaling. The check box
Individual Scaling is initially set to off.
The process can be stopped by clicking the STOP button below the preview.
Note: If the instrument motors are currently moving, the process will stop after this movement.
Note: No sample data are stored for the row processed. Sample data are stored for completed rows only.
No analysis, peak calling, or report/export are performed. Thus, the stored sample data contains raw
data only.

Actions after the process has finished:
Process has finished.

The next process can be started by returning to the process wizard by clicking the Back to Wizard button
below the preview.
To inspect the sample data, switch to the Analysis environment. For information on how to do that, refer
to sections Environments, Handling samples and experiments and Viewing sample data, respectively.
Return to the Process environment and click the Back to Wizard button to start the next process.

Provide sample information
To access the Sample Information screen, the Provide Sample Information check box must be checked in
the Sample Selection screen.
Use the Sample Information screen to:
enter sample information, typically sample IDs
enter comments
import sample information and comments for all plate positions from a file
save sample information (without comments) for later reuse
The sample information grid becomes automatically active upon entering the Sample Information step. To
switch to sample comments, click the Sample Comments tab. To switch back to the sample information
grid, click the Sample Information tab.
Entering sample information in the Sample Information screen; size marker at A1.
Note: The size marker positions are marked by a "ladder" symbol.

Editing sample information
To provide sample information manually, enter the sample information into the grid. Position A1 is
preselected by default. Confirm the information for each position by pressing the Enter or the Tab key; the
next position will be selected automatically for the next input. To provide sample information for a specific
position, click the position and enter the sample information.
The sample information grid supports an auto-increment functionality. To number sample information texts
consecutively:
1. Write the main sample information in the left uppermost cell.
2. Drag the small black square at the lower right corner of the cell border to extend the selection to all
wanted cells.
3. Release the selection square. All selected cells will be filled with the main sample information entered in
step 1. The cells will be numbered consecutively, starting with number 1.
To navigate through the sample information grid, use the arrow and Tab/Shift+Tab keys (just as in a
Microsoft Excel® table).
To select multiple cells:

Starting with one or more selected cells, hold Ctrl and left-click cells to add or remove them from the
selection.
Left-click in a cell and, starting in the cell with the cursor, drag to select a rectangular area of cells.
To copy the text of one selected cell into multiple cells:

1. Select the (source) cell.
2. Use the context menu item Copy or press the Ctrl-C key combination to copy the text into the clipboard.
3. Select the target cells.
4. Right-click one of the selected cells, but not the one with the cursor, and use the context menu item Paste.
The text will be pasted from the clipboard into all selected cells. In addition, the first selected cell will
remain highlighted after the text has been pasted.
To copy a column:
1. Select all cells of the column you want to copy.
2. Use the context menu item Copy to copy the text of all selected cells into clipboard.
Note: The Ctrl-C key combination captures the text of the last selected cell only.
3. Left-click on the first cell of the column from which you want the text to be pasted.
4. Use the context menu item Paste or press the Ctrl-V key combination. The cells from the clipboard will be
pasted to the column starting with the cell selected in the last step.
Note: In the same way, it is possible to copy rows or other selected areas. To start pasting, click the
uppermost cell to the left.
To copy multiple cells from a Microsoft Excel table:

1. Copy the cells from the Microsoft Excel table into the clipboard.
2. In the Sample Information screen, click on the most left cell to paste.
3. Use the context menu item Paste or press the Ctrl-V key combination. The cells from the clipboard will be
pasted to the cells starting with the cell selected in the last step.
Text that is too long (more than 30 characters) that has been pasted into the cells.
Note: If the length of the pasted text exceeds the maximum value (30), the cell background will change.
To clear sample information, click the Reset Sample Information button.
Note: Users who are allowed to revise sample information (see User management) may edit the sample
information after the run using the context menu of the Experiment Explorer. In the analysis environment,
select the sample in the Experiment Explorer, right-click the sample, and select the context menu option
Revise Sample Information, then enter the new sample information.
Editing sample comments

To enter sample comments, click Sample Comments. To enter a comment for a specific position, click the
relevant cell in the Sample Comments tab and enter the text.
To sort the plate positions by row or by column, click the column headers Row and Col, respectively.

To copy a comment from one cell into another cell:
1. Click the (source) cell.
2. Select the text to be copied using the mouse or by holding down the Shift key while using the end, left-
arrow or right-arrow key.
3. Select the context menu item Copy or press the Ctrl-C key combination to copy the text into the clipboard.
4. Click the target cell.
5. Select the context menu item Paste or press the Ctrl-V key combination. The text will be pasted from the
clipboard into the cell.
To clear all sample comments, click the Reset Sample Comment button.
Sample comments can also be imported from a file together with the sample information.
Note: Sample comments are restricted to 150 characters.
Importing sample information

The QIAxcel ScreenGel Software provides the possibility to import sample information, with or without
sample comments, from files. Three file types are supported: Microsoft Excel files (Excel 97–2003
Workbook (*.xls), Excel Workbook 2007–2010 (*.xlsx)), QIAGEN rack files, and QIAGEN qdef files, the
QIAGEN data exchange format used in both QIAsymphony® and QIAgility® applications.
Note: The QIAGEN rack file format does not support sample comments.
To import sample information and/or sample comments from a file, click the Import button. In the lower
part of the dialog that appears, select the type of file to be imported. The dialog lists all available files of
this type. Alternatively, navigate to the directory where the sample information was stored, select the file
and click OK. The imported data overwrites all sample information and comments previously provided.
Note: Examples of all file types can be found under the File menu by selecting Open Data Directory and
then Sample Information.
Note: Imported sample information is read-only if the settings option Prevent modification of imported
sample information is selected (see Settings).
For the import of sample information from Microsoft Excel files, the following options are available:
Row-wise Select this option if the sample list in the Microsoft Excel file follows this
order: A1, A2, ..., A12, B1, B2, ..., B12, ..., H1, ..., H12. All samples
names must be listed in the first column, starting in the first line of the table.
Sample names for all plate positions must be listed in the file. Optional
sample comments should be listed in the second column.
Column-wise Select this option if the sample list in the Microsoft Excel file follows this
order: A1, B1, ..., H1, A2, B2, ..., H2, ... , A12, ... H12. All sample
names must be listed in the first column, starting in the first line of the table.
Sample names for all plate positions must be listed in the file. Optional
sample comments should be listed in the second column.

Matrix Select this option if the sample information in the Microsoft Excel file is
written in matrix format spanning cells A1 to L8 in the table. That is: A1,
A2, ..., A8 in the first row, and A1, B1, ... ,H1 in the first column.
This option does not support sample comments.
Note: The QIAxcel ScreenGel Software imports sample information from the first worksheet in an
alphabetical listing of all worksheets of the Microsoft Excel file. That is, if you rename the worksheets of the
Microsoft Excel file, ensure that the relevant sample information is entered in the worksheet that would
appear first, when arranged alphabetically by worksheet name.
Saving sample information

To save the provided sample information in rack file format for later reuse, click the Save as button. In the
resulting dialog, navigate to the directory where the sample information should be stored, enter a unique
file name, and click OK.
Note: The Save as button will be disabled if one or more cells contain more than 30 characters.
Note: The QIAGEN rack file format does not support sample comments.
Modifying a process profile
Note: Only users with the assigned role Advanced User and Basic User can modify process profiles.
Restrictions apply to users with the role Basic User as they, for example, cannot save the modified process
profile. Restrictions are annotated in this manual, where they apply.
To modify a process profile proceed as follows:
1. Launch the Process environment.
If not already open, switch to the Process environment by clicking the Process environment icon. Select the
Process Profile screen.

Steps to modify a process profile.
Note: If the last process only just finished, click the Back to Wizard button on the right bottom.
2. Select the process profile to be modified.
Use the Process Profile drop-down list to select a profile.
Note: Each process profile is related to a certain cartridge type. Therefore, the system can ensure that a
process (i.e., data acquisition) can be started only if the correct cartridge type is inserted.
If the process profile you want to select is not listed, make sure that the correct cartridge type is selected. If
the instrument is connected, the system automatically detects the inserted cartridge type. If you want to
modify a process profile to use with another cartridge type, remove the cartridge, or at least the cartridge
key. Select the correct cartridge type. The process profile you want to modify should now be listed in the
Process Profile drop-down list. Select the process profile and proceed.

3. Change the process profile options as required.
Screens for process

profile definition.
See the Process profile options section for detailed information.
4. Save the modified process profile under a new name.
Click the Save Process Profile as button below the process setup and enter a new unique profile name in the
dialog that appears.
Note: This is possible for users only with the assigned user role Advanced User.
Note: If there are process profile screens containing incomplete or inconsistent data highlighted in yellow,
the Save process profile as button is disabled. Select the marked process profile screens and correct the
data. If all data are correct, the Save process profile as button becomes enabled and the process profile
can be saved.
Note: You can start a process or leave the Process environment without saving your changes. QIAxcel
ScreenGel Software will not remind you to save a process profile or the embedded analysis profile, report/
export profile, or peak calling instruction. If you leave the Process environment, log out, or exit the
application, you should save your changes if they are to be reused.

Process profile options
The process profile options are grouped into several screens. To specify the complete process profile,
follow the screen order as described below. To switch to the Run Parameters screen, click the screen name:
Defining a process profile.

Note: You can return to each screen by clicking the screen name. You can skip screens if modifications are
not necessary.
Note: Screens with incomplete or incorrect options are highlighted in yellow. There is no need to correct
them straight away, but you cannot save or start an incomplete or incorrect process profile.

The Process Profile screen options are described below.
Process Profile Specifies the process scope. In addition to data acquisition, it is possible to
include additional steps such as analysis and report. For detailed
information, refer to the Selecting general process options section.
Run Parameters Specifies the data acquisition details such as method used, rows to be
processed, and size marker position. For detailed information, refer to the
Selecting run parameters section.
Analysis Parameters Specifies the analysis parameters for fully automated analysis after data
acquisition. For detailed information, refer to the Selecting analysis
parameters section.
Note: This screen is disabled if analysis is not in the process scope.
Marker Specifies the markers, alignment marker, and size marker used for analysis.
For detailed information, refer to the Selecting marker section.
Note: This screen is disabled if analysis is not within the process scope.
Peak Calling Specifies the parameters for peak calling based on the peak result table.
For detailed information, refer to the Selecting peak calling instructions
section.
Note: This screen is disabled if peak calling is not within the process scope.
Distribution Analysis Specifies the parameters for distribution analysis based on the smear result
table. For detailed information, refer to the Selecting distribution profiles
section.
Note: This screen is disabled if distribution analysis is not within the process
scope.
Report/Export Specifies the report and/or export parameters for fully automatic report and
export as last step during process. For detailed information, refer to the
Selecting report/export parameters section.
Note: This screen is disabled if report/export is not in the process scope.
Note: In DNA mode, the peak calling screen or the distribution analysis screen are available only if the
corresponding features (peak calling or the distribution analysis) are active. To activate, select the
corresponding option from the View menu. Note that only one set of features can be active at a given time.
Selecting general process options
1. Select the Process Profile screen.
Refer to the Process profile options screen for information on how to select the screen.
2. Specify the process scope.
Select the additional steps:

Analysis Includes analysis in the process. This means after data acquisition is complete,
the software analyzes the sample data automatically in the background, based
on the process options set in the Analysis and Marker screens (described in the
Selecting analysis parameters and Selecting marker sections).
The Analysis Parameters and Marker screens become enabled.

Peak Calling Includes peak calling in the process, based on the analysis peak result table.
This means that after analysis, peak calling will be automatically performed,
based on the process options set in the Peak Calling screen (described in the
Selecting peak calling instructions section).
Note: This step is disabled if Analysis is not within the process scope.
Note: In DNA mode, this option is available only if peak calling features are
active. To activate peak calling features, select Activate Peak Calling Features
from the View menu.
Distribution Analysis Includes distribution analysis in the process, based on the analysis smear result
table. This means that after analysis, distribution analysis will be automatically
performed based on the process options set in the Distribution Analysis screen
(described in the Selecting distribution profiles section).
Note: This step is disabled if Analysis is not within the process scope.
Additionally, the used analysis profile must have the option Smear Analysis
Profile selected.
Note: In DNA mode, this option is available only if distribution analysis features
are active. To activate distribution analysis features, select Activate Distribution
Analysis Features from the View menu.
Report Includes report and/or export as the last step in the process. This means that
the software automatically generates report and export.
3. Optional: Change the directory where the experiment will be saved.
Note: This can be a directory on the network. However, during the process, the experiment will always be
saved to a local directory first (refer to Settings), and then copied to the experiment directory defined here,
when the process finished.
4. Optional: Allow directory selection.
Select the option to allow directory selection in the Sample Selection screen while preparing a process.
Using this option, the run can be customized even by a user with the assigned user role Routine User.
5. Optional: Edit a note in the process profile.
Use this note field to add a short description about the intended use of the profile. This note is displayed
each time the process profile is selected. The note field is limited to maximal 2.000 characters and 25 lines.

Selecting run parameters
Define the methods and the rows that have to be processed with the methods. Select at least one method. In
addition, the position of the size marker can also be specified.
Note: During processing, the list will be processed consecutively. For information about the correlation
between run parameters and result structure, refer to the Run parameters and result structure section.
Proceed as follows:
1a. If the Method Details list is empty, click the Add button to start the first definition. A new empty entry
appears in the Method Details list. Proceed with step 2 to specify the entry.
Note: This option is only available for users with the assigned user role Advanced User.
Empty Method Details list after the Add button has been clicked.

1b. If the Method Details list is not empty you have the following options:
Add Click the Add button to add a new entry at the bottom of the list. Proceed with step 2 to
specify the entry.
Insert Select an entry by left-clicking and then click the Insert button to insert a new entry before
the selected one. Proceed to step 2 to specify the entry.
Modify Select the entry you want to modify. Proceed to step 2 to modify the entry.
Delete Select the entry you want to delete, then click the Delete button. The entry will be deleted
from the list. Proceed to step 6.
Note: This option is only available for users with assigned user role Advanced User.
2. Select the rows to be processed.
In the Sample Row Selection view to the right, left-click this view to add or remove a sample row to the
plate. The Range field shows the row selection you have made.
Note: For DNA mode only. If you later refine a process profile that uses Distribution analysis, note the
following:
If you reduce the rows to process in the sample row selection in this screen, these rows will be removed
automatically also in the Distribution analysis screen to ensure a consistent process profile.
If you add rows later, there's no automatic adaptation in the Distribution Analysis screen.
Optional: Define the number of runs per row in the editable field Runs per row. The method will be applied
as often as you specify here.
3. Optional: Define the size marker position.
Note: This position will be used for automatic analysis if the size marker is to be run side by side with the
samples.
Right-click to define the position that will contain the size marker. The Marker field shows the position of the
marker you set.
Note: Only one size marker position can be defined for an entry in the Method Details list. If you want to
specify the process profile for a plate run containing a size marker at each row, create an entry for each
row separately in the Method Details list.

4. Select the appropriate method from the Method drop-down list.
Note: The Method drop-down list only contains methods that are allowed for the cartridge type that the
process profile is defined for.
Note: A number of default methods are available for each QIAxcel Kit. For a complete list, please refer to
Appendix B. Refer to the Viewing method details section if you want to look at the details of the method you
have selected.
If required, change the sample injection time in the Injection Time editable field. This time will be applied
instead of the sample injection time defined in the method.
Modified sample injection time.

5. Click OK to confirm.
Note: The OK button becomes enabled as soon as the rows are defined and a method is selected.
The specified parameters appear in the entry created entry in the Method Details list.
Note: Click Cancel to discard all specifications made during steps 2 to 5. The entry will not be created/the
selected entry will not be modified.
Note: The column Runs in the Method Details list contains the total number of runs specified by this entry: if
Range is A–C and RpR ("Runs per Row") is 2, Runs will therefore be 3*2=6.
6. Define all entries in the Method Details list repeating steps 1 to 5.
7. Optional: Allow row deselection.
Select the option to allow row deselection in the Sample Selection screen while preparing a process. Using
this option, the run can be customized even by a user with assigned user role Routine User. This option is
useful to, for example, prepare the process profile for a complete plate but only run the rows needed.
8. Optional: Allow marker definition.
Select the option, to allow the size marker position to be redefined in the Sample Selection screen while
preparing a process. Using this option, the run can be customized even by a user with assigned user role
Routine User.

Selecting analysis parameters
Note: The Analysis screen is enabled only if analysis is within the scope of the process profile. For details,
refer to the Selecting general process options section.
Specify the analysis parameters as follows:
1. Select an analysis profile.
Use the Profile drop-down list to select the analysis profile. The analysis parameters of the selected profile
are shown below the drop-down list.
Selecting an analysis profile to modify.
Note: The analysis profile will be used for fully automatic analysis of all samples.

Note: In order to perform a distribution analysis in the process, the used analysis profile must have the
option Smear Analysis Profile selected.
Note: Select NewAnalysisProfile to define the analysis parameters from scratch. This is only possible for
users with the assigned user role Advanced User.
Note: All analysis parameters currently set in the selected analysis profile will be copied to the process
profile. Further modifications of the underlying analysis profile do not affect the analysis parameters in this
process profile. This prevents the process profile from unwanted changes and ensures process stability. If
modifications in the underlying analysis profile are to be included in this process profile as well, include the
modified analysis profile again by selecting it from the Profile drop-down list.
2. Optional: Modify the analysis parameters. You can modify the analysis parameters according to your
needs in this screen as described in the Modifying an analysis profile section.
Note: This is only possible for users with the assigned user role Advanced User.
Note: If you define the Suspend Integration intervals using relative migration time, make sure that the relative
migration times match the marker mode. See Modifying an analysis profile for details.
Note: The modifications will only be included in this process profile. If the modified parameters are also to
be included in the selected analysis profile, save the analysis profile as described below.
3. Optional: Save the modified analysis parameters.
The modified analysis parameters can be saved by clicking the Save as button. A dialog appears, which
includes the name of the selected analysis profile. You have two options:
Click OK if you want the modifications to be saved in the selected analysis profile; enter a new unique
analysis profile name to save the modified analysis parameters as a new analysis profile, then click OK.
The name of this new analysis profile and all of its analysis parameters will be included in the process
profile.
Selecting marker
Note: The Marker screen is only enabled if analysis is within the scope of the process profile. For details,
refer to the Selecting general process options section.

Marker selection.
Define the markers to be used when running this process profile.
1. Select one of the size marker options.
2. Select the correct marker for the selected option.
For information about marker options, see the descriptions below:
No Marker Select this option if automatic analysis is for peak detection only.
Note: No size marker will be used during automatic analysis, therefore

determination of size and concentration is not possible.
Reference Marker
Table If analysis of size and/or determination of concentration is to be performed, select
this option. The determination of size and/or concentration is based on a
previously saved reference marker table.
Select the reference marker table to be used from the Reference Marker Table drop-
down list.

Note: To ensure compatibility, the drop-down list contains only reference marker
tables whose size markers were processed with the same method as defined in this
process profile. The drop-down list is marked as invalid and empty if there is no
compatible reference marker table. In this case, run a process with size marker
side by side with the samples or create a reference marker table from a previous
process (refer to the Creating a reference marker section).
Note: If no cartridge is currently inserted, the system cannot check the compatibility
of the selected reference marker table. The drop-down list is marked as invalid and
empty, or it contains a previously selected reference marker table only. Insert the
cartridge to be processed by the profile and select a reference marker table
compatible for this cartridge and method defined in this process profile.
Note: See the table below for explanation of the symbol at the right of the
Reference Marker Table drop-down box:
The selected reference marker table is fully compatible.
This means that the size marker used for the reference marker table was
processed no more than 90 days (DNA)/60 days (RNA) before with the
cartridge that is currently inserted and with the same method as defined in
this process profile.
The size marker used for the reference marker table was processed more
than 90 days (DNA)/60 days (RNA) before with the cartridge that is
currently inserted and with the same method as defined in this process
profile.
The size marker used for the reference marker table was processed with the
same method as defined in this process profile, but with a cartridge other
than that currently inserted.
The reference marker table is not compatible with the method defined in this
process profile. This can happen if the method was changed in the Run
Parameters screen and the reference marker table was not yet changed
correspondingly. Select another reference marker table from the drop-down
list that is compatible with the newly selected method.

Run size marker Select this option if the plate requires a size marker.
side by side
Select the size marker to be used from the Size Marker drop-down list.
with sample
Optional: Change the total concentration of the size marker above the Size Marker
table to the right, if needed. The individual concentrations of the fragments are then
recalculated automatically.
In the Alignment Marker drop-down list, select the alignment marker to be used in
the MARKER1 position in the buffer tray.
Note: If the Run size marker is selected side by side with sample option, but size
marker and/or alignment marker is not specified, the Marker screen would be
considered as invalid.
Note: For DNA mode only: Using the correct size marker will increase the accuracy
of size and concentration determination. Select the marker containing DNA
fragments close to the size of your targeted DNA fragments. The DNA fragments to
be analyzed must fall within the smallest and largest fragment size of the size
marker.
Note: For DNA mode only: In addition, the range of the alignment marker must
cover the range of the size marker. If not, the Size Marker table to the right shows
this discrepancy with rows highlighted in yellow and the Marker screen would be
considered as invalid.
Note: Refer to the Selecting run parameters section for information on how to define
the position of the size marker.
Selecting peak calling instructions
Note: The Peak Calling screen is enabled only if analysis and peak calling are within the scope of the
process profile. For details, refer to the Selecting general process options section.
Refer to the Peak Calling section for an explanation of the peak calling concept.
Define the instruction for peak calling:
1. Select a peak calling instruction.
Use the Peak Calling Instruction drop-down list to select a predefined peak calling instruction. The instruction
definition is shown below the drop-down list.
Note: All parameters currently set in the selected peak calling instruction will be copied to the process
profile. Further modifications of the underlying peak calling instruction do not affect the peak calling
parameters in this process profile. This protects the process profile from unwanted changes and ensures
process stability. If modifications in the underlying peak calling instruction are also to be included in this
process profile, include the modified peak calling instruction again by selecting it from the Peak Calling
Instruction drop-down list.

Note: Select NewPeakCallingInstruction to create a new instruction (for Advanced Users only). The Peak
Calling screen is highlighted in yellow because the new peak calling instruction is still empty. Proceed to
step 2 to define the instruction.
2. Modify the peak calling instruction. The peak calling instruction can be modified as required in this
screen as described in the Modifying a peak calling instruction section.
Note: This can only be carried out by users with the assigned user role Advanced User.
Note: If the position of a peak is defined to be found using the relative migration time, make sure that the
relative migration times match the marker mode. See Modifying a peak calling instruction for details.
Note: The modifications will only be included in this process profile. If the modifications are also to be
included in the selected peak calling instruction, save the peak calling instruction as described below.
3. Save the modified peak calling instruction.
The modified peak calling instruction can be stored by clicking the Save as button. A dialog appears
containing the name of the selected peak calling instruction. You have two options: Click OK if the
modifications are to be stored in the selected peak calling instruction; enter a new unique peak calling
instruction name to save the modifications to a new peak calling instruction, then click OK. The name of this
new peak calling instruction and all of its parameters will be included to the process profile.
Selecting distribution profiles
Define the distribution profiles to be used in the process and assign the rows to be analyzed with those
profiles. Select at least one distribution profile. A sample row can be analyzed with one distribution profile
only. Selections made are listed in the Assignment of Distribution Profiles list, where each row defines the
use of one distribution profile.
Distribution analysis is performed automatically in the process after smear analysis. Therefore, the Default
Smear DNA profile should have been selected in the Analysis screen, and a size or reference marker must
have been selected in the Marker screen. For more information, refer to Distribution analysis.
Note: This screen in the Process Setup is enabled only if analysis and distribution analysis are within the
scope of the process profile. For details, refer to Selecting general process options.
To define the use of distribution profiles:
1a. If the Assignment of Distribution Profiles list is empty, click the Add button to make the first assignment.
An empty entry appears in the assignment list. Proceed with step 2 to specify the entry.

Empty Assignment of Distribution Profiles list after the Add button has been clicked.
1b. If the Assignment of Distribution Profiles list is not empty, the following options are available:
Add Click the Add button to add a new assignment at the bottom of the list. Proceed with step
2 to specify the assignment.
Note: This option is available for users with the assigned user role Advanced User only.
Modify Select the assignment to be modify. Proceed to step 2 to modify the assignment.
Delete Select the assignment and click the Delete button to remove it from the list. Proceed to step
6.
Note: This option is only available for users with assigned user role Advanced User.
2. Select the desired distribution profile from the Distribution profile drop-down list.
Note: All parameters set in the selected distribution profile are copied to the process profile. Further
modifications of the Distribution profile in the Analysis environment do not affect the distribution parameters
in this process profile. This protects the process profile from unwanted changes and ensures process
stability. If modifications in the underlying distribution profile are to be included in the process profile, add
the modified distribution profile by selecting it from the Distribution Profile drop-down list again.

3. Select the sample rows to be analyzed with the distribution profile.
In the Sample Row Selection panel, left-click sample rows to select or deselect them. The Range field shows
the row selection made. It is possible to select only rows to be run in the process, that is, that have already
been selected in the Run Parameters screen.
Note: A row that has already been assigned to a distribution profile in the assignment list, cannot be
selected anymore.
Note: If the rows to be processed have been reduced in the Run Parameters screen while refining a process
profile, those rows are removed automatically in this screen. If rows have been added in the Run
Parameters screen, one would need to adapt the row selection in this screen if you would want to use
Distribution analysis for the added rows as well.
4. Click OK to confirm.
Note: The OK button becomes enabled as soon as rows are defined and a distribution profile is selected.
The specified parameters appear in the created entry in the Assignment of Distribution Profiles list.
Note: Click Cancel to discard all entries made during steps 2 and 3. The entry will not be created or the
selected entry will not be modified.
5. Repeat steps 1 through 4 to define all assignments in the Assignment of Distribution Profiles list.
The parameters of distribution profiles cannot be viewed or edited in this screen. To view or edit the
distribution profile parameters, switch to the Analysis environment.
If the underlying distribution profile is modified after being selected for the process profile, the name of the
distribution profile is preceded with an "*". This indicates that the parameters that will be used by this
process profile are not the same those visible in the Analysis environment. To view the distribution profile
parameters that are defined for the current process profile:
1. Select the row with the distribution profile that is modified.
2. Click the Save as button below the Distribution Profile drop-down box and save the distribution
parameters using a new distribution profile name.
3. Switch to the Analysis environment to inspect the parameters of the saved distribution profile.
4. You can delete obsolete distribution profiles using the Profile Manager in the Configuration environment.

Selecting report/export parameters
Note: The Report/Export screen is enabled only if Report is within the scope of the process profile. For
details, refer to the Selecting general process options section.
Specify the report and export parameters as follows:
1. Select a report/export profile.
Use the Report/Export Profile drop-down list to select the report/export profile. The parameters of the
selected profile are shown below the drop-down list.
Selecting a report/export profile.

Note: All report/export parameters currently set in the selected report/export profile will be copied to the
process profile. Further modifications of the underlying report/export profile do not affect the report/export
parameters in this process profile. This prevents the process profile from unwanted changes and ensures
process stability. If modifications in the underlying report/export profile are also to be included in this
process profile, include the modified report/export profile by selecting it from the Report/Export Profile
drop-down list.
Note: Report/export profiles with the option Use Images as Displayed selected are not listed in the Report/
Export Profile drop-down list. This option is available in the analysis environment only. Refer to the Report/
Export options section for more information.

Note: In DNA mode, report/export profiles that include selected distribution analysis options are not listed
in the Report/Export Profile drop-down list if peak calling features are active. Similarly, report/export
profiles with selected peak calling options are not listed if distribution analysis features are active.
2. Modify the report/export parameters.
The report/export parameters can be modified as required in this screen. Refer to the Report/Export options
section for more information.
Note: The modifications will only be included in this process profile. If the modified parameters are also to
be included in the selected report/export profile, save the report/export profile as described below.
Note: A report/export profile is only applicable if at least one format check box (PDF or RTF) and one of the
content options (Overview or Sample Details) is selected for report, or if one check box is selected for
export. The check boxes and the Report/Export screen are highlighted in yellow if no selection is made.
3. Save the modified report/export parameters.
The modified report/export parameters can be saved by clicking the Save as button. A dialog box
appears, which includes the name of the selected report/export profile. You have two options: Click OK if
the modifications are to be stored in the selected report/export profile; enter a new unique report/export
profile name to save the modified report/export parameters to a new report/export profile, then click OK.
The name of this new report/export profile and all of its parameters will be included in the process profile.

Run parameters and result structure
This section provides an example so that the relation between process definition and the structure of the
result can be described:
With a QIAxcel DNA Screening Cartridge:
Rows A and B will be run twice with Method AM320, with size marker at position A1
Rows C and D will be run 3 times with Method AH420, with the same size marker at position C1
The same alignment marker will be used for both methods.
See the Run Parameters and Sample Selection screens of the process definition:
Run Parameters screen.

Two entries were defined because of the different methods. The rows and size marker positions were
defined for each method, as well as for the runs per row (column RpR in the Method Details list). In the Runs
column the total number of runs for each method is listed.

During the process, the software first runs Method AM320 in the order row A and B (first run), and row A
and B (second run). It then runs Method AH420 in the order row C and D (first run), row C and D (second
run), and row C and D (third run).
The Plate ID will be used as the name of the results.
The Sample row selection shows a summary of the run definition in the Run Parameters screen.
The total number of runs (Total Runs) in this example is 10:
2 times A and B = 4 runs for Method AM320
3 times C and D = 6 runs for Method AH420

When the process is finished, the sample data are presented in the Analysis environment in the Experiment
Explorer:
Experiment generated by the process.

All sample data generated by the process are combined into one experiment and named according to the
Plate ID, which was specified in the Sample Selection screen.
All sample data are grouped by so called "plates" as they were generated by the process.

The name of the plate identifies the run. It is combined with:
Experiment name The experiment name is created from the Plate ID specified in the Sample Selection
screen.
R# Run number, where "#" represents a number, starting from 1. In this example for method
AM320, the run numbers R1 and R2 are generated.
E# Entry number (entry in the Method Details list of the Run Parameters screen), where "#"
represents a number starting from 1. In this example, the entry numbers E1 and E2 are
generated, because the Method Details list contained 2 entries.
Therefore, the sample data for Method AM320 for rows A and B are listed first and also separately for
each run.
Creating a new process profile
Note: Only users with the assigned role Advanced User can create a new process profile.
To create a new process profile, proceed as follows:
1. Open the Process environment.
If not open, switch to the Process environment by clicking the Process environment icon. Select the Process
Profile screen.

Main steps for creation of a new process profile.
Note: If the last process was just completed, click the Back to Wizard button at the bottom right.

2. Select cartridge type.
Select the cartridge type that is to be used for the new process profile.
Note: Each process profile is related to a certain cartridge type. Therefore, the system can ensure that a
process (i.e., data acquisition) can be started only if a cartridge with correct cartridge type is inserted.
Note: If the instrument is connected, the system automatically detects the inserted cartridge and the cartridge
type cannot be changed. If you want to create the process profile for another cartridge type, remove the
cartridge, or at least the cartridge key, or disconnect from the instrument.
3. Select a process profile.
Use the Process Profile drop-down list to select a process profile. The selected profile serves as a template
for the creation of the new profile.
Note: Select NewProcessProfile to create a process profile from scratch. The system will show *
NewProcessProfile after selection. This can only be carried out by users with the assigned role Advanced
User.
3. Set the process profile options according to your needs.
See section Process profile options for detailed information.
4. Save the modified process profile under a new name.
Click the Save Process Profile as button below process setup and enter a new unique profile name in the
dialog that appears.
Note: If there are process profile screens containing incomplete or inconsistent data highlighted in yellow,
the Save process profile as button is disabled. Select the marked process profile screens and correct the
data. If all data are correct, the Save process profile as button becomes enabled and the process profile
can be saved.
Viewing method details
During definition of a process profile, it is possible to view the details of a method.
Note: This function is available for users with the assigned role Advanced User and Basic User only.
Proceed as follows:
1. Select a process profile in the Process Profile screen.
2. Switch to the Run Parameters screen. Select the entry containing the method you want to view in the Plate
Definition tab .
3. Switch to the Method Details tab.
4. Select another method to view, if required.
Note: Selecting another method modifies the entry in the Plate Definition tab you came from. Ensure you
have selected the correct method you want to process.

Method Details screen.
All actions defined in the method are listed. During the run, the actions will be performed sequentially.
For more information about what the position abbreviations mean, see the Instrument Status section of the
Status Information panel to the left of the Process environment.

Status information panel
The left panel of the screen in the Process environment is called the Status Information panel. It is divided
into:
A toolbar at the top
Instrument Status
Cartridge Status
Status Information panel.
Instrument Status and Cartridge Status can be collapsed and expanded. The toolbar buttons and status icons
are explained in the following table:
Load Position button. Click the button to move the buffer tray to the front of the instrument
to load samples and buffer.
Note: The motors will not move if either the sample door or cartridge door is open.
Wash Park Position button. Click the button to move the cartridge to the wash park
position of the buffer tray.
Note: The motors will not move if either the sample door or cartridge door is open.
Indicates that the currently inserted QIAxcel gel cartridge is latched. Click the button to
unlatch the QIAxcel gel cartridge.
Important: If the Pressure 1 status is low, increase system pressure before unlatching.
Releasing the cartridge latching with reduced pressure may damage the instrument!
Indicates that the currently inserted QIAxcel gel cartridge is unlatched. Click the button to
latch the QIAxcel gel cartridge.
Important: If the Pressure 1 status is low, increase system pressure before unlatching.
Releasing the cartridge latching with reduced pressure may damage the instrument!

Pressure 1 status: OK/Low. OK indicates adequate pressure for the sample run. LOW
indicates that the N2 pressure is sufficient for the current sample run; however, the N2
cylinder should be replaced once the run of the current sample row has finished.
Pressure 2 status: OK/Low. OK indicates adequate pressure for the sample run. LOW
indicates that the N2 pressure is insufficient for the current sample run and the analysis
will not be performed. The N2 cylinder should be replaced.
Sample door: Closed/Open.
Cartridge door: Closed/Open.
Connection status: Connected, disconnected, and connection is being established with the
QIAxcel Advanced instrument.
Note: If disconnected, the icon can be clicked to connect to the instrument.
The Instrument Status panel displays the buffer tray and sample plate. The current position of the capillaries
of the QIAxcel gel cartridge is highlighted when the process is running. In the example below, the sample
rows A–D are processed with the same method.
Instrument Status panel.

The Cartridge Status panel displays information about the QIAxcel gel cartridge currently inserted, such as
cartridge ID, cartridge type, remaining number of runs, remaining number of calibration runs, expiration
status, and calibration status. When opening the Calibration Details expander, additional calibration details
are shown.
Cartridge Status panel.
Note: Calibration status NOT OK means that the cartridge is not calibrated and needs calibration. For
information about calibration, refer to the Calibrating a cartridge section.
Note: The Status Information panel is shown in the Process environment and the Service environment.

Analysis
The Analysis environment provides sophisticated visualizations and analysis algorithms for
electropherograms acquired by the QIAxcel Advanced instrument.
The software provides several customizable views for sample raw data, for example, a gel view, a single
electropherogram view, and electropherogram superposition view. Electropherogram views also visualize
analysis results, enabling fast assessment of the results.
The analysis algorithms provided by the QIAxcel ScreenGel Software automatically determine a variety of
peak properties. Analysis algorithms can be applied to single samples or collections of samples (called
experiments), and can be customized by the user. The size and concentration of analytes can be
determined. The DNA mode includes functions that enable quality assessment of samples, for example, after
a target enrichment step in a workflow. These functions include checking for the presence of certain
fragment sizes (peak calling), and determining and assessing the molarity and size distribution of DNA
fragments (distribution analysis). The RNA mode provides the RNA Integrity Score (RIS) as a tool to
objectively asses the quality of eukaryotic RNA samples. In addition, parameters such as 28S/18S ratio
and concentration of total RNA can be calculated.
Analysis environment with active Electropherogram screen, Experiment Explorer to the left, and Analysis
panel to the right.

The Experiments panel on the left displays functions for Handling samples and experiments. The middle
panel displays several graphical views and result tables. For more information, refer to Viewing sample
data.
On the right is the Parameters panel, where analysis parameters and report/export options can be
specified.
If it is not visible, you can display it using the View menu (selecting the menu item View/Show Analysis
Parameters) or by clicking the icon at the extreme right of the view selection bar:
Introduction into analysis
Before (re)analysis of samples can start, the experiment must be loaded in the Experiment Explorer on the
left and the samples must be visualized in the middle area. Additionally, the samples that shall be analyzed
must be selected for analysis. Refer to Handling samples and experiments and Viewing sample data and its
sub sections for more details.
The analysis of samples is performed using a two-step approach. First, peaks are detected in the raw data.
As a result, the alignment marker peaks are found and the first, very basic peak properties are available,
e.g., peak start and peak end, peak apex as a function of time, as well as peak area. After peak
detection, the samples can be viewed and aligned according to the alignment marker peaks found in the
Gel view or the Electropherogram overview. Because peak detection is the basis of the analysis, ensure that
the peaks and especially the alignment marker peaks have been found correctly. For details, see Peak
detection.
In a second step, the peak sizes and peak concentrations are determined by mapping the detected peaks in
the sample to peaks of a reference markerwhich is created based on a size marker that has been used in
this or a previous run. To use a size marker from a previous run for analysis, it is important that the same
cartridge, method, instrument and alignment marker are used. For size and concentration, see section Size
and Concentration determination. The software allows you to combine the first and the second analysis
step.
Optionally, a third analysis step is possible. Either Peak Calling or Distribution analysis can be used based
on peak detection and size determination. These analyses can be used to check whether the samples meet
certain defined expectations.
Follow the instructions in Analysis of DNA samples and Analysis of RNA samples for step-by-step guidance
for your specific samples.
One can benefit from fully automated processing by including analysis steps already into the process of
data acquisition. Starting with analysis parameters initially provided by the software, customize the
parameters such that the analysis gives good and reliable results for your samples. Save them into Profiles
and use them to create fully automated customized Process Profiles.

Handling samples and experiments
The Experiment Explorer in the Analysis environment displays samples in a concise manner and provides
functionality to load and manage samples.
After a process is completed, the result data are saved in an experiment. If the Analysis environment is
selected, the experiment is automatically loaded in the experiment explorer.
An experiment groups samples by plates and rows in the order that they were processed. For detailed
information, refer to the Run parameters and result structure section.
Several experiments can be loaded, but only one experiment can be active at a time. The samples in the
experiment can be visualized and analyzed. A note for the active experiment can be entered in the note
field at the bottom of the explorer.
Customized experiments can be created to combine sample result data from different experiments. Refer to
the Customizing experiments section for detailed information.

Experiment Explorer.
The experiment explorer toolbar has the following buttons:
Load experiment from disk: Refer to the Loading sample data section for detailed
information.
Save: Save the active experiment to disk. Refer to the Saving an experiment section for
detailed information.

Move/rename: Save the active experiment; it allows the name and directory to be changed.
Refer to the Saving an experiment section for detailed information.
Note: This function does not create a copy of the experiment.

Create new experiment: Refer to the Creating a new experiment section for detailed
information.
Meaning of sample icons
In the Experiment Explorer, samples are symbolized by a well and size markers by a ladder .
These symbols vary slightly according to the analysis, visualization, and selection status:
Analyzed Meaning Not analyzed

Not visualized, not selected.
Visualized, not selected.
Not visualized, selected.
Visualized, selected.
The current focus sample has, in addition, a border . This sample is displayed in the single
electropherogram view and you can inspect its properties.
The Size Marker property of a sample can be changed by using the sample context menu. Use the Size
Marker option to toggle.
A reference marker can be created afterward from samples with the Size Marker property.
Loading sample data
To load samples from the disk, proceed as follows:
1. Click at the top of the Experiment Explorer.
2. A file dialog appears, showing all experiments that were created in the current run mode (e.g., in DNA
mode, you will not see RNA experiments). Navigation starts in the most recently opened directory, or
otherwise in the default experiment directory. You can navigate to a different directory.
Note: To open calibration results, select the path ending with "[Calibration Results]"

3. Select the experiment from the list by double-clicking it, or clicking it with the mouse and clicking Load
file.
4. The experiment will be loaded and displayed in the Experiment Explorer.
Note: If there were experiments already loaded in the Experiment Explorer, the experiment just opened will
be displayed as the last experiment, at the bottom. The newly loaded experiment automatically becomes
active.
Note: In DNA mode, loaded experiments that include peak calling or distribution analyses trigger the
software to automatically activate peak calling or distribution analysis features, respectively.
Alternatively, you can open one or more experiments via drag and drop from the Windows Explorer. To do
so, navigate to the folder where the experiments to be opened are located and drag and drop them into
the Experiment Explorer. All experiments dragged and dropped into the Experiment Explorer that can be
opened in the given mode (e.g., in DNA mode, only DNA experiments can be opened) will be loaded and
displayed. Files that cannot be opened by the application will be ignored.
Note: Close experiments after analysis and reporting is completed.
The file dialog for loading an experiment.

Representation of an experiment on disk
An experiment is represented on disk as a file with the name of the experiment. The file extension depends
on the mode used to create the experiment (.xdrx for DNA, .xrrx for RNA, and for calibration data created
during cartridge calibration, .xcdrx, and .xcrrx, respectively).
Loading experiments of previous software versions

To load an experiment that was created with a previous QIAxcel ScreenGel Software version, proceed as
described above. The loaded experiments will be automatically converted (migrated) to the newest version.
Note: Experiments which were created by previous software versions in protein mode can no longer be
opened.
Note: A migrated experiment cannot be opened by previous software versions any more.
In version 1.0.x of QIAxcel ScreenGel, an experiment was represented on disk as a folder with the name of
the experiment. The folder contained a file with the name of the experiment, describing the experiment
structure. The extension of this file was dependent on the mode used to create the experiment (.xdr for DNA,
.xrr for RNA, .xcr for calibration data created during cartridge calibration). In addition, the folder
contained several files, each containing the sample data of a sample row. The file names were extended
based on the experiment name.
When an experiment created with QIAxcel ScreenGel Software version 1.0.x is loaded to QIAxcel
ScreenGel Software versions 1.1 or higher, it is automatically converted (migrated) to the newest version.
After saving the experiment, the folder with the experiment and sample files is replaced by a single
experiment file with the appropriate new file extension (see above).
When a RNA experiment created with QIAxcel ScreenGel Software version 1.0.x is loaded to QIAxcel
ScreenGel Software versions 1.1 or higher, the search criteria for the 18S and 28S peak in the reference
marker table are automatically converted to a peak calling instruction.
For loading experiments from the BioCalculator Software, refer to the Importing BioCalculator Data section.
Selecting samples
In the Experiment Explorer samples inside the active experiment can be selected. For more information
about activating an experiment, see the Activating an experiment section.
Select an individual sample with a left-click.

To select multiple single samples, simultaneously hold
the Ctrl key and left-click the samples.
To select multiple samples in a rectangular area,

simultaneously hold the Shift key and — for this
example — left-click the samples A3 and B5.
To select all samples in a row, left-click the row

letter.
To select multiple rows, hold the Ctrl or Shift keys

simultaneously.
To select all of the samples of a plate, right-click the

plate name and select the context menu option Select
Whole Plate.
To select all of the samples of the experiment, right-

click the experiment name and select the context
menu option Select all Samples.
Switch the focus by left-clicking a sample. During sample selection, the last sample selected has the focus.
If samples from different experiments need to be selected, create a new customized experiment containing
these samples. For more information about customized experiments, see the Customizing experiments
section.

Selecting samples for analysis or report
Here, the selection inside the view is relevant — not the selection in the Experiment Explorer. The selection
of samples depends on the view. Descriptions are provided below:
View Single sample selection Multiple sample selection
Gel Image Select a single sample by Selection of multiple samples

clicking the gel lane header of can be performed by clicking
the sample. Selection of a the gel lane headers using the
sample for analysis in the Shift or Ctrl key (just as in the
Experiment Explorer is not Windows Explorer).
possible in this environment. Alternatively, you can select
all visualized gel lanes by
clicking the Select all key in
the tool bar.
Single Electropherogram Select a single sample in the Not possible in this view.
Experiment Explorer. In this
view, the visualized sample
will be analyzed.
Electropherogram Overview Select a single sample by Selection of multiple samples

clicking the electropherogram can be performed by clicking
of the sample. Selection of a the electropherograms using
sample for analysis in the the Shift or Ctrl key (just as in
Experiment Explorer is not the Windows Explorer).
possible in this environment. Alternatively, you can select
all visualized
electropherograms by clicking
the Select all key in the tool
bar.
Electropherogram Not possible in this view. All samples included in the

Superposition diagram are selected
automatically.

Expanding and collapsing
For a better overview, you can collapse experiments or plates, regardless of whether the experiment is
active or not.
To collapse an experiment:
1. Click to the left of the experiment name. The entire experiment collapses down to the experiment name
only.
2. Click to expand it again.
Note: You can collapse a single plate inside an experiment by clicking to the left of the plate name. The
plate collapses down to the plate name only. Click to expand it again.
Activating an experiment
Only one experiment can be active at a time. The samples in the active experiment can be visualized and
analyzed.
To activate an experiment in the Experiment Explorer, right-click the experiment and select Activate from the
context menu or double-click the experiment header.
Activating an experiment using the context The experiment is now active.

menu.

The previously active experiment will be deactivated automatically. If this experiment was modified, the
system asks whether the changes should be saved or not. Click Yes to save or No to discard the changes.
Select Cancel to cancel activation. For more information about saving experiments, see the Saving an
experiment section.
Note: Experiments from older software versions cannot be deactivated. Instead, they will be closed if you
activate another experiment. Avoid this by saving them in the new format. Note, however, that once saved
with the current software version, the experiments can no longer be opened with older software versions.
Note: In DNA mode, activated experiments that include peak calling or distribution analyses trigger the
software to automatically activate peak calling or distribution analysis features, respectively.
Saving an experiment
To save the active experiment to the disk, click the Save button at the top of the Experiment Explorer.
All modifications made to this experiment will be saved, as specified in the settings. This includes analysis
results, as well as information about the configuration of the visualization.
Note: Sample data cannot be saved individually.
If you want to save the active experiment to another directory, use the Move/rename button . This will
open a file dialog for choosing a different directory and experiment name.
Note: To avoid data redundancy, the previous experiment file will be removed.

The same file dialog opens if the experiment was created in the experiment explorer and has not yet been
saved to disk.
The file dialog for saving an experiment.
The file dialog enables navigation to the directories of the disk, creation of a new directory, and allows the
user to choose the new name of the experiment. The appropriate file extension will be appended
automatically.
Note: The experiment name is restricted to 40 characters.
Information stored in the experiment
The following information is stored in the experiment:
Experiment structure
Visualization information: visualization status of the samples (not for superimposition), sample order in the
visualization.

The following information is saved in each sample since it can differ from sample to sample:
Run information: all run parameters, including cartridge information, parameters of the method used,
sample injection time, and separation time. The run information is stored immediately after the process
has finished and will not be changed later.
Analysis information, if the sample has been analyzed: includes analysis parameters, reference marker
table used during analysis, and peak calling information.
For more details about samples refer to the Inspecting sample properties section. For details about settings
and directory configuration, refer to the Settings section.
Closing an experiment
You can close an experiment by clicking to the right of the experiment name, regardless of whether the
experiment is active or not.
If the experiment was modified, the system asks you whether to save the changes or not. Click Yes to save
or No to discard the changes. Select Cancel to cancel closing.
For more details about saving experiments, see the Saving an experiment section.
Importing BioCalculator Data
Data files from the BioCalculator Software (the QIAxcel Software version prior to QIAxcel ScreenGel
Software) can be imported into the QIAxcel ScreenGel Software.
Proceed as follows:
1. Select Import BioCalculator Data from the File menu.
Opening the File menu.
Note: This menu option is available in the Analysis environment only.
2. A dialog appears enabling selection of the BioCalculator data files to be imported. Navigation starts
initially with the most recently used BioCalculator import directory or the user's My Documents directory.
Navigate to the directory that the BioCalculator data files will be imported from. Use the file type to
filter.

3. Select the files to be imported from the list and click Import.
Note: Only one file of type .hff can be imported at a time. The .hda files referred to by the selected .hff file
are expected to be located in the same folder as the .hff file.
Note: Change the file type to HDA, to select multiple .hda files.
4. The files will be converted and displayed in the Experiment Explorer.
If a .hff file was selected, an experiment will be created containing as many rows and samples as in the .hff
file. Repeats will be represented by separate plates.
The experiment will be saved in the default experiment directory, as defined in the user settings.
Note: If there are incomplete rows, the empty sample positions remain empty.
Note: If a sample position is referred to multiple times, separate plates are also generated.
Note: If there were experiments already loaded in the Experiment Explorer, the newly opened experiment
will be displayed as the last experiment, at the bottom). This experiment automatically becomes active.
Note: If the mode (DNA or RNA) of the selected files is different to the current mode, the files cannot be
imported.
5. Visualize the samples.
Note: To see the imported analysis parameters and reference marker table in the analysis parameters tab,
right-click a sample in the experiment explorer and select the context menu option Transfer Analysis
Instructions.
To load an experiment that was created with the QIAxcel ScreenGel Software, use the Load function as
described in the Loading sample data section.
Revising sample information
To revise sample information or sample comments after the run, select the sample in the experiment
explorer, right-click the sample, and select the context menu option Revise Sample Information or Sample
Comment. Enter the new sample information and/or comment in the dialog that appears.
Note: The context menu option Revise Sample Information or Sample Comment is enabled only if the user
has the right to revise the sample information. The administrator can grant the right in the User management.
Note: The report will indicate that a sample name or comment has been revised.

Handling an incomplete experiment
An experiment can be incomplete if the process stopped during data acquisition. This is indicated in the
experiment explorer with a yellow lock icon. Hover with the mouse over the lock icon to display a tooltip
with further information.
Incomplete experiment.
You can remove this icon from the experiment (for example, because you could successfully reprocess the
missing runs). Right-click the experiment name and select the context menu option Accept Corrupt Experiment
.
Accept an incomplete experiment.
Note: This option is available only for users who have this right (based on their user role). The administrator
can grant the right May accept incomplete experiments using the User Management system.
The report will contain information about the incomplete process and the acceptance in the report overview
section.

Viewing sample data
The Analysis environment offers several options for visualization of raw data and analysis results:
A gel view, which can display several samples — see Gel view.
A single electropherogram view, which visualizes a single sample along with its analysis results — see
Electropherogram view.
An electropherogram overview, which visualizes several electropherograms in a gallery — see

Electropherogram overview.
An electropherogram superposition view, which visualizes several electropherograms in one plot — see
Electropherogram superposition view.
All views allow data exploration by zooming and scaling the data.
Adding samples to views
Note: A maximum of 97 samples can be visualized at a time in the gel view and electropherogram
overview. If this limit is reached, visualization of more samples is disabled.
Samples can be added to a view by dragging samples from the Experiment Explorer to:
The gel view
The electropherogram overview
The electropherogram superposition view (see description at the end of this section)
Proceed as follows:
1. In the Experiment Explorer select the samples to be visualized.
2. Left-click the selected samples, drag to the view, and drop. All selected samples will be displayed in the
view.
Note: In gel view and electropherogram overview a marker is shown that indicates the position when
dropping. All samples will be displayed at the selected position. See also Changing lane order.

Dragging sample A1 to the gel image, to the right of D9.

Alternatively, samples can be added to the views through the sample context menu of the experiment
explorer. Use the Visualize Selected Samples option to add the selected samples to the views.
Visualize selected samples.
Finally, to visualize a plate, right-click the plate name and select the context menu option Visualize Whole
Plate. To visualize the whole experiment, right-click the experiment name and select the context menu
option Visualize Whole Experiment.
Unlike all other views, the superposition view does not automatically display all samples selected for
visualization.
To add samples to the superposition view:
1. In the Experiment Explorer select the samples to be added.
2. Open the context menu of the selected samples in the Experiment Explorer.

3. Select the Superimpose option.
Adding sample C4 to superposition.
The selected samples will be added to the superposition view. In the Experiment Explorer all samples that
are displayed in the superposition view are marked by a colored rectangular according to their color in the
superposition.
Note: Up to 12 electropherograms can be superimposed. A warning will be displayed if the limit is

exceeded.
Alternatively, drag and drop up to 12 selected samples from the Experiment explorer to the superposition
view.

Removing samples from views
Samples can be removed from the views by dragging the selected samples from the view back to the
Removing samples E7 and E9 from the gel image.

Note: You can drop the samples elsewhere in the Experiment Explorer.
Alternatively, use the context menu of the samples in the Experiment Explorer:
1. Select the samples that should no longer be visualized.
2. Right-click a selected sample and uncheck the Visualize Selected Samples option to remove samples from
the views.

Removing selected samples E7 and E9 via the context menu.
Finally, if a whole plate or a whole experiment is visualized, you can remove all the samples from the view.
Right-click the plate name or the experiment name and uncheck the Visualize Whole Plate or Visualize Whole
Experiment option from the appropriate context menu.
To remove samples from the superposition view, proceed as follows:
1. In the Experiment Explorer select the samples to be removed.
3. Unselect the Superimpose option.

Exporting view to clipboard
Sample views can be copied to the clipboard.
1. Select the lanes/electropherograms to be copied (in gel view or electropherogram overview).
2. Right-click the selected sample and select from the menu item Copy to clipboard the resolution you want
have the image with.
3. Switch to the application you want the view to appear in and paste.
Note: You can use the keyboard shortcut Ctrl+C to copy selected images to clipboard. Keep in mind that
using of key shortcut applies the default resolution value (96 dpi), not the last used one.
Note: When you paste the image in an application, make sure that it uses the right resolution. QIAxcel
ScreenGel puts the pixel array on clipboard which adapted for desired resolution (this means that the
image has the appropriate pixel size). The application you paste the image in, shall be able to interpret this
information correctly.
Note: The samples that have been copied to clipboard, have the same image settings as in the visualization
view (such as color palette, contrast, noise cutoff, and zoom factor).
Note: In the single electropherogram view and electropherogram superposition view the gel lane and C-
channel diagram will be copied to clipboard too if they are displayed in visualization. If you hide both gel
lane and C-channel diagram, only samples will be copied to clipboard. You can access the Copy to
clipboard pop-up menu from gel lane and C-channel diagram as well.

Copying the gel image of the selected samples C1,
C2, and C4 to the clipboard.
C1, C2, and C4 pasted.
Direct printing view
You can directly print images of selected samples:
1. Select the lanes/electropherograms to be printed.
2. Right-click the selected sample and select the context menu item Print.
This function works in a similar way to the 'copying to clipboard' function with default image resolution; the
selected samples will be sent to the default printer. They have the same image settings as in the
visualization view (such as contrast, noise cutoff, and zoom factor).
The image sent to the printer is identical to the image you would copy to the clipboard; if the gel lane and
C-channel diagram are displayed in the single electropherogram view and electropherogram superposition
view, they will be printed as well.

Result table
The analysis result table of a sample is displayed in the Analysis environment below the electropherogram
views or the gel view. Sample information, sample comment (if entered), position of the sample on the
plate, and plate ID are displayed at the top of the result table. When an analyzed sample is selected, the
results are shown in the result table. The displayed columns depend on the mode. Right-click the header line
of the table, select Show column, and then select the property you are interested in.
DNA result table.

The Peak Result table lists the detected peaks of the sample. Use this result table for Standard DNA analysis
, for the Fast Analysis of DNA samples and for RNA analysis. Refer to the Peak result columns section for
detailed information on available peak properties.
The Peak Calling Result table lists the peak calling result of the sample. Use this result table also for RNA
quality control. Refer to the Peak calling result columns section for detailed information.
In DNA mode, the Smear/gDNA Result table lists the detected smear peaks of the sample and shows
properties that are specific for smear peaks. Smear peaks are detected only when the analysis profile
option Smear or gDNA had been selected in the Analysis Properties panel at the right of the Analysis
environment (Smear DNA analysis, gDNA analysis). Refer to the Smear result columns section for detailed
information on smear peak properties.
If a distribution analysis was performed on DNA mode, the Distribution result table is visible instead of the
Peak Calling Result table. Refer to the Distribution result columns for detailed information.
Note: Peak calling and distribution analysis generate an additional overview result table in the middle
panel of the Analysis environment. For more information, refer to Peak Calling or Distribution result,
respectively.
Modifying the result table
The information displayed in the result table can be customized for the electropherogram single view and
overview independently. The customization applies to all further viewing of the results.
Note: In the electropherogram superposition view, a small non-customizable result table is displayed.
Adding a column
To add a column:
1. Right-click the table header.

2. Select the column to be displayed from the Show Column selection.
Note: Select the Show all Columns option to display all columns. Select the Restore Default Columns option
to display the default for the application.
Removing a column
To hide a column:
1. Right-click the column header.
2. Unselect the column from the Show Column selection.
Changing column order

The order of the displayed columns can be changed by dragging a column header to the desired position.
While dragging, a marker is displayed that indicates the position of the column when dropping it.
Note: Columns of the peak calling and distribution result tables cannot be reordered.
Resizing column width

The column width can be changed by dragging a vertical cell border in the table header.
Note: Column widths of the peak calling and distribution result tables cannot be changed.
Interacting with the result table
Selecting and removing a peak

When selecting a peak in the result table, the peak is highlighted in the electropherogram (single
electropherogram view and electropherogram overview). To select a peak in the result table, left-click the
peak number in the # column. To unselect the peak, use the context menu option Unselect Peak or just click
to another cell. To remove the selected peak from the result table, use the context menu option Delete
Selected Peak. To remove multiple selected peaks from the result table, first select the peaks to delete by
holding the Ctrl key and left-clicking the corresponding peak numbers in the # column. Alternatively, hold
the Shift key and left-click the first and last peak numbers in the # column. All peaks in between will be
selected. Right-click the selection and click Delete Selected Peaks.
Exporting analysis results

The contents of the result table can be exported to other applications using the Windows clipboard. There
are several ways to select the table cells:
Select the cells with the mouse while holding down the left mouse button.
Click the first column of a row to select a row. You can also select multiple columns using the Shift and
Ctrl key.
Click the column header to select a column.

Click the column header of the first column to select all cells.
To copy your selection:
1. Select cell(s).
2. Right-click a selected cell.
3. Click the Copy selected cells to clipboard.
4. Paste the data to other applications, for example, Microsoft Excel®.
Note: The result data are exported using the local settings of the Windows system. Make sure that the
target application also uses the local settings to interpret the numbers.
Peak result columns
The following columns are available:
# Number of peaks in the sample.
Size [bp] For DNA mode only. Fragment size in base pairs.
Size [nt] For RNA mode only. Fragment size in nucleotides.
Conc. [ng/µl] Concentration of the fragment in ng/µl.

Note: This value is not calculated for alignment marker peaks.
Mol. [nmol/l] Molar concentration (molarity) in nmol/l. The calculation is based on the fragment size
and concentration.
Saturated Indicator whether the peak intensity reaches the maximum possible intensity (see
Saturated Signals section). The calculated height, area and concentration of saturated
peaks are not correct.
S/N Signal-to-noise ratio of the peak. The noise is approximated with three times the
standard deviation of the noise data points from the baseline.
NA Normalized area, also called corrected peak area. This is the peak area divided by the
migration time of the peak apex.
Area Peak area (integration of the area under the signal and above the baseline).
NA % Normalized peak area relative to the sum of all normalized peak areas.
Ratio NA The area ratio with respect to the previous peak. The alignment marker peaks and the
first data peak in the table will have an empty field here.
Height Height of the peak at its maximum.

Height % Peak height relative to the sum of all peak heights.
Res. The separation resolution relative to the next peak.

FWHM [sec] The peak width at half the maximum intensity (full width at half maximum), which is a
parameter for peak resolution and thus the precision of size calculation.
Start [min] Start time/X-value of the peak in minutes.
Time [min] Time/X-value for the peak maximum.
Stop [min] Stop time/X-value of the peak in minutes.
Rel. Time Relative time/X-value for the peak maximum. This value is mode-dependent:
In DNA mode, in case of 2 alignment marker peaks, the relative position of the peak
between lower alignment marker and upper alignment marker is mapped to the interval
from zero to one, i.e. all peaks have a Rel. Time between zero and one. The alignment
markers have a Rel. Time of zero and one, respectively. In case of one alignment
marker peak, the relative migration time is calculated as in RNA mode.
In RNA mode, the relative position of the peak in relation to the lower alignment marker
is calculated, i.e. the alignment marker has a Rel. Time of 1 and all other peaks have
Rel. Time higher than one.
Peak calling result columns
Each row in the table corresponds to a sample; the columns Pos. and Sample Info identify the sample. The
Pos column is fixed. The following columns are defined by the peak calling instruction. Aggregated columns
over all peaks of interest appear if they were selected in the Calculated Columns panel of the peak calling
instruction. The following columns are grouped by the names of the peaks of interest and show several
peak properties. To change the properties listed for each peak of interest, right-click the table header and
select/unselect the property with the Show Column option. The change takes effect in the entire table.
Note: If a sample was not analyzed, it is not present in the peak calling result overview.
Parts of the peak calling result table can be copied to the clipboard. Select the cells to be copied and then
press Ctrl+C. To copy the complete result of a peak calling instruction, right-click in the peak calling result
table and select the Copy Peak Calling Result of [...] option.
Smear result columns
The following smear peak properties are available:
# Number of peak in sample.

Note: As alignment marker peaks are no smear peaks, the peak number in this table
usually starts with 2.
Median Size Determines the fragment size that corresponds to the median of the area of interest. The
[bp] median is the point in the peak curve, where geometrically the left part of the peak area
has the same size as the right part. The value is given in base pairs.
Conc. Area of Continuously calculated concentration of the fragments corresponding to the area of
Interest [ng/µl] interest. Value is given in ng/µl.
Mol. [nmol/l] Molar concentration (molarity) of the fragments corresponding to the area of interest. This
Area of Interest calculation is based on the continuously calculated fragment size and concentration, not
Median Size, and is given in nmol/l.
Start Area of Start of the area of interest given in base pairs.
Interest [bp]
End Area of End of the area of interest given in base pairs.
Interest [bp]
% Conc. Area Percentage of concentration of fragments in the area of interest relative to the concentration
of Interest of the smear peak (defined by the start and end of the peak).
NA Area of Normalized area based on the area of interest. Area of the smear peak normalized by the
Interest migration time.
% NA Area of Percentage of the normalized area relative to the normalized area of the smear peak
Interest (defined by the start and end of the peak).
Note: All values listed in the table above refer to the area of interest assigned to a smear peak. Moving the
borders of the area of interest of a smear peak will trigger the recalculation of the corresponding
properties.
In addition, two properties are calculated for the entire sample. The values are displayed just above the
smear result table:
Total Concentration Total concentration of the fragments across the entire sample. The calculation is
[ng/µl] performed continuously for all data points with a signal above the baseline. The
calculation starts after the end of the lower alignment marker peak and ends at the
beginning of the upper alignment marker peak. The value is given in ng/µl.
Total Molarity Total molarity of the fragments across the entire sample. The calculation is based
[nmol/l] on continuously calculated fragment size and concentration for all data points with
a signal above the baseline. The calculation starts after the end of the lower
alignment marker peak and ends at the beginning of the upper alignment marker
peak. The value is given in nmol/l.
If the value is not visible, scroll the horizontal table scroll bar to the right to see
the value.

Distribution result columns
Each row in the table corresponds to a sample, with the columns Pos. and Sample Info identifying the
sample. Columns relevant to the entire sample appear first. Thereafter, columns are grouped according to
the names of the defined areas of interest and display several smear peak properties. The remaining
columns are then grouped by the name of defined ratios. Find a detailed description in the section
Distribution result columns.
To change the properties listed, right-click the table header and select or unselect the property with the
Show Column option. The change takes effect in the entire table.
Note: If a sample was not analyzed with a smear or gDNA analysis profile, it will not appear in the
distribution result overview. If a sample was not analyzed with a reference marker, the distribution values
cannot be calculated. In this case, the sample Quality is listed as "Review." In both cases, follow the
instructions in Analysis of DNA samples to check and correct the analysis steps that are required before
Distribution analysis. Ensure using Analysis parameters as described in Smear DNA analysis and gDNA
analysis, respectively.
The distribution result table can be copied to the clipboard. To copy the complete result of a distribution
profile, right-click in the distribution result table and select the Copy Distribution Result of [...] option.
Columns relevant to the entire sample:
Pos Position on the plate.
Sample Info Sample information
Total Conc. [ng/µl] Total concentration of the fragments across the entire sample. Refer to Smear
result columns for details. The column displays "n/a" for size marker samples.
Total Mol. [nmol/l] Total molarity of the fragments across the entire sample. Refer to Smear result
columns for details. The column displays "n/a" for size marker samples.
Quality The overall quality assessment of the sample.
The column reports "Passed" if all ratio assessments and height checks passed (if
applicable). That is, if one sub-assessment failed, the overall quality reported is
"Review" as well. The column displays "Not Analyzed" for size marker samples.
Note: If the sample was not analyzed with a reference marker table, i.e., if the Size and concentration
determination procedure was unsuccessful, the Quality reported will be "Review," and Total Conc. and Total
Mol. will display "n/a."
Columns relevant to an area of interest (grouped by name of the area of interest):
Mol. [nmol/l] Molar concentration (molarity) of the fragments corresponding to the area of
interest. Refer to Smear result columns for details. The column displays "n/a" for
size marker samples.

Conc. [ng/µl] Concentration of the fragments corresponding to the area of interest. Refer to
Smear result columns for details. The column displays "n/a" for size marker
samples.
Height [S/N] Maximum signal height of the area of interest, given as a Signal-to-noise ratio
[S/N]. The noise is approximated by taking three times the standard deviation of
the noise data points from the baseline. The column displays "n/a" for size
marker samples.
Height Check The quality assessment of an area of interest with regards to the Height [S/N].
The column reports "Not Analyzed" if the height of the area is not to be checked;
"Passed" when the checked height of the area of interest is above the defined
minimum height for that area; and "Review" when not. The column displays "Not
Analyzed" for size marker samples.
Size Start [bp] Start size of the area of interest given in base pairs. The column displays "n/a"
for size marker samples.
Note: The size may differ slightly from the start size defined in the distribution
profile. The area of interest starts at the data point with a size nearest to the
defined start size.
Size End [bp] End size of the area of interest given in base pairs. The column displays "n/a" for
size marker samples.
Note: The size may differ slightly from the end size defined in the distribution
profile. The area of interest ends at the data point with a size nearest to the
defined end size.
determination procedure was unsuccessful, the Height Check reported will be "Not Analyzed" and all other
columns will display "n/a."
Note: If the signal in an area of interest does not exceed the baseline at any point (indicating that the area
of interest is not present in the sample), the Height Check reports "Not Analyzed" when the height of the area
is not to be checked, and "Review" when it is to be checked. All other columns display "n/a."
Columns relevant to a ratio (grouped by name of the ratio):
Ratio (Molarity) This column is present only if the calculation basis Molarity has been selected for
ratios.
The value of the molarity ratio. That is, the molarity of the area of interest defined
as the Numerator divided by Denominator, which may be either the molarity of
another area of interest or the Total Molarity. The column displays "n/a" for size
marker samples.
Ratio (Concentration) This column is present only if the calculation basis Concentration has been
selected for ratios.

The value of the concentration ratio. That is, the concentration of the area of
interest defined as the Numerator divided by Denominator, which may be either
the concentration of another area of interest or the Total Concentration. The
column displays "n/a" for size marker samples.
Ratio Quality The quality assessment of the ratio. The column reports "Not Analyzed" if the
quality of the ratio is not to be checked; "Passed" when the value of the ratio is
within the defined range; and "Review" when not. The column displays "Review"
for size marker samples.
Numerator Defined in the distribution profile. This is the area of interest, of which the molarity
or the concentration is used as numerator of the ratio, depending on the selected
calculation method.
Denominator Defined in the distribution profile. Either Total Sample or another area of interest,
of which either the molarity or the concentration is used as denominator of the
ratio, depending on the selected calculation method.
determination procedure was unsuccessful, the Ratio Quality reported will be "Review" and the Ratio will
display "n/a."
Note: If the signal of the area of interest used for the numerator does not exceed the baseline at any point
(indicating that the area of interest is not present in the sample), the molarity/concentration value is
assumed to be "0." If the signal of the area of interest used for the denominator does not exceed the
baseline, the column Ratio Quality displays "Review." In both cases, the column Ratio displays "n/a."
For information about defining the distribution profile, refer to the Modifying a distribution profile section.

Gel view
The gel view displays the gel images of the samples.
The lanes in the gel view can be displayed in four view modes:
Normal mode
Inverted mode
False color rendering mode
Gel view with ruler, sample labels, and peak annotation.

The y-axis on the left-hand side is the main scale for the whole image. When the size scale is selected, it is
based on the bands of the reference marker applied to all samples (see sample A1 in the image above).
The y-axis on the right-hand side describes the detected bands of the selected sample only (see above:
highlighted with the black border, in the image above sample A7). It is available in the application only,
not in report/export images (also not if the Use Images as Displayed option is selected).
Above each gel image the sample position is displayed (e.g., A1, A2, and so on). For a gel image a tool
tip can be displayed by moving the mouse pointer to the sample number. This tool tip has information
about the plate, the number of the run, and method that the sample was processed with.

If the mouse pointer hovers over the gel lanes, the values at the current cursor position are shown in the
upper left corner of the view.
The result table of one sample is displayed below the gel view. This sample is marked in the Experiment
Explorer and outlined with a black border in the gel view (see sample A7 in the image above). Select the
sample to display in the result table by left-clicking it in the Experiment Explorer or in the gel view.
To view a sample in detail, double-click its gel lane. The view changes to single electropherogram view. To
return to the gel view, select the Gel Image tab again.
You can interact with the gel view mainly through the buttons above the view:
Toggles zoom mode on/off.
In zoom mode (button pressed), the mouse is used to select a region for zooming into (Rubber
band function — see General software usage). In addition, you can use the scroll wheel of the
mouse to zoom in and out.
If this button is not pressed, the drag-and-drop function is activated to change the lane order.
Note: The controls in the lower left corner of the gel view can be used to set the zoom region to
absolute values, independently of the zoom mode.
Note: The drag-and-drop function is always possible if the mouse cursor is over the gel lane label,
even in the zoom mode (button pressed).
Auto scale.
Resets the zoom region to the overall data range, undoing all zooming.
Undo zoom.
Returns to the previous zoom state.
Toggles a horizontal ruler at cursor position.
To configure the gel view, click the Image options button for the following options:
Unit of y-axis Use this option to select the units of the y-axis scale on the left-hand side of the gel
view.
If you select Size, the y-axis will show a size scale based on the reference marker.
The lanes in the gel image will be aligned according to the alignment markers.
Note: The size scale can be created only if all selected samples have been run with
the same alignment marker, have been analyzed with the same reference marker
table, and the alignment markers have been correctly identified. Otherwise, a
message will appear instead. In this case, reanalyze the samples with the same
reference marker table and ensure that the alignment markers have been correctly
identified, or remove from the view the samples that have a different alignment
marker or those samples for which alignment markers could not be correctly
identified.

If you select Relative migration time, the y-axis will show relative migration time. The
lanes in the gel image will be aligned according to the alignment markers.
Note: The relative time scale can be created only if all selected samples have been
run with the same alignment marker, have been analyzed, and the alignment
markers have been correctly identified. Otherwise, the lanes cannot not be aligned
and the y-axis will display a corresponding message. In this case, reanalyze the
samples so that the alignment markers have been correctly identified, or remove
from the view the samples that have a different alignment marker or those samples
for which alignment markers could not be correctly identified.
If you select Absolute migration time, the lanes will not be aligned and the y-axis will
show an absolute time scale.
Individual scaling Select this option to auto-scale the contrast for each gel lane individually.
Unselect this option for a comparison of samples.

Show sample Select this option to display sample information at the top of each gel lane.
information
Show plate ID Select this option to display the plate ID at the top of the gel lane.
Show method Select this option to display the method applied at the top of each gel lane.
Show analysis
Highlight alignment Select this option to highlight the alignment marker bands
details
markers in green.
Note: This highlighting is only possible for analyzed

samples if the alignment markers have been correctly
identified
Show peak size If this option is selected, the y-axis on the right-hand side
will describe the sizes of the detected bands of the
selected sample.
Note: If the sample was not analyzed with a reference

marker, the y-axis on the right hand will display "n/a." If
the sample was not analyzed, a corresponding message
will appear.
Note: This option is always selected in the RNA mode.
Show median of size For DNA mode only. Select this option to show the
median size of detected smear peaks for the selected
sample.
Note: If the sample was not analyzed with a DNA smear

analysis profile or a reference marker, the y-axis on the
right hand will display "n/a." If the sample was not
analyzed, a corresponding message will appear.
Controls for contrast settings are located below the gel view to the right. The functions are described
below:

Contrast Use the slider to change the contrast according to your needs. The contrast value will
be saved together with the experiment. Thus, you can customize the gel images
independently of other experiments.
Noise cutoff Use the slider to customize display of the noise in the signal. Move the slider to the
extreme left position to see all signals. Move the slider to the right to suppress small
signals, eliminating the noise. As for contrast, the noise cutoff value will be saved
together with the experiment.
Changing lane order
The gel lanes can be reordered by drag-and-drop. The lane order takes effect for all views where the
samples are visualized. The changed order will be saved when saving the experiment.
To change the lane order:
1. Select one or more lanes in the gel view.
2. Left-click the header of the selected lane or lanes and drag it to the new position. While dragging, a
marker is shown indicating the new position of the lane(s) when dropping.
3. Drop the lane(s) when the marker indicates the correct new position. The lane(s) will be placed in that
position. If more than one lane was selected, the lanes will be inserted in the same order as they were in
before.
Note: If the zoom button is toggled off, dragging can start also inside a gel lane.
Electropherogram view
The electropherogram view is activated by clicking on the Electropherogram tab in the analysis
environment. Three electropherogram views can be selected using the following buttons in the tool bar:
Single electropherogram view.
Overview mode with several single electropherograms.
Superposition view with several superimposed electropherograms.
The single electropherogram view is described in this section. The overview and superposition mode are
described in the following sections.

Single electropherogram with peak annotation and
displayed electrical current.
The single electropherogram view consists of a plot showing the recorded signal and the gel representation
of the signal below the main plot.
Controls for the zoom region size and contrast settings of the gel view are located below the graphical
representations of the signal. The current cursor position is shown in the upper left corner of the view.
The analysis result of the sample is displayed below the electropherogram view. Refer to section Result
table for detailed information about the different types of result tables.
You can mainly interact with the electropherogram through the buttons in the tool bar (all buttons in this
table are listed in "not pressed" state, left-click the button to press/release):
Toggles zoom mode on/off. For details, see Zooming and scaling.
Auto scale. For details, see Zooming and scaling.
Undo zoom. For details, see Zooming and scaling.

Insert peak. For details, see Adding a peak.
Manual integration of a time range. For details, see Manual range integration.
Toggles ruler.
Activates vertical and horizontal rulers used to compare peak heights and positions.
To configure the electropherogram view, click the Image options button for the following options:
Unit of x-axis Use this option to select the units of the x-axis scale.
If you select Size, the x-axis will show a size scale based on the reference marker, if
the sample has been analyzed with a reference marker table and the alignment
markers have been correctly identified. Otherwise, a message will be shown
instead.
If you select Rel. Time, the x-axis will show relative migration time, if the sample has
been analyzed and the alignment markers have been correctly identified. Otherwise,
a message will be shown instead.
If you select Abs. Time [min], the x-axis will show an absolute time scale.
Note: If the relative time scale is not created, reanalyze the sample so that the
alignment markers are correctly identified. If the size scale is not created, reanalyze
the sample with a reference marker table so that the alignment markers are correctly
identified.
Show gel lane Select this option, to display the gel representation below the electropherogram in
alignment with the x-axis.
Show electrical Select this option to display the diagram of the electrical current measured during
current curve data acquisition below the gel representation, if present, in alignment with the x-axis.
Show analysis Select this option to display analysis details for analyzed samples. Additional
details options can be selected.
Mark detected peaks Select this option to display the apex markers of detected
peaks.
If the option With label is selected, peak labels are

displayed at the apex of each peak.
Note: Only peak labels that do not overlap with an

adjacent label are displayed. Hover the mouse cursor
over the peak apex to get a tool tip with the peak label.
Select the label units: Size, or absolute or relative

migration time.

Note: The label can be displayed as Size only if the
sample was analyzed with a reference marker (for details
refer to Size and Concentration determination).
Otherwise, "n/a" is displayed.
Note: In DNA mode, a second option Mark median of

size is available. If the sample was analyzed with a DNA
smear analysis profile, select this option to display the
marker with the median size of detected smear peaks.
You can switch the corresponding label on and off.
Select the option Mark peak start and end to mark the
start and end points of detected peaks.
Show areas of interest For DNA mode only. If the sample was analyzed with a
DNA smear analysis profile, select Show areas of interest
to display the areas of interest of detected smear peaks.
Show suspend Select this option to display the suspend integration
integration intervals intervals.
Show threshold Select this option to display the peak threshold (shown in
blue).
Note: The threshold parameter can be interactively

changed by moving the threshold with the mouse. For
details, see Modifying the threshold.
Show baseline Select this option to display the baseline (shown in red).
Below the gel view at the right, controls for contrast settings are located. The controls are described below:
Contrast Use the slider to change the contrast according to your needs. Contrast changes
apply for further display of the gel lanes below electropherograms in single view for
all experiments, but do not affect the contrast settings of the gel overview.
Noise cutoff Use the slider to customize display of the noise in the signal. Move the slider to the
extreme left position to see all signals. Move the slider to the right to suppress small
signals, eliminating the noise. As for contrast, changes to the noise cutoff value do
not affect the settings of the gel overview.

Zooming and scaling
The Electropherogram view allows exploration of the data via zooming and scaling.
Toggles zoom mode on/off.
When the button is clicked, the mouse is used to select a region for zooming into. For
information on how to use the Rubber band function, see General software usage. Additionally,
you can use the scroll wheel of the mouse to zoom in and out.
Auto scale.
Resets the zoom region to the overall data range (both in time and RFU dimension), undoing all
zooming.
Undo zoom.
Returns to the previous zoom state.
Independent of the zoom mode, all electropherograms can be panned using the axes. You can shift the
zoom region horizontally by dragging the x-axis. To shift the zoom region horizontally drag the y-axis.
Dragging the x-axis.

In addition to the tool buttons, the controls in the lower left corner of the Electropherogram view can be
used to set the zoom region to absolute values.
Input fields to set the zoom region to absolute values.

Note: For RFU values, only the values are permitted that are inside of the actual values. The values lying
outside of the range of actual values range are not accepted and the background of the input field
becomes yellow.
Note: For time values, the input of the upper range value up to an hour is allowed.
Peak annotations
In an analyzed sample the analysis result is displayed along with the raw signal. Each peak has peak
markers for start (green), apex (red '+', green for alignment marker peaks), stop (turquoise), and a peak
label. In DNA mode, if smear or gDNA analysis has been performed, i.e., if the sample has been analyzed
with selected analysis profile option Smear or gDNA, the median of the peak can be marked (with a pink
'x') instead of the apex.

Peak annotations showing the apex.
In addition to the peaks, the detected baseline (in red) and the threshold for peak detection above the
baseline (in blue) are displayed in the electropherogram.
The peak markers and units of the peak label can be configured by clicking the Image options button.
Whether peak markers, the baseline or the threshold are displayed or hidden can be configured under
Image options. For details, refer to Electropherogram view.
The functions are described below:
Selecting a peak In the electropherogram, left-click the apex marker of the peak.
Alternatively, in the result table, left-click the peak number in the # column.
The peak will be marked with a red circle in the electropherogram and
highlighted in the result table.
Unselecting a peak In the electropherogram or in the result table, open the context menu of the
selected peak and select the Unselect Peak option.
The red circle in the electropherogram disappears as well as the

highlighting in the result table.
Adding a peak See Adding a peak for information on how to add a peak.
The peak will be added to the result table.
Deleting a peak See Deleting a peak for information on how to delete a peak.
The peak will be removed from the result table, and the markers of the peak
in the electropherogram disappear.

Manual range integration
The manual integration of a time range is possible using the range integration tool ( ).
After clicking the Range Integration button, you need to specify a region. To do so, first click the left border
of the region, then click the right border of the region.
Selection of a region for manual integration.
After selecting the region, a dialog is displayed which shows the selected time range borders, the
normalized area sum of the region, and the percentage of normalized area in relation to the overall
normalized area.
Note: The calculated values can be copied to the clipboard using the context menu of the dialog.
Note: The alignment marker peaks are not included in the normalized area calculation.
Electropherogram overview
The electropherogram overview displays several electropherograms in a gallery view. Twelve samples are
always displayed on one page, arranged in a 3 x 4 matrix. It is intended for an overview inspection of the
acquired data. In the electropherogram overview the ruler tool is especially useful. It provides a
means to compare peak positions between several samples, both for alignment marker peaks and sample
peaks. For analyzed samples, each peak has a peak marker for apex time (sample peaks are red,
alignment marker peaks are green).

Overview after analysis using the ruler tool.
The zooming and scaling functionality is very similar to the single electropherogram view (see Zooming and
scaling). The only difference is that zooming affects all electropherograms.
Use the forward and backward buttons at the bottom of the gallery view to navigate through the pages of
the overview. Clicking on a sample in the experiment explorer will also navigate to the corresponding
electropherogram in the gallery view. Use the scrollbars to navigate through the electropherograms on one
page.
To enlarge the overview, collapse the parameters panel on the right side.
A result table displaying information on one sample appears below the electropherogram overview. Refer
to the sections Interacting with the result table and Result table for more information.
To inspect an electropherogram in detail, double-click it. The view changes to single electropherogram
view. To return to the overview, click again.

You can interact with the electropherogram mainly through the buttons in the tool bar:
Toggles zoom mode on/off. For details, see Zooming and scaling.
Auto scale. For details, see Zooming and scaling.
Undo zoom. For details, see Zooming and scaling.
Toggles ruler.
To configure the electropherogram overview, click the Image options button for the following options:
Unit of x-axis Use this option to select the units of the x-axis.
If you select Size, the x-axis will show a size scale based on the reference marker.
The electropherograms will be aligned according to the alignment markers.
table, and the alignment markers have been correctly identified. Otherwise, the x-
axis will show a corresponding message. In this case, reanalyze the samples with
the same reference marker table and ensure that the alignment markers have been
correctly identified, or remove from the view the samples that have a different
alignment marker or those samples for which alignment markers could not be
correctly identified.
If you select Rel. Time, the x-axis will show relative migration time. The
electropherograms will be aligned according to the alignment markers.
markers have been correctly identified. Otherwise, the electropherograms will not be
aligned and the x-axis will display a corresponding message. In this case,
reanalyze the samples so that the alignment markers have been correctly identified,
or remove from the view the samples that have a different alignment marker or those
samples for which alignment markers could not be correctly identified.
If you select Abs. Time [min], the electropherograms will not be aligned and the x-
axis will show an absolute time scale.
Show sample Select this option to display the sample position in the upper left corner of each
position electropherogram.
Show sample Select this option to display the sample information at the top of each
information electropherogram.
Show plate ID Select this option to display the plate ID at the top of each electropherogram.
Show method Select this option to display the method applied at the top of each
electropherogram.

Note: Only one of the options Show sample information, Show plate ID or Show
method can be selected at a time.
Show analysis Select this option to show analysis details for analyzed samples. Additional options
details can be selected.
Mark detected peaks Select this option to display the apex markers for
detected peaks.

size is available. If the samples were analyzed with a
DNA smear analysis profile, select this option to display
the marker with the median size of detected smear peaks.

integration intervals intervals.
Changing order
Remove samples from the electropherogram overview by dragging them from the overview into the
experiment explorer.
Add samples to the electropherogram overview by dragging them from the experiment explorer into the
overview. Added samples will be inserted at the end of the gallery.
To change the order of the electropherograms, switch to gel overview and reorder the samples there. See
Changing lane order for details. Then switch back to the electropherogram overview.
Below the electropherogram overview, the result table of one sample is displayed. This sample is marked in
the Experiment Explorer and outlined with a black border in the gallery overview (see sample A6 in the
image below). Select the sample in the Experiment Explorer or in the electropherogram overview by left-
clicking it to view its result table.

Inspecting result table of sample A6.
The functions are described below:
Selecting a peak In the electropherogram, left-click on the marker of the peak apex. Alternatively, in
the result table, left-click the peak number in the # column.
The peak will be marked with a red circle in the electropherogram and highlighted
in the result table.
Unselecting a peak In the result table, open the context menu of the selected peak and select the
Unselect Peak option.
The red circle in the electropherogram disappears as well as the highlighting in the
result table.
Deleting a peak Select the peak to be deleted in the result table. Open the context menu of the result
table and select the option Delete selected peak.
The peak will be removed from the result table, the marker of the peak in the
electropherogram overview disappears.

Electropherogram superposition view
The electropherogram superposition view displays up to 12 electropherograms in one plot. It allows an

easy comparison of several measurements.
In order to make the signals from different samples distinguishable, each sample has a distinct color.
Electropherogram superposition view.
In the lower part of the superposition view, small result tables of all samples are shown along with the
corresponding colors. The order of the result tables is the same as the sample order in the gel view or
electropherogram overview.

You can interact with the electropherogram through the buttons in the tool bar:
Toggles zoom mode on/off. For details see Zooming and scaling.
Auto scale. For details see Zooming and scaling.
Undo zoom. For details see Zooming and scaling.
Toggles ruler.
To configure the electropherogram superposition view, click the Image options button for the following
options:
Unit of x-axis Use this option to select the units of the x-axis.
If you select Size, the x-axis will show a size scale based on the reference marker.
The electropherograms will be aligned according to the alignment markers.
table, and the alignment markers have been correctly identified. Otherwise, the x-
axis will display a corresponding message. In this case, reanalyze the samples with
the same reference marker table and ensure that the alignment markers have been
correctly identified, or remove from the view the samples that have a different
alignment marker or those samples for which alignment markers could not be
correctly identified.
If you select Rel. Time, the x-axis will show relative migration time. The
electropherograms will be aligned according to the alignment markers.
markers have been correctly identified. Otherwise, the electropherograms will not be
aligned and the x-axis will display a corresponding message. In this case,
reanalyze the samples so that the alignment markers have been correctly identified,
or remove from the view the samples that have a different alignment marker or those
samples for which alignment markers could not be correctly identified.
If you select Abs. Time [min], the electropherograms will not be aligned and the x-
axis will show an absolute time scale.
Show electrical Select this option to display the diagram of the superimposed electrical current
current curve measured during data acquisition below the electropherogram superposition in
alignment with the x-axis.

Show size marker If this option is selected, and if exactly one size marker is among the superimposed
peak labels samples, the peak labels will be displayed for detected peaks of the marker sample.
Select the units of the peak labels in the drop-down list.
Adding and removing samples
The superposition view does not automatically display all samples selected for visualization.
To add samples to the superposition view:
1. In the Experiment Explorer select the samples to be added.
3. Select the Superimpose option.
Adding sample C4 to superposition.
The selected samples will be added to the superposition view. In the Experiment Explorer all samples that
are displayed in the superposition view are marked by a colored rectangular according to their color in the
superposition.
Note: Up to 12 electropherograms can be superimposed. A warning will be displayed if the limit is

exceeded.
Alternatively, drag and drop up to 12 selected samples from the Experiment Explorer to the superposition.
To remove samples from the superposition view, proceed as follows:

1. In the Experiment Explorer select the samples to be removed.
3. Unselect the Superimpose option.
Inspecting sample properties
To view sample properties:
1. Select the sample in the Experiment Explorer.
2. View the properties of the sample on the right-hand side of the analysis environment. If the toolbar on the
right is not displayed, open it by clicking on the following icon:

In the properties view, there
are six sections containing the
following information:
Sample
This section contains
general information about
the sample and the
acquisition, for example,
the date, experiment ID,
and plate ID.
Analysis instructions
The analysis instructions
section shows the analysis
parameters, alignment
marker, and the reference
marker used for the
analysis.
Peak Calling Instruction or

Distribution profile
This section shows the
peak calling instruction or
distribution profile that was
last applied to the sample.
Method
method name and actions
used during the acquisition.
Cartridge
The cartridge section
shows information about
the cartridge, such as the
cartridge ID and the
cartridge type.
Platform
software version and the
instrument information
(firmware version and
serial number) for the run.
Note: It is not possible to perform peak calling and distribution analysis in the same experiment. Thus, either
a peak calling instruction or a distribution profile is applied to a sample, but never both.

Saturated signals
Identifying a saturated signal

Overloading the signal by injecting highly concentrated DNA will cause the detector to saturate. Saturated
signals are those in which the signal level exceeds the maximal detector limit.
A saturated signal will usually display a flat top in its electropherogram. These signals are also referred to
as “clipped.”
An example saturated signal.
Preventing a saturated signal

There are 2 ways to prevent overloading or saturation of the signal: dilute the samples in QX DNA Dilution
Buffer or inject less sample. A smaller amount of sample can be injected by reducing the injection time (see
section Operating the QIAxcel). A nonsaturated signal will display a sharp peak in the electropherogram.

An example normal (nonsaturated) signal.
Peak detection
This section describes the peak detection procedure.
Unanalyzed raw data.

Analysis parameters for peak detection are provided in Analysis Profiles.
Raw data after peak detection, without determination of size and concentration.
Alignment marker peaks are marked in green. It is important that the correct peaks are marked as
alignment marker peaks because this is the basis for all other analysis functions.
Note: In the image above, the Analysis parameter Alignment Marker Threshold (see dark blue line in the
image above) was greater than the Threshold parameter. This leads to a peak in the threshold line at
alignment marker positions.
Peak detection procedure
To perform peak detection, proceed as follows:
1. Load the samples you want to analyze using the Experiment Explorer. For details, refer to the Loading
sample data section.
2. Visualize the samples you want to analyze. See the Viewing sample data section for details on data
inspection.
3. Select the samples for analysis.

Note: Here, the selection inside the middle view is relevant — not the selection in the experiment
explorer. See the Selecting samples for analysis or report section for details.
4. Open the Analysis parameters panel to be able to specify the analysis properties.

In the Analysis properties panel, define the parameters to use for analysis. This can be done by selecting a
predefined analysis profile, which can be either a default (e.g., "Default DNA") or a user defined parameter
set.
Refer to Analysis of DNA samples and Analysis of RNA samples for getting guidance as to which Analysis
profile should be selected initially and how to use the analysis options for your specific samples.
Alternatively, a new analysis profile can be created. To modify or create an analysis profile, refer to
sections Modifying an analysis profile and Creating a new analysis profile, respectively. The analysis
parameters of the selected profile are shown below the profile drop-down list. For general peak detection,
no reference marker is required. Check No Marker in the Reference Marker section, as illustrated in the
following figure.

No marker selected.
Note: If loaded samples have already been analyzed, the analysis parameters from the selected sample
can be transferred to the Analysis parameters panel. To do this, right-click the sample in the Experiment
Explorer and select the menu item Transfer analysis parameters from the context menu, as shown in the
following figure.

Note: The alignment marker of a plate can be changed. To change the alignment marker, select the menu
item Overwrite alignment marker from the context menu in the Experiment Explorer (the mouse cursor should
be over the plate name). The Overwrite Marker dialog appears. Select the alignment marker from the drop-
down list and confirm your choice by clicking OK.
5. Start the analysis by clicking the Start Analysis button.
6. View the analysis results. For each analyzed sample, the results are shown in tabular form at the bottom
of the Analysis environment in the Peak Result tab (see Result table section) and in the plot of the single
electropherogram view (see Electropherogram view).
Note: In the case of a smear or gDNA analysis, the Smear Result tab at the bottom of the Analysis
environment shows the calculated properties that are specific to smear peaks. For more details, see the
Result table section.
7. Make sure that the right peaks were detected. Firstly, it is important that the correct peaks are marked as
alignment marker peaks (marked with a green '+') because this is the basis for all other analysis
functions. If not, adapt the analysis parameters and repeat steps 5 to 7.
As a last option, use the Insert/Delete Peak options described in the Manually modifying analysis results
section.
8. Save the analysis results by clicking the Save button in the Experiment Explorer.

It is possible to automate the analysis (peak detection) during the data acquisition process. To do so, save
any changes in the analysis parameters into a customized analysis profile. Make sure that these analysis
parameters work for all samples. Then create a process profile. In the Process Profile step, select the
option Analysis in the Included steps section. In the Analysis step, select the customized analysis profile.
Save the process profile with these settings for reuse.
Modifying an analysis profile
To modify an analysis profile proceed as follows:
1. Open the Analysis tab at the right side of the Analysis environment.
2. Select the analysis profile to be modified in the Profile drop-down list in the Analysis Properties panel .
3. Change the analysis parameters as described below.
4. To save the modified profile click the Save as button to the right of the Profile drop-down list.
Note: The parameters of an analysis profile can be modified by users with assigned user role Advanced
User only.
Parameters can be changed by:
1. Clicking the parameter.
2. Changing the value (and unit if possible).
3. Clicking OK.

Changing the threshold parameter.
For example, to raise the threshold parameter to 7% starting from 4 minutes, perform the following:
1. Click the Add button below the parameters.
2. Select the parameter type Threshold.
3. Adjust the starting time (4 minutes), the threshold value (7), and its unit (%).
4. Accept the changes by clicking OK.

Each parameter displayed in the figure above has a corresponding time point. This is necessary because all
parameters, except for Alignment Marker Threshold, can be changed with respect to time.
Note: The time of the initial parameter at 0.0 minutes cannot be changed. The suspend integration
parameter is an exception. It is turned off by default and can be turned on to ignore a defined range of
data during peak detection. This region does not necessarily start from 0.0 minutes.

The descriptions of the parameters and instructions on how to deduce suitable settings are in the table on
the next page. Refer to sections Standard DNA analysis, Fast Analysis DNA analysis, Smear DNA analysis,
gDNA analysis, and Standard RNA analysis for information on which parameters work best for your
samples. More information about the analysis algorithms in QIAxcel ScreenGel and the respective
parameters can be found in Appendix D.
Parameter Description Adjusting the value

Peak For DNA mode only. This parameter Select this option if the profile has to
establishes the given profile as a DNA be used for Standard DNA analysis
profile for sharp peaks. or Fast Analysis DNA analysis.
Smear For DNA mode only. This parameter Select this option if the profile has to
establishes the given profile as a DNA be used for Smear DNA analysis of
smear profile. DNA libraries.
gDNA For DNA mode only. This parameter Select this option if the profile has to
establishes the given profile as a gDNA be used for gDNA analysis.
profile.
Baseline Filter This parameter governs the baseline The default value for the Window
detection (shown as a red line in parameter should be sufficient for most
electropherograms). samples.
Note: In case of a DNA smear and gDNA If the baseline starts following the
analysis, the software detects the baseline data, increase this value. Generally,
automatically and no parameterization by the value should be set to twice the
the user is needed. Thus, for smear and width of a single peak, but it must not
gDNA analysis profiles no baseline be larger than half of the total
parameter is shown. migration time.
If peak widths differ a lot over time,

use distinct values for the Window
parameter in different time intervals.
For an example, see the "Default
RNA" analysis parameter settings and
Analyze RNA samples.

Threshold The threshold parameter is used during The default setting is a good starting
peak detection. Signals that exceed the point for most samples. The threshold
baseline by the threshold value are should be lowered if relevant peaks
detected as peaks. The threshold can be are below the threshold and not
given in RFU, as percentage of the recognized as peaks.
highest signal in the sample, or as a You can specify the threshold using
multiple of the (estimated) noise level of different units. Use the RFU unit to set
the electropherogram. the threshold to a fixed RFU value. Use
the % unit to specify the threshold as a
Note: The software uses the threshold for
percentage of the highest signal in the
detection of alignment marker peaks
sample. Use the S/N unit to specify
whenever no higher alignment marker
the threshold as a multiple of the
threshold is set.
noise level, which is estimated from the
sample data.
Note: For DNA smear and gDNA

analysis, a higher S/N value is
required as threshold.
Note: The threshold parameter can be

interactively changed in the single
electropherogram view. Simply drag
the threshold (displayed in blue) with
the mouse. When doing so, the
sample is re-analyzed using the new
threshold (all other parameters are
taken from the sample properties).
Minimum Distance The minimum distance parameter is used The default setting is suitable for most
during the plausibility check of peaks. It samples.
defines the minimum distance two peak For very noisy data with fronting or
clusters must have to be detected as two tailing, in order to prevent the
distinct peaks. detection of noise peaks at cluster
In noisy data with heavy tailing or borders, increase the value.
fronting, noise spikes can cross the
minimum peak threshold several times at
the border of peaks. Detection of these
noise peaks is prevented by this
parameter.
Suspend Integration The suspend integration parameter turns In the default setting, Suspend
off peak detection for a defined period of Integration is turned off, meaning that
time. The affected areas are marked with peak detection is performed on the
a grey bar in the single electropherogram entire duration of migration time.
view as well as in the electropherogram The time interval for Suspend
overview. Peaks that overlap with this Integration can be specified via
bar are ignored by the analysis. absolute or relative migration time. In
case the relative time unit is used,
alignment marker peaks are not
affected by Suspend Integration.

Note: The suspend integration interval
is shaded gray in the
electropherogram single view and
overview.
Note: If relative time is chosen to

describe the suspend integration
interval, the following constraints
apply: in case of 2 alignment marker
peaks, all relative times must be
between 0 and 1. In case of 1
alignment marker peak, all relative
times must be above 1.
Smoothing Filter The smoothing filter parameter defines the The default window width is a good
smoothing window width, i.e., the setting for most samples. If two close
strength of the smoothing. The smoothing peaks cannot be resolved, the
filter improves the signal-to-noise ratio (S/ smoothing filter parameter can be
N) of the data but lowers the resolution. lowered or disabled (i.e., set to 0 pts)
to obtain the optimal resolution. One
example for disabled smoothing is the
Default Fast Analysis profile.
Note: A different smoothing algorithm

is applied in DNA smear analysis (
Appendix D). The window length
parameter of this algorithm is given in
seconds.
Alignment Marker This parameter allows to set a higher A value between 5 and 10 should be
Threshold threshold for alignment marker peaks. It is suitable for most samples. If the
useful to avoid that low intensity peaks alignment marker peaks have a lower
are detected as alignment marker peaks, S/N value, you can lower this
e.g., primer dimers before the lower threshold, or disable it by setting it to
alignment marker peak or noise peaks on a value below the Threshold
the tail of the upper alignment marker. parameter.
Note: For DNA smear and gDNA

analysis, a higher S/N value is
required as alignment marker
threshold.

Creating a new analysis profile
To create a new analysis profile:
1. Open the Analysis tab in the toolbar on the right-hand side of the Analysis environment.
2. Select an existing analysis profile from the Profile drop-down list. The selected profile serves as a
template for the creation of the new profile. Select NewAnalysisProfile to start with default parameters.
3. Change the analysis parameters according your needs as described in the Modifying an analysis profile
section.
4. Store the new profile by clicking the Save as button to the right of the Profile drop-down list.
5. Assign a unique name to the profile and click OK.
Note: Only users with assigned user role Advanced User can create new analysis profiles.
Size and concentration determination
For a sample with detected peaks, the sizes and concentrations of the underlying analytes are calculated
by referencing to a sample containing fragments of known size and concentration. The figures below show
how a so-called reference marker (middle picture) is used to derive the sizes and concentrations for detected
peaks (upper and lower picture). A reference marker can be created in two ways: either a size marker
sample is run side by side with the samples that are being analyzed or a previously saved reference marker
is selected in the Reference Marker section in the analysis tab. For details, see Creating a reference marker.
Sample with detected but not annotated peaks.

Each detected peak is mapped to a corresponding reference marker peak. For peaks without unique
corresponding reference marker peaks, the adjacent reference marker peaks are taken as reference (e.g.,
peaks with known size 310 bp and 603 bp, respectively).

Reference marker sample. Sizes and concentrations of contained molecules are known.
Sample with detected and annotated peaks.
The sizes for the newly detected peaks are either directly transferred from the matching reference marker
peaks (15 bp peak) or interpolated using the two adjacent reference marker peaks (562 bp peak
interpolated from 310 bp and 603 bp).
Similarly, the concentrations of detected analytes are referred from the known concentrations underlying the
corresponding reference marker peaks.
This section describes how to proceed to determine size and concentration.

Note: Sample analysis can be performed by users with the assigned user roles Basic User and Advanced
User only.
Size and concentration determination procedure
To determine size and concentration, proceed as follows:
1. Load the samples you want to analyze using the Experiment Explorer. For details, refer to the Loading
sample data section.
2. In the Analysis parameters panel at the right side of the Analysis environment, define the parameters to
use for analysis.
It is possible to reuse the analysis parameters and the reference marker table of an analyzed sample. This
can be helpful if samples have already been analyzed during the data acquisition process, but analysis
shall be reviewed or repeated. To do so, right-click one of the samples in the Experiment Explorer and
select the context menu option Transfer Analysis Instruction. The analysis parameters and the reference
marker table, if present, from the sample will be transferred to the analysis parameters tab.
Otherwise, select a predefined analysis profile in the Analysis properties panel.
To modify or create an analysis profile, refer to sections Modifying an analysis profile and Creating a new
analysis profile, respectively.
3. If the size marker was run side by side with samples, create a new reference marker as described in
Creating a reference marker. If samples should have been analyzed during data acquisition process, but
either an error message has been shown or sample results are not as expected, use the procedure to
check the correctness of the created reference marker step by step and recreate the reference marker, if
needed. If the reference marker needs to be recreated, all other samples need to be reanalyzed too, as
described in the next steps, using this new reference marker in step 6.
4. Visualize the samples you want to analyze. See the Viewing sample data section for details on data
inspection.
5. Select the samples for analysis.

Note: Here, the selection inside the middle view is relevant – not the selection in the Experiment Explorer.
See the Selecting samples for analysis or report section for details.
6. Define the reference marker to be used in the Reference Marker section of the Analysis panel. If you just
created or recreated a reference marker in step 2, it is preselected for use. Proceed with step 7.
Otherwise, check Reference Marker Table and select a previously saved reference marker. Details of the
reference marker are shown below the combo-box.

Reference marker checked.

Note: To ensure compatibility, the reference marker drop-down list contains only reference marker tables
that match the alignment marker of the selected samples. The drop-down list is marked as invalid and empty
if there is no matching reference marker table or no sample has been selected for analysis. In this case,
select a sample. If the drop-down list is still marked as invalid, check the sample alignment marker and
correct it if required (refer to Checking alignment marker), or create a new reference marker (refer to
Creating a reference marker).
Note: If no sample is selected for analysis, the reference marker drop-down list is empty. Select the samples
to analyze before selecting the reference marker. For details, see Selecting samples for analysis or report.
Note: See the table below for explanation of the symbol at the right of the Reference Marker Table drop-
down list:
The selected reference marker table is fully compatible.
That means that the size marker used for the reference marker table was processed no earlier or later
than 90 days (DNA)/60 days (RNA) as the sample, and with the same cartridge and method as the
sample. For analysis, it is not necessary to run the size marker first. The user can analyze older
samples with a newer reference marker as well.
The size marker used for the reference marker table was processed more than 90 days (DNA)/60
days (RNA) earlier or later than the sample, with the same cartridge and method as the sample.
The reference marker table was processed with the same method as the sample, but with another
cartridge of the same cartridge type.
The reference marker table is not compatible with the sample. This can happen if no reference marker
matches the cartridge type, method and alignment marker of the sample.
It is also shown when the software cannot check the compatibility because no sample has been
selected for analysis.
Important: Selecting the correct size marker will increase the accuracy of the size and concentration
determination. Use the marker containing DNA fragments closest to the size of your targeted DNA
fragments. The DNA fragments to be analyzed must fall within the smallest and largest fragment size of the
size marker. In addition, the range of the alignment marker must cover the range of the size marker.
7. Start the analysis by clicking the Start Analysis button at the bottom of the Analysis Parameters panel.
8. View the analysis results. For each analyzed sample, the results are shown in tabular form at the bottom
of the Analysis environment in the Peak Result tab. In the case of a smear or gDNA analysis in DNA
mode, the Smear/gDNA Result tab shows the calculated properties that are specific to smear peaks. For
more details, see the Result table section. The single electropherogram view is most suitable for checking
peak detection. (see Electropherogram view).
Note: If the samples had been analyzed before with Peak Calling or Distribution analysis, these results will
be automatically updated as well, based on the new calculations for peaks/smear peaks.

In case the sample was earlier analyzed with distribution analysis in DNA mode, the single
electropherogram view shows smear peaks corresponding to the areas of interest as defined in the
distribution profile. In order to see a plot of the peak detection, the distribution analysis needs to be
removed temporarily. To do so, right-click the sample in the Experiment Explorer to the right and select the
option Transfer Distribution Profile to copy the parameters that had been used for distribution analysis into
the Distribution panel to the right for later reuse. Then right-click the sample again and select the option
Remove Distribution Analysis Data to remove the results of distribution analysis from the sample. The single
electropherogram now shows the result of peak detection. It shows the alignment marker peaks (marked
green at the apex) and the smear peaks according to the Smear/gDNA Result table.
9. Make sure that the right peaks were detected. First of all, it is important that the correct peaks are
marked as alignment marker peaks (marked with a green '+') because this is the basis for all other
analysis functions. If not, adapt the analysis parameters and repeat the steps 5 to 9.
As a last option, use the Insert/Delete Peak options as described in the Manually modifying analysis results
section.
10.In case the distribution analysis needs to be removed temporarily, it has to be repeated manually by
using the distribution profile parameters that had been transferred before. Refer to Distribution analysis for
instructions.
11.Save the analysis results by clicking the Save button in the Experiment Explorer.
It is possible to automate the peak detection and size and concentration determination during the data
acquisition process. To do so, save any changes in the analysis parameters into a customized analysis
profile. Make sure that these analysis parameters work for all samples and also for the size marker sample.
Then create a process profile. In the Process Profile step, select the option Analysis in the Included steps
section. In the Analysis step, select the customized analysis profile. If the size marker is to be run side by
side with samples, define the size marker position for a run in the right part of the screen in the Run
Parameters step, select the option Run size marker side by side with sample in the Marker step, and select
the alignment marker and the size marker. If instead, a previously created reference marker shall be reused
for several runs, select the option Reference Marker Table and select the previously created reference
marker. For further details, refer to Process profile options. Save the process profile with these settings for
reuse. During each run setup, ensure to select the alignment marker in the Sample Selection step.
Creating a reference marker
To create a new reference marker, an analyzed size marker sample with annotated peak times and areas is
required. A reference marker is formed by matching the peaks of the size marker sample to a size marker
table (including alignment marker).
Proceed as follows:

1. In the Experiment Explorer select the sample that contains the size marker. If it is not flagged as a size
marker (i.e., its symbol is or ), flag it with a right-mouse click and by selecting the Size Marker
option from the context menu that appears. The icon changes to or .
Analyzing the size marker sample.
2. Open the size marker sample in single electropherogram view by clicking the Electropherogram tab at
the top of the middle view. If the size marker sample is already analyzed (i.e., its symbol is ),
proceed with step 6.
3. Select a profile in the Analysis Properties toolbar.

Note: It is possible to reuse the analysis parameters of an analyzed size marker sample. This can be helpful
if the sample has already been analyzed during the data acquisition process, but analysis shall be
reviewed or repeated. Right-click the sample in the experiment explorer and select the context menu option
Transfer Analysis Instruction. The analysis parameters and the reference marker table, if present, from the
sample will be transferred to the analysis parameters tab.
4. Select No Marker as reference marker in the Reference Marker toolbar below.
5. Start the analysis by clicking the Start Analysis button.

The result of the analysis is a sample with annotated peak times and areas.
6. Make sure that the right peaks were detected. If not, adapt the analysis parameters and reanalyze the
size marker sample.
As a last option, use the Insert/Delete Peak options described in the Manually modifying analysis results
section.
7. Switch to the Reference Marker screen by clicking the Reference Marker tab on the top of the middle
view.
The peak table (with the Rel. Time and NA columns) of the size marker sample is displayed at the left side
of the screen.
Note: The panel is empty if no size marker sample is selected in the Experiment Explorer or if the selected
size marker sample is not analyzed. In this case, repeat the steps above first.

Creating the reference marker.
Note: Depending on cartridge and method, a size marker creates different gel lanes. As the gel lane for the
size marker (right-hand side) is a calculation based on the size marker table only, this image may differ
from the gel lane from the actual run (left-hand side).
8. In the Reference Marker screen, check the alignment marker and select the size marker used in the size
marker sample.
A comparison of the sample gel view (left) and the theoretical reference marker gel view (right) is
displayed in the middle of the screen.
Note: If the alignment marker is not correct, change it as described in Checking alignment marker.
Note: Creating new size markers is described in Creating a new size marker table.
9. If the number of peaks in the size marker sample matches the number of peaks in the reference marker
(two alignment marker peaks plus the size marker peaks), the reference marker can be used for sample
analysis. Click the Apply button at the top of the Reference Marker screen to copy the created reference
marker to the bottom of the Reference Marker panel of the Analysis parameters screen.
Optionally, save the reference marker using the Save as button at the top of the screen if you want to use
the reference marker table for the analysis of further experiments.

Note: The Apply and Save as buttons are disabled and a warning is displayed at the top of the screen if the
reference marker is invalid, e.g., if the number of peaks on the left and on the right does not match.
If more peaks than expected were detected in the size marker sample, you can delete them using the Delete
button below the size marker samples peak table (with Rel. Time and NA).
Alternatively, switch to the single electropherogram view and check that the correct peaks were detected.
Use the Insert/Delete Peak options described in the Manually modifying analysis results section or change
the analysis parameters and reanalyze the size marker sample.
Note: A reference marker can be created by users with the assigned user role Basic User and Advanced
User only.
It is possible to automate the creation of the reference marker during the data acquisition process if the size
marker is to be run side by side with samples. To do so, save any changes in the analysis parameters into
a customized analysis profile. Make sure that these analysis parameters also work for the samples. Then
create a process profile defining the size marker position for a run in the Run Parameters step and selecting
the customized analysis profile in the Analysis step. Save the process profile with these settings for reuse.
To continue sample analysis, refer to step 3 of the Size and Concentration determination procedure.
Creating a new size marker table
To use a custom size marker, a new size marker table has to be created manually.
Proceed as follows:
1. In the Experiment Explorer select the sample that contains the size marker. If it is not flagged as a size
marker (i.e., its symbol is or ), flag it with a right-mouse click, selecting the Size Marker option
from the context menu that appears. The icon changes to or .
2. Open the Reference Marker screen of the Analysis environment.

Editing a new size marker.
3. Select NewSizeMarker from the size marker drop-down list to create an empty size marker table.
4. Click the Add button below the table to add a new row to the table.
5. Define the size and optionally the concentration.
6. Click OK to save the changes to the table. Repeat the steps from step 4 to define all rows.
7. Save the new size marker by clicking the Save Size Marker as button below the size marker drop-down
list.
Note: A new size marker can be created by users with the assigned user role Advanced User only.

Note: If a sample is selected which is flagged as a size marker, a warning about mismatch of the number of
rows of the size marker and peak table of the selected sample may be displayed. Ignore the warning and
proceed with adding fragment sizes to the size marker table. If you entered all size marker fragments and
the warning persists, switch to single electropherogram view and check that all peaks have been detected
correctly.
Peak Calling
Based on the peak table, which is the result of the sample analysis, a peak calling step can be performed.
Peak calling shows whether corresponding peaks (e.g., because of the same size) are present in analyzed
samples, and provides peak data for comparison.
To trigger peak calling, the definition of the peaks of interest must be provided by the user. Refer to the
Creating a new peak calling instruction section for information on how to create it.
Note: Peak calling can be performed by users with the assigned user roles Basic User and Advanced User
only.
To perform peak calling proceed as follows:
1. Load and activate the experiment for which sample peak calling should be carried out.
2. If not yet analyzed, analyze the samples of interest as described in Standard DNA analysis.
Note: The samples must be analyzed before performing peak calling.
3. Select the visualized samples that the peak calling instruction shall be applied to.
4. Open the Peak Calling tab located on the right-hand side of the Analysis environment.
Note: In DNA mode, the Peak Calling tab is available only if peak calling features are active. Refer to
Activating peak calling features for information on how to activate peak calling features.
5. Select the peak calling instruction from the Peak Calling Instruction drop-down box, which contains the set
of peaks to search for.
6. Start peak calling by clicking the Start Peak Calling button at the bottom of the Peak Calling tab. The
peak calling instruction is assigned to the selected samples and the Peak Calling screen in the middle of
the Analysis environment is filled with the peak calling result.
Note: If you click Start Peak Calling the next time with the same unchanged peak calling instruction, the
previous peak calling result for this instruction is completely replaced by the new one. If you would like to
apply the same peak calling instruction to different data and don't want to overwrite the first set of results,
save the instructions under different names, and apply them subsequently to the different sets of samples.

7. Switch to the Peak Calling screen in the middle of the Analysis environment to view the result. The
structure of the result is described below.
Separate RNA analysis for row A and B with RNA peak calling.
8. To save the result of peak calling, save the experiment by clicking the Save button in the
Peak calling result

Every sample can be analyzed individually (by means of peak calling). Therefore, the peak calling result
overview is grouped by peak calling instructions, each of them named as the applied peak calling
instruction (see image above). The result for each peak calling instruction can be collapsed individually. It
has the following structure: the table peak calling instruction is placed at the top, followed by the list of the
samples to which the peak calling instruction has been applied. The list of the samples is grouped by the
plates to which the samples belong.

Each row in the table corresponds to a sample; the columns Pos. and Sample Info identify the sample. The
Pos column is fixed. The following columns are defined by the peak calling instruction. Aggregated columns
over all peaks of interest appear if they were selected in the Calculated Columns panel of the peak calling
instruction. The following columns are grouped by the names of the peaks of interest and show several
peak properties. To change the properties listed for each peak of interest, right-click the table header and
select/unselect the property with the Show Column option. The change takes effect in the entire table.
Note: If a sample was not analyzed, it is not present in the peak calling result overview.
Parts of the peak calling result table can be copied to the clipboard. Select the cells to be copied and then
press Ctrl+C. To copy the complete result of a peak calling instruction, right-click in the peak calling result
table and select the Copy Peak Calling Result of [...] option.
Removing peak calling result

To remove the result of peak calling from a sample, right-click the sample in the experiment explorer and
select Remove Peak Calling Data from the context menu that appears, as shown in the figure below. This
menu item is only active if peak calling has been performed for the sample.
Remove the result of peak calling from a sample.

It is possible to automate peak calling during the data acquisition process. Ensure you have already
automated the Size and concentration determination procedure for your samples using Standard DNA
analysis, Fast Analysis DNA analysis or Standard RNA analysis. To automate peak calling, save any
changes in the peak calling instructions into a customized peak calling instruction. Make sure that these
parameters work for all samples. Then modify the process profile you have created to automate the size
and concentration determination procedure for your samples. In the Process Profile step, select the option
Peak Calling in the Included steps section additionally. If distribution analysis features are still active,
activate peak calling features now. See the section Activating distribution analysis features. In the Peak
Calling step, select the customized peak calling instruction. For further details, refer to Process profile
options. Save the process profile with these settings for reuse. During each run setup, ensure selecting the
alignment marker in the Sample Selection step.
Activating peak calling features
In DNA mode, either peak calling or distribution analysis features can be applied to samples of an active
experiment.
To activate peak calling features for the current experiment, select Activate Peak Calling Features from the
View menu. The peak calling result tables replace the distribution result tables and the peak calling
parameter panel replaces the distribution parameter panel. The software keeps this setting until an
experiment that used distribution analysis is activated or opened.
Note: It is not possible to activate peak calling features if a distribution analysis has already been
performed in the current experiment. In this case, remove the distribution analysis data first.
Modifying a peak calling instruction
Peak calling instructions contain a set of parameters, defining the peaks to search for (peaks of interest).
Note: Peak calling instructions can be modified by users with the assigned user role Advanced User only.
To modify a peak calling instruction proceed as follows:
1. Open the Peak Calling tab at the right of the Analysis environment.
2. Select the peak calling instruction to be modified from the Peak Calling Instruction drop-down box.
3. Change the definitions for the peaks of interest according to your needs as described below.

Modifying a row.
Note: The name in the Peak Calling Instruction drop-down box will appear with an asterisk to the left,
indicating that the table has been changed.
4. Save the modified peak calling instruction by clicking the Save as button to the right of the Peak Calling
Instruction drop-down box.

Peak calling configuration:
Include size marker samples If this option is chosen, peak calling can be performed on
the size marker sample too. Otherwise, peak calling

will be skipped for size marker samples.
Find centered / highest peak in interval If more than one peak is found within the tolerance interval,
this setting determines whether the centered peak (nearest
to the sought position) or the highest peak is chosen.
To add a peak of interest:

1. Click the Add button. A new row with empty fields will appear at the bottom of the table.
2. Specify the peak of interest in the edit area below.
Name Specifies the name of the peak of interest. This will be the column header in the peak
calling result table.
Note: The names of the peaks must be different.
Position Specifies the position of the peak to search for and the unit of the position (Size, Rel. Time,
or Time).
Note: The positions of the peaks must be different.
Note: If Rel. Time is chosen to describe the position, the following constraints apply: In case
of 2 alignment marker peaks, all relative times must be between 0 and 1. In case of 1
alignment marker peak, all relative times must be above 1.
Tolerance Tolerance for peak searching. In a sample the peak will be considered as detected if its
position difference is less than the given tolerance from the defined position.
3. Click OK to add the new peak of interest to the table.
Note: The peaks of interest are sorted by position in the peak calling instruction table.
To delete a peak of interest:

1. Select the peaks row in the table.
2. Click the Delete button.

To modify a peak of interest:
1. Select the row of the peak of interest to be modified.
2. Edit the values of the peak of interest in the edit area below.
3. Click OK. The values in the selected row are changed.
Note: The peaks of interest are sorted by position in the peak calling instruction table.
Calculated columns:
In addition to finding the specified peaks, depending on the run mode, the following parameters can be
calculated during peak calling:
Total Concentration For RNA mode only. The total concentration of the RNA over the whole
sample.
RNA Integrity Score For RNA mode only. RNA integrity score (RIS) is a value from 0 to 10, where
a value of 10 indicates completely intact RNA. This is especially useful for
RNA QC.
Note: The value is not calculated if the 18S peak was not found.
Ratio Normalized Choose two peaks of interest. If both are found in the sample, the ratio of
Area their normalized areas is calculated. This is especially useful for RNA QC
using the 28S and 18S peaks.
Relative Abundance For each peak of interest, the normalized area relative to the highest
normalized area of corresponding peaks over all samples is calculated. (For
the sample in which the normalized area of the peak is highest, the relative
abundance is 100%. For all other samples, it is the percental fraction of its
normalized area relative to the highest value.)
Creating a new peak calling instruction
To create a new peak calling instruction:
1. Open the Peak Calling tab at the right of the Analysis environment.
2. Select a peak calling instruction from the Peak Calling Instruction drop-down box. The selected peak
calling instruction serves as a template for the creation of the new one. Select NewPeakCallingInstruction
to start with an empty table.
3. Specify the peaks of interest according to your needs as described in the Modifying a peak definition
table section.
4. Save the new peak calling instruction by clicking the Save as button to the right of the Peak Calling
Instruction drop-down box. Enter a new unique peak calling instruction name and click OK.

Peak pattern matching
Based on a peak calling step, a peak pattern matching step can be performed.
Peak pattern matching shows whether certain patterns of peaks (determined in the peak calling step) are
present in analyzed samples.
Note: Peak pattern matching can be performed by users with the assigned user roles Basic User and
Advanced User only.
A peak pattern matching step is always based on a peak calling step. In order to perform peak pattern
matching, proceed as follows:
1. Complete steps 1–5 described in the Peak Calling section.
2. In the Peak Pattern Matching panel, click the Add button to add a new pattern.
3. Entering a name for the new pattern and define the pattern. The definition of the pattern is done via the
checkboxes presented for all peaks defined in the current peak calling instruction. Check the box for
each peak to include in the pattern. Unchecked peaks will not be included in the pattern.
4. Click OK to confirm the pattern definition. By clicking Cancel, the definition step is canceled and no
changes are made.
Note: You can define more than one pattern for a given peak pattern matching step. To add further
patterns, repeat steps 2–4.
Note: To delete a pattern, click on it and press the Delete button.
5. Start peak calling and switch to the Peak Calling screen in the middle of the Analysis environment to view
the results. For details see steps 6 and 7 of section Peak Calling.
The peak calling result will indicate which pattern matches to each sample. Results are listed in the sample-
specific column Pattern of the peak calling result table. If the peak calling result of a sample does not match
any defined pattern, "n/a" will be displayed in the column and the result will be highlighted in light yellow.
For details about viewing the Peak calling result, refer to section Peak Calling.
Note: Peak pattern matching is an extension to the peak calling instruction and is saved along with the
peak calling instruction. It will also appear in any reports, exports, or print outs of the peak calling
instruction.

Result of a peak pattern.
Analysis of DNA samples
This section describes how to analyze a DNA sample. Instructions are given for 4 types of analyses: (1)
standard analysis of DNA samples, (2) analysis of samples using the high voltage method (fast analysis), (3)
analysis of samples containing DNA libraries, and (4) analysis of samples containing genomic DNA. For all
4 samples types, perform steps 1–6 and follow the instructions corresponding to the relevant analysis type.
1. Select the DNA mode if this is not already selected. Check the current mode in the bottom right corner
of the software screen. If another mode than DNA is selected, select File/Logout from the application
menu bar to log out and then log in with selected DNA mode. For details, refer to section User
authentication.
Note: Only users with user role Advanced User can modify and save parameters of an analysis profile.
Users with user role Basic User can select another analysis profile which is more suitable for the type of
samples.
2. Switch to the Analysis environment by selecting the Analysis icon in the main toolbar.

3. If the samples you want to analyze are not yet listed in the Experiment Explorer at the left, select the
Load experiment icon from the Experiment Explorer's toolbar. If the samples are listed, but not active
(grayed out), right click it's experiment name and select Activate. For further details, refer to the Loading
sample data or Activating an experiment section.
4. For the Fast Analysis of samples, or if the samples to analyze contain DNA libraries, or to perform
quality control on gDNA purified with silica-based technologies, or for standard analysis of DNA
samples for which size and concentration shall be determined, follow the instructions from the Size and
concentration determination procedure.
For information on which Analysis profile should be used as a starting point and which analysis
parameters are required for your samples, refer to the respective sections: Fast Analysis DNA analysis
for the Fast Analysis of samples, Standard DNA analysis for standard analysis of DNA samples, Smear
DNA analysis for samples that contain DNA libraries, and gDNA analysis for samples containing
gDNA purified with silica-based technologies.
Follow the Size and concentration determination procedure also if samples should have been analyzed
during data acquisition process, but either an error message has been shown or sample results are not
as expected. In this case, use the procedure to check the analysis step by step and correct if needed.
Follow the instructions to reuse the analysis parameters that have been used for the samples.
If no size calculation shall be performed, follow the instructions of the Peak detection procedure.
5. Optional: For the Fast Analysis of samples or standard analysis of DNA samples for which size and
concentration have been determined, peak calling can be performed. Follow the instructions described
in section Peak Calling.
6. For DNA libraries with specific distribution expectations or to asses the quality of a library in routine
use, or to assess the quality of gDNA, perform Distribution analysis. Follow the instructions described
in Distribution analysis. For information on which Distribution profile should be used as a starting point
for gDNA samples, refer to section gDNA analysis.
The result table summarize all properties that the QIAxcel ScreenGel Software calculates for detected
peaks. Right-click the header line of the table, select Show column, and then select the property you are
interested in. Alternatively, right-click the header line of the table and select Show all columns. This option
displays all the properties calculated by QIAxcel ScreenGel. For more information, refer to section Result
table and sections Standard DNA analysis, Fast Analysis DNA analysis, Smear DNA analysis, and gDNA
Standard DNA analysis
During the Size and concentration determination procedure or the Peak detection procedure select the
Default DNA v2.0 analysis profile as a starting point.
Note: The QIAxcel ScreenGel Software, version 1.2 and higher, comes with an improved default profile,
named Default DNA v2.0. To be independent from the highest signal in the sample, in the new profile, the
threshold parameter is defined as a multiple of the noise level which is estimated from the sample data.

The single electropherogram view is most suitable for checking peak detection. Ensure that the plot shows a
red "+"-sign at the peak apex for all peaks between/after the alignment marker peak(s). If a pink "x"-sign is
shown instead, click the Image Options button of the electropherogram toolbar and select the options Mark
peak apex and With Label, with Size [bp] selected. Click OK to close the dialog. The electropherogram
plot of the analyzed samples will show the size of the detected DNA molecules in base pairs above the
apex of the corresponding peaks. Peak properties are shown in the Peak Result table below the
electropherogram. For details, refer to the Result table section.
To switch the sample to be shown in the electropherogram, click on the next sample in the Experiment
Explorer on the left.
Ensure that the peak detection has worked as expected. Firstly, it is important that the correct peaks are
marked as alignment marker peaks (marked with a green '+') because this is the basis for all other analysis
functions. If not, adapt the analysis parameters in the Analysis parameters panel on the right side of the
Analysis environment. To do so, open the Analysis Properties section and then open the Parameters section.
For details on how to change the parameters that are mentioned below, refer to section Modifying an
analysis profile.
Note: Collapse and expand parts of the analysis properties by clicking and , respectively.

Analysis profile for standard DNA analysis.
Ensure that the Peak option is selected.
If the raw data being analyzed are too noisy, increase the Smoothing Filter window. Click this parameter
line and set the window size to 25 pts, for example, in the edit area below the parameters list and click
OK to confirm. To apply time-dependent smoothing, add one or more smoothing filter parameter lines. To
do so, click the Add button, select Smoothing Filter, and set the values for start time and window size.
Click OK to confirm this setting. An example of time-dependent smoothing is represented by the Default
RNA analysis profile in RNA mode.

If peaks were detected before or after the alignment marker peak, increase the Alignment marker
threshold. Click on the field and change the value.
If peak detection is too sensitive, increase the Threshold. Click this parameter line and increase the value
in the Value field in the edit area below the parameters list, and click OK to confirm.
If in a certain range of migration time, peak detection is too sensitive, increase the Threshold in this
region. To do so, click the Add button below the parameters list and select Threshold from the Define
parameter drop-down list. As a starting point, set the time where the region for which to increase the
threshold starts, and define a threshold of, for example 5 S/N. Click the OK button to confirm this
setting. Then at the end of the affected region, reset the threshold to the default value (e.g., 2 S/N in
Default DNA) by adding a third threshold definition. Set the start time of this threshold to the end of the
affected region and set the threshold value to that of the first threshold parameter line. Click the OK
button to confirm this setting.
Click the Start Analysis button again to start a new analysis according to this modified analysis profile.
In some cases, it may be necessary to repeat the adaptations to the analysis profile iteratively. If the peak
detection worked as expected with the modified analysis profile, save this analysis profile and try to use
this new profile instead of the Default DNA v2.0 analysis profile for future DNA analyses of similar samples.
Fast Analysis DNA analysis
For a run that contains the size marker, follow the Size and concentration determination procedure. During
the procedure, create and save a reference marker from the size marker sample. Use the Default Fast
Analysis analysis profile as a starting point. If the run contains the size marker only, leave the procedure
after the reference marker has been saved. If the run contains samples as well, continue the procedure to
analyze the samples: in the Reference Marker section, check Reference Marker Table and select use the just
created and saved reference marker.
For a run that contains samples only, follow the Size and concentration determination procedure. During the
procedure, use the Default Fast Analysis analysis profile as a starting point, and in the Reference Marker
section, check Reference Marker Table and select the previously created reference marker.
red "+"-sign at the peak apex for all peaks between the alignment marker peaks. If a pink "x"-sign is shown
instead, click the Image Options button of the electropherogram toolbar and select the options Mark peak
apex and With Label, with Size [bp] selected. Click OK to close the dialog. The electropherogram plot of
the analyzed samples will show the size of the detected DNA molecules in base pairs above the apex of
the corresponding peaks. Peak properties are shown in the Peak Result table below the electropherogram.
For details, refer to the Result table section.
analysis profile.

Analysis profile for Fast Analysis.
Ensure that the Peak option is selected.
If you're analyzing samples, in the Reference Marker section, check Reference Marker Table and select a
previously saved reference marker. If you're creating the reference marker, in the Reference Marker
section, check No Marker.
If peaks were detected before or after the alignment marker peak, increase the Alignment marker

If peak detection is too sensitive, increase the Threshold. Click this parameter line and increase the value
in the Value field in the edit area below the parameters list, and click OK to confirm.
When analyzing Fast Analysis data, it may be that the default baseline filter window (40 seconds) is too
large. In this case, a notification will arise suggesting to decrease the baseline filter window. To do so,
click the Baseline filter line and set the Window size to 39 in the edit area below the parameters list, and
click OK to confirm. In most cases, this will work.
If in a region with many peaks close together, some peaks are not detected, decrease the minimum
distance by clicking on the Minimum Distance parameter line and setting the distance Value from default
0.25 to 0.1 seconds, for example, in the edit area below the parameters list. Click OK to confirm this
setting. If you do not need minimum distance between peaks, set the minimum distance value to 0
seconds.
For Fast Analysis samples, smoothing should be deactivated as set in the Default Fast Analysis analysis
profile. Here, in the Smoothing Filter parameter line, the Window value is set to 0 pts.
this new profile instead of the Default Fast Analysis analysis profile for future Fast Analysis samples.
Smear DNA analysis
Use the analysis options described below to obtain basic information about DNA libraries in samples, such
as minimum and maximum fragment sizes, molarity or concentration.
During the Size and concentration determination procedure, select the Default Smear DNA analysis profile
as a starting point.
pink "x"-sign for all smear peaks between the alignment marker peaks. If a red "+"-sign is shown instead,
click the Image Options button of the electropherogram toolbar and select the options Mark median of size
and With Label. Click OK to close the dialog. The electropherogram plot of the analyzed samples will mark
the median of size in base pairs of the corresponding peaks.
Smear peak properties are shown in the Smear/gDNA Result table below the electropherogram. For details,
refer to the Result table section.

analysis profile.
Analysis profile for smear analysis.

Ensure that the Smear option is selected.
If peaks were detected before the first or after the last alignment marker peak, increase the Alignment
marker threshold. Click on the field and change the value.
If signals were incorrectly detected as peaks, increase the threshold. Because the smoothing algorithm
was optimized for the typical shape of smear data, a high S/N value is required as threshold.
Click the Start Analysis button again to start a new analysis using the modified analysis profile.
In some cases, it may be necessary to repeatedly adapt the analysis profile. If the peak detection worked
as expected with a modified analysis profile, save and use the modified analysis profile for future DNA
analyses of similar samples, instead of using the Default Smear DNA analysis profile.
Smear analysis distinguishes samples marked as size marker and does not define smear peaks for these
samples. For all other samples, the analysis distinguishes between alignment marker peaks and smear
peaks. The software assigns a so called area of interest to each detected smear peak. The borders of an
area of interest are marked by two vertical pink lines and, by default, are the same as the borders of the
corresponding peak. In case the detected peak borders do not describe the actual area of interest, move
the borders to the correct positions. All properties displayed in the Smear Result table refer to the area of
interest defined by the vertical pink lines.
Note: Upon clicking the Start Analysis button, the borders of the normalized areas will be reset to match the
borders of the detected smear peak, even if they were previously corrected manually. Moving the threshold
does not affect the borders of the area of interest.

Result of smear analysis.
However, for routine use, use Distribution analysis instead. There you can define the areas of the distribution
you are interested in and use these settings for all samples in one step. For information on how to setup
distribution analysis, refer to section Distribution analysis. Distribution analysis can only be performed after
the Size and concentration determination procedure has been completed successfully.
gDNA analysis
Use the analysis options described below for analysis of genomic DNA quality.
Note: Make sure to use the 15 bp alignment marker. For details, refer to Checking alignment marker.
During the Size and concentration determination procedure, select the Default gDNA analysis profile as a
starting point.
pink "x"-sign for all smear peaks between the alignment marker peaks. If a red "+"-sign is shown instead,
click the Image Options button of the electropherogram toolbar and select the options Mark median of size
and With Label. Click OK to close the dialog. The electropherogram plot of the analyzed samples will mark
the median of size in base pairs of the corresponding peaks.

After the Size and concentration determination procedure, the results are shown in the Smear/gDNA Result
table below the electropherogram. Find the size estimation of the gDNA in base pairs in the column Median
Size [bp]. The concentration estimation of the gDNA is displayed as Total Concentration just above the
Smear/gDNA Result table. For further details, refer to the Result table section.
analysis profile.

Analysis profile for gDNA analysis.
Ensure that the gDNA option is selected.
If the first detected peak is not the alignment marker peak, as a first step, increase the Alignment marker
threshold. Click on the field and change the value. If this is not sufficient, click the Add button below the
parameter list and select Suspend Integration from the Define parameter drop-down list. Use the Absolute
time unit and define the starting point as 0 minutes. Set the ending point of this parameter to shortly
before the start of the alignment marker peak (e.g., set end to 2 minutes if the first alignment marker peak
appears at 2.5 minutes).

If signals were incorrectly detected as peaks, increase the threshold. Click this parameter line and
increase the value in the Value field in the edit area below the parameters list and click OK to confirm.
Because the smoothing algorithm was optimized for the typical shape of smear data, a high S/N value
is required as threshold.
Click the Start Analysis button again to start a new analysis using the modified analysis profile.
In some cases, it may be necessary to repeatedly adapt the analysis profile. If the peak detection worked
as expected with a modified analysis profile, save and use the modified analysis profile for future DNA
analyses of similar samples, instead of using the Default gDNA analysis profile.
To assess the quality of the gDNA, perform Distribution analysis. Select the Default gDNA distribution profile
as a starting point. For information on how to perform distribution analysis, refer to section Distribution
analysis. Distribution analysis can only be performed after the Size and concentration determination
procedure has been completed successfully.
Distribution analysis
Use this analysis type to assess the quality of DNA libraries or genomic DNA in routine use based on the
size distribution.
Note: Distribution analysis is available in DNA mode only.
If the parameters panel is not yet open, open it by clicking the icon on the right-hand corner of the tab:
Note: If peak calling features are still active, activate distribution analysis features now. See the section
Activating distribution analysis features.

To perform the distribution analysis:
1. Before distribution analysis can start, ensure that the Size and concentration determination procedure has
been performed using analysis profile parameters as described in the sections Smear DNA analysis or
gDNA analysis, respectively.
Intermediate result after the size and concentration determination procedure.
2. Open the Distribution tab located on the right side of the Analysis environment.
3. In case, the distribution analysis needs to be removed temporarily during the Size and concentration
determination procedure, use the distribution profile parameters that had been transferred before - they
should be visible in the Distribution parameters tab at the right.
Otherwise, select the distribution profile relevant for the samples from the Distribution Profile drop-down
box. For gDNA quality analysis, select the Default gDNA distribution profile. A distribution profile defines
the areas of interest that are, for example, expected for the library. For DNA libraries, refer to the
section Creating a distribution profile for information on how to create the profile.

4. Select the samples to be analyzed with this distribution profile.
Note: Here, the selection inside the middle view is relevant — not the selection in the Experiment Explorer
. See the Selecting samples for analysis or report section for details.
5. Click the Start Analysis button at the bottom of the Distribution tab at the right to start the distribution
analysis.
6. The result for one sample is displayed in the Distribution Analysis Result table below the electropherogram
and an overview result table for all samples is available in the Distribution screen in the middle of the
Analysis environment. Refer to the section Distribution result for a description of the result structure and to
the section Distribution result columns for a description of the available columns.
7. To save the result of the distribution analysis, save the experiment by clicking in the Experiment
Explorer at the left.
Sample with completed distribution analysis.
Note: After distribution analysis, the single electropherogram shows the areas of interest as defined in the
Distribution profile and the borders of areas of interest cannot be moved anymore.
Note: In some cases, the signal in an area of interest does not exceed the baseline at any point, indicating
that the area of interest is not present in a sample.

It is possible to automate distribution analysis during the data acquisition process. Ensure that you have
already automated the Size and concentration determination procedure for your samples using Smear DNA
analysis or gDNA analysis. To automate also the distribution analysis, save any changes in the distribution
analysis parameters into a customized distribution profile. Make sure that these parameters work for all
samples. Then modify the process profile you have created to automate the size and concentration
determination procedure for your samples. In the Process Profile step, select the option Distribution Analysis
in the Included steps section additionally. If peak calling features are still active, activate distribution
analysis features now. See the section Activating distribution analysis features. In the Distribution Analysis
step, select the customized distribution profile. For further details, refer to Process profile options. Save the
process profile with these settings for reuse. During each run setup, ensure to select the alignment marker in
the Sample Selection step.
Activating distribution analysis features
In DNA mode, either peak calling or distribution analysis features can be applied to samples of an active
experiment.
To activate distribution analysis features for the current experiment, select Activate Distribution Analysis
Features from the View menu. The distribution result tables replace the peak calling result tables and the
distribution parameter panel replaces the peak calling parameter panel.The software keeps this setting until
an experiment that used peak calling is activated or opened.
Note: It is not possible to activate distribution analysis features if peak calling has already been performed
in the current experiment. In this case, remove the peak calling data first.
Distribution result
In the Analysis environment, each sample can be analyzed individually by means of distribution analysis.
Therefore, the distribution result overview is grouped by distribution profiles and each group is labeled with
the name of the applied distribution profile. The result for each distribution profile can be collapsed
individually.
The result of each distribution profile lists the samples to which the profile was applied. This list is
organized into groups of samples belonging to the same plate. Thus, in the screenshot below, a second
group of samples from another plate might appear within the collapsible area of the distribution profile
under a second heading MO_V-1192 R1|E1.
Each row in the table corresponds to a sample, with the columns Pos. and Sample Info identifying the
sample. Columns relevant to the entire sample appear first. Thereafter, columns are grouped according to
the names of the defined areas of interest and display several smear peak properties. The remaining
columns are then grouped by the name of defined ratios. Find a detailed description in the section
Distribution result columns.
To change the properties listed, right-click the table header and select or unselect the property with the
Show Column option. The change takes effect in the entire table.

Note: If a sample was not analyzed with a smear or gDNA analysis profile, it will not appear in the
distribution result overview. If a sample was not analyzed with a reference marker, the distribution values
cannot be calculated. In this case, the sample Quality is listed as "Review." In both cases, follow the
instructions in Analysis of DNA samples to check and correct the analysis steps that are required before
Distribution analysis. Ensure using Analysis parameters as described in Smear DNA analysis and gDNA
The distribution result table can be copied to the clipboard. To copy the complete result of a distribution
profile, right-click in the distribution result table and select the Copy Distribution Result of [...] option.
Distribution result overview with size marker at B2.
Note: If the distribution profile was modified but not saved, and then used for a subset of previously
analysed samples, two distribution results will be listed with the same distribution profile name. To identify
the differences between the used profiles, right-click one of the samples in the Experiment Explorer on the left
and select the Transfer Distribution Profile item from the context menu. Inspect the parameters in the
Distribution tab on the right. Do the same with a sample from the second distribution result.
Modifying a distribution profile
A distribution profile specifies the quality criteria for a DNA library or genomic DNA. The profile defines
areas of interest by start and end size, as well as molarity or concentration ratios between defined areas of
interest or against the total molarity or total concentration of the sample.
Note: Distribution profiles can only be modified by users with the assigned user role Advanced User.
Note: Distribution analysis is available in DNA mode only.

To modify a distribution profile proceed as follows:
1. Open the Distribution tab on the right of the Analysis environment.
Note: The Distribution tab is available only if distribution features are active. Refer to Activating distribution
analysis features for information on how to activate distribution analysis features.
2. Select the distribution profile to be modified from the Distribution Profile drop-down box.
Selected distribution profile.

3. Follow the instructions below to change definitions of areas of interest and/or of ratios as needed.
Note: The name of the profile in the Distribution Profile drop-down box will appear preceded by an "*",
indicating that the profile has been modified.
4. Save the modified distribution profile by clicking the Save as button to the right of the Distribution Profile
drop-down box.
Note: At least one area of interest must be defined.
Note: Collapse and expand parts of the distribution profile by clicking and , respectively.
To add an area of interest:

1. Click the Add button. A new empty row appears at the bottom of the table.
2. Define the area of interest in the editable fields:
Name A unique name for the area of interest. This will be the column header in the
distribution result table, grouping all columns relevant to this area.
Note: Names of the areas must be unique and can have a maximum length of 20
characters. Total Molarity or Total Concentration cannot be used as a name for an
area of interest.
Start [bp] Define in base pairs the size where the area of interest starts.
End [bp] Define in base pairs the size where the area of interest ends.
Check smear height Select this option to check that the signal of the area of interest is above the
threshold defined by Min Height (below).
Min Height Enabled if the option Check smear height has been selected.
[S/N]

Defines the threshold for the area of interest as a multiple of the noise level, which
is estimated from the sample data.
Note: If Check smear height is not selected, "n/a" will appear in the table of areas
of interest.
Note: Areas of interest may not overlap. The start or end field appears yellow in case of overlapping sizes.
An area may, however, start at the size where another area ends.
Note: Make sure that size definitions of the areas of interest are in within the sizes of the alignment marker.
Either use a suitable alignment marker or adapt the areas of interest. The distribution analysis will fail,
otherwise, because all areas of interest are assumed to be within the range of the alignment marker. For
gDNA analysis, refer to the Default gDNA distribution profile for the maximum size.
Example: Use areas of interest to distinguish between wanted (library) and unwanted (small or large
artifacts) fragments during a library preparation reaction and use the option Check smear height for the
library.
3. Click OK to add the new area of interest to the table.
Note: The areas of interest are sorted in the table by start size.
Note: At least one area of interest must be defined.
Modifying an area of interest.

To delete an area of interest:
1. Select the corresponding row in the table.
2. Click the Delete button.
Note: If the deleted area of interest was used in the definition of a ratio, the ratio becomes invalid. Then
delete the ratio as well.
To modify an area of interest:
1. Select the row of the area of interest to be modified.
2. Modify the values of the area of interest in the editable fields.
Note: Areas of interest are sorted by position in the Areas of Interest table.
The QIAxcel ScreenGel allows to define ratios to assess the relationship between wanted and unwanted
fragments in a distribution.
To add a ratio:
1. Expand the Ratio section.
2. Ensure that the Ratios option is selected.
3. If the QIAxcel ScreenGel shall include an assessment of the defined ratios into the overall sample quality,
select the option Check Quality. In this case, you are forced to enter limits for the ratio value (see below).
Select Show Values, otherwise, if you want to see the ratio calculations in the distribution result table
without quality assessment based on the ratios.
4. Select the calculation basis for the ratios to be defined. It is possible to select Concentration or Molarity.
This calculation basis will be used for all ratios.
5. Click the Add button. A new empty row will appear at the bottom of the Ratio Definitions list.
6. Define the ratio in the editable fields:
Ratio Name A unique name for the ratio. This will be the column header in the distribution
result table, grouping all columns related to this ratio.
Note: Names of ratios must be unique and have a maximum length of 20

characters. The same name may not be used for ratios and for areas of interest.
Calculate ratio for Define the nominator and denominator of the ratio by selecting the respective
areas of interest from the drop-down boxes. In addition, the denominator drop-
down box offers the option to select the Total Sample, which means the Total
Molarity or Total Concentration, respectively, depending on the selected
calculation method.
Acceptance range These fields are available only if the option Check Quality has been selected.

Enter a minimum and maximum value in the Min. and Max. fields. The quality of
the ratio will be considered as "Passed" for samples where the value of the ratio
falls within this range, as "Review" otherwise.
Example: Select Check Quality and calculation basis Concentration, and define a ratio against the Total
Sample for an area of unwanted fragments, and enter low values for the acceptance range.
Often, it is an iterative process to find out the acceptance range for a certain type of samples. If you find
values that work for your samples, save the changes into this or a new distribution profile for reuse. If the
ratio quality is frequently assessed as "Review" although the samples are good enough for downstream
application, consider broadening the acceptance range or continuing without a quality check for ratios.
7. Click OK to add the new ratio to the list.
Note: Ratios appear in the list in the same order as in the distribution result table.
Note: Ratio names or range values that are too long may not be fully displayed in the list. A tool tip
appears with the complete name by hovering the mouse over the truncated name or value.
Modifying a ratio.

To delete a ratio:
1. Select the ratio row in the list.
2. Click the Delete button and approve the confirmation message.
3. If you deleted the last ratio, uncheck the Ratios option at the top of the Ratios section.
To modify a ratio:
1. Select the row of the ratio to be modified.
2. Modify the values of the ratio in the editable fields.
Note: Ratios appear in the list in same order as in the distribution result table.
Creating a distribution profile
Note: Distribution analysis features must be active to create a distribution profile. Refer to Activating
distribution analysis features for information on how to activate distribution analysis features.
To create a new distribution profile:
1. Open the Distribution tab on the right of the Analysis environment.
2. Select a distribution profile from the Distribution Profile drop-down box. The selected distribution profile
serves as a template for the creation of the new one. Alternatively, select NewDistributionProfile to start
with an empty profile.
3. Define the distribution profile as needed. Refer to the section Modifying a distribution profile for details.
4. Save the new distribution profile by clicking the Save as button to the right of the Distribution Profile drop-
down box. Enter a unique distribution profile name and click OK.
Note: Only users with assigned user role Advanced User can create new distribution profiles.
Removing distribution results
To remove results of a distribution analysis from one or more samples:
1. Select the samples in the Experiment Explorer. Refer to the section Selecting samples for information on
how to select multiple samples.
2. Right-click the selection and select Remove Distribution Analysis Data from the context menu.
The distribution analysis results for these samples are cleared from the distribution result tables. The
electropherograms of the samples are updated because the areas of interest are no longer defined by a
distribution profile.

In the experiment explorer, the samples will still appear as "analyzed."
Analysis of RNA samples
This section describes how to analyze an RNA sample. It distinguishes between two different kinds of
analyses: size and concentration determination and RNA quality control. For both types of analyses,
perform the steps below. Follow the instructions corresponding to the desired type of analysis.
1. Switch to RNA mode if this is not already selected. Check the current mode in the bottom right corner of
the software screen. If another mode than RNA is selected, select File/Logout from the application menu
bar to log out and then log in with selected RNA mode. For details, refer to section User authentication.
Note: Only users with user role Advanced User can modify and save parameters of an analysis profile.
Users with user role Basic User can select another analysis profile which is more suitable for their type of
samples.
2. Switch to the Analysis environment by selecting the Analysis icon in the main toolbar.
3. If the samples you want to analyze are not yet listed in the Experiment Explorer at the left, select the
Load experiment icon from the Experiment Explorer's toolbar. If the samples are listed but not active
(grayed out), right click it's experiment name and select Activate. For further details, refer to the Loading
sample data or Activating an experiment section.
4. To determine the size and concentration of RNA molecules, or to perform quality control for RNA
samples with a size marker, follow the instructions of the Size and concentration determination
procedure. If quality control for RNA samples without a size marker shall be performed, follow the
instructions of the Peak detection procedure.
For both procedures refer to section Standard RNA analysis for information on which Analysis profile
should be used as a starting point and which analysis parameters are required for your samples.
Follow the Size and concentration determination procedure or Peak detection procedure also if samples
should have been analyzed during data acquisition process, but either an error message has been
shown or sample results are not as expected. In this case, use the procedure to check the analysis step
by step and correct if needed. Follow the instructions to reuse the analysis parameters that have been
used for the samples.
5. To perform quality control for RNA samples with or without a size marker, perform peak calling. Follow
the instructions described in section Peak Calling. For information on which peak calling instruction
should be used as a starting point, refer to section RNA quality control analysis.
The result tables summarize all the properties that the QIAxcel ScreenGel Software calculates for detected
peaks. Right-click the header line of the table, select Show column, and then select the property you are
interested in. Alternatively, right-click the header line of the table and select Show all columns. This option
displays all the properties calculated by the QIAxcel ScreenGel. For more information, refer to section
Result table and sections Standard RNA analysis and RNA quality control analysis, respectively.

Standard RNA analysis
During the Size and concentration determination procedure or the Peak detection procedure, select the
Default RNA analysis profile as a starting point.
red "+" sign at the peak apex for all peaks after the alignment marker peak. If not, click the Image Options
button of the electropherogram toolbar and select the options Mark peak apex and With Label, with Size [nt]
selected. Click OK to close the dialog. To switch the sample to be shown in the electropherogram, click on
the next sample in the Experiment Explorer at the left.
Peak properties are shown in the Peak Result table below the electropherogram. For details, refer to the
Result table section. After the Size and concentration determination procedure has been completed, the
single electropherogram views of the analyzed samples will show the size of the detected RNA molecules in
nucleotides above the apex of the corresponding peaks.
The correct concentrations can be examined in the peak result table. If the concentrations are not shown by
default, right-click the header line of the table, choose Show column and then select the concentration
column, which displays the concentrations in ng/µl.
analysis profile.

Analysis profile for RNA analysis.
If the first detected peak is not the alignment marker peak, as a first step, increase the Alignment marker
If this is not sufficient, use the Suspend Integration parameter. To do so, click the Add button below the
parameters list and select Suspend Integration from the Define parameter drop-down list. Select Absolute
from the drop-down list next to End to use the Absolute time unit. Define the starting point as 0 minutes. Set
the ending point of this parameter to shortly before the start of the alignment marker peak (e.g., set end
to 2 minutes, if the first alignment marker peak appears at 2.5 minutes). Click the OK button to confirm
this setting.

If the analysis profile is too sensitive and detects peaks where there is only noise, increase the Threshold
(e.g., from 2 S/N to 5 S/N). Click this parameter line and increase the value in the Value field in the
edit area below the parameters list and click OK to confirm.
If the baseline follows the 28S peak, increase the baseline filter window size for roughly the last third of
the migration time. To add a second interval to the baseline filter parameter, click the Add button below
the parameters list and select Baseline Filter from the Define parameter drop-down list. Then, e.g., set
start to 6 minutes and the window size to 80 seconds. Click the OK button to confirm this setting.
this new profile instead of the Default RNA analysis profile for future RNA analyses.
RNA quality control analysis
This section provides instructions to investigate the integrity of RNA molecules. The RNA integrity check can
be done with or without a size marker. Both approaches are described below.
If the parameters panel is not yet open, open it by clicking on the icon appearing on the right:
Performing quality control of RNA with a size marker

1. Ensure that the Size and concentration determination procedure has been performed using analysis
profile parameters, as described in the section Standard RNA analysis.
2. Switch to the Peak Calling tab of the parameters panel and select one of the provided peak calling
instructions: Default RNA QC, Default RNA prokaryote, or Default RNA rat_mouse_human.
3. To determine the RNA integrity, select the RNA Integrity Score option and choose the 18S peak. To
examine the 28S-to-18S-ratio in one sample, select the Ratio Normalized Area option and choose the
28S and the 18S peak. For prokaryotic RNA, choose the 23S and 16S peak, respectively. For detailed
information on how to define peak calling instructions, refer to Modifying peak calling instructions.

Peak calling instruction for RNA QC.
4. In the gel image overview, select all samples.
5. Click the Start Peak Calling button appearing at the bottom of the Peak Calling tab on the right.

6. Inspect the peak calling result in the peak calling result overview.
Each row in this table represents the peak calling result for one sample. The RNA integrity score is given in
the column RIS. The 28S-to-18S-ratio, is given in the column Ratio. In addition, the total concentration of
RNA is given in the column Total RNA concentration. Furthermore, for the 18S and 28S peak, it is listed
whether or not this peak was found, based on the criterion given in the peak calling instruction. For
detailed information on the peak calling result table, refer to Peak Calling.
Performing quality control of RNA without the size marker

1. Ensure that the Peak detection procedure has been performed using analysis profile parameters as
described in the section Standard RNA analysis.
2. Switch to the Peak Calling tab of the parameters panel and select one of the provided peak calling
instructions: Default RNA QC, Default RNA prokaryote, or Default RNA rat_mouse_human.
3. As the analysis was performed without the reference marker, adapt the peak calling instruction to
search for peaks based on relative migration time instead of size. Click on the line of the 18S peak and
update the position criterion in the parameter area below. Set the Position value to an average of the
relative migration times that is shown in the result tables for the 18S peak of the selected RNA samples
and change the unit from Size to Rel. Time in the drop-down list. Confirm this setting by clicking the OK
button. Adjust the tolerance parameter, if the relative migration times differ from sample to sample. Do
the same for the 28S peak. For prokaryotic RNA, change the 23S and 16S peak, respectively. For
detailed information on how to define peak calling instructions, refer to section Modifying peak calling
instructions.
4. To determine the RNA integrity, select the RNA Integrity Score option and choose the 18S peak. To
examine the 28S-to-18S-ratio in one sample, select the Ratio Normalized Area option and choose the
28S and the 18S peak.
5. In the gel image overview, select all samples.
7. Click the Start Peak Calling button appearing at the bottom of the Peak Calling tab on the right.
8. Inspect the peak calling result in the peak calling result overview.
Each row in this table represents the peak calling result for one sample. The RNA integrity score is given in
the column RIS. The 28S-to-18S-ratio, is given in the column Ratio. In addition, the total concentration of
RNA is given in the column Total RNA concentration. Furthermore, for the 18S and 28S peak, it is listed
whether or not this peak was found, based on the criterion given in the peak calling instruction. For
detailed information on the peak calling result table, refer to section Peak Calling.

Manually modifying analysis results
The QIAxcel ScreenGel Software algorithms analyze the data fully automatically. The user can only
influence the automated analysis through the analysis parameters.
After the analysis, the results can be modified manually by the user.
Modifying the threshold
In the single electropherogram view, the threshold parameter can be interactively changed by moving the
threshold with the mouse. When doing so, the sample is reanalyzed using the analysis parameters of the
sample properties and the new threshold value.
Deleting a peak
Deleting a peak is possible in the Single Electropherogram View only.
To delete a peak, proceed as follows:
1. Switch to the Single Electropherogram View.
2. Right-click the top of the peak in the electropherogram and select Delete Peak from the context menu that
appears. The peak will be deleted.
To delete multiple peaks, proceed as follows:
2. Using the Ctrl key, left-click the top of the peaks to be deleted in the electropherogram.
3. Right-click in the electropherogram and select Delete Selected Peaks from the context menu that appears.
The peaks will be deleted.
Note: After new analysis, deleted peaks may be detected again depending on the analysis parameters.
Repeat the steps above to delete them again.
Note: A peak can be deleted by users with the assigned user roles Basic User and Advanced User only.
Adding a peak
Adding a peak is possible in the Single Electropherogram View only.
To add a peak, proceed as follows:
2. Right-click the electropherogram and select Insert Peak from the context menu that appears.
3. A marker is displayed that moves along the signal while the mouse is being moved. Move the marker to
the left border of the peak that is to be added. Left-click to set the left border.

4. Accordingly, left-click to set the right border of the peak to be added. If a peak can be found in the
marked area, the peak is added to the result table and the visualization is updated.
Specifying the peak area.

Note: Adding a peak before the first alignment marker peak or after the second alignment marker peak is
only possible if the signal rises above the alignment marker threshold in the corresponding region.
Note: If the sample was analyzed with smear analysis, a new smear peak can be added as described
above. The newly inserted peak may not overlap with the area of interest of another peak.
Note: A peak can be added by users with the assigned user roles Basic User and Advanced User only.
Removing analysis results
Removing the analysis result from samples is only possible using the Experiment Explorer.
To remove the analysis result from samples:
1. Select the samples in the Experiment Explorer. Refer to the Selecting samples section for information on
how to select multiple samples.
2. Right-click the selection and select Remove Analysis Data from the context menu that appears.

Removing the analysis result of C5.
The result tables for these samples become empty. The representation of the sample in gel image and
electropherogram view is updated: all peak annotations as well as baseline and threshold lines disappear.
If peak calling or distribution analysis was performed on the samples, the peak calling or distribution result
tables for these samples also become empty and the samples are removed from the peak calling or
distribution overview tables.
Note: To restore peak calling or distribution analysis results, reanalyze the samples with an analysis profile
and reference marker, and repeat the peak calling or distribution analysis.
Refer to the sections Peak Calling and Removing distribution results for information on how to remove peak
calling results or distribution analysis results independently.
Note: Only users with the assigned user roles Basic User and Advanced User can remove analysis results.

Checking alignment marker
To check the alignment marker of a sample:
1. Select the sample in the Experiment Explorer.
2. View the sample properties at the right side of the Analysis environment, in the Analysis Instructions panel.
Refer to Inspecting sample properties for detailed information about how to view the properties.
3. Check if the alignment marker of the sample is correct. If not, the alignment marker of a plate can be
changed. In the Experiment Explorer, right click the plate name. Select the context menu option Overwrite
alignment marker. Select the correct alignment marker in the Overwrite Marker dialog that appears and
confirm by clicking OK.
Note: Upon switching from one alignment mode to another (two alignment marker peaks vs. one alignment
marker peak), the analysis data of the plate will be removed and the samples must be analyzed again.
Note: To ensure analysis compatibility, the reference marker drop-down list contains only reference marker
tables that match the alignment marker of the samples.
Modifying areas of interest
In the single electropherogram view, if the sample was analyzed with a smear analysis profile and at least
one smear peak was detected, the borders of the area of interest for each peak can be interactively
changed. To do so, use the mouse to click and drag the pink vertical lines indicating the area borders to
the desired position. The lines may be moved independently of any peak start or end point.
Note: Area of interest may not overlap. Thus, it is not possible to drag a vertical line into the area of
interest of another peak.
After moving a border, the properties corresponding to the given area of interest are recalculated using the
newly defined borders.
Reusing used analysis parameters
It is possible to reuse the analysis parameters of an analyzed sample.
1. Right-click the sample in the Experiment Explorer.

2. Select one of the following options to transfer the parameters used for analysis of the sample into the
toolbar on the right-hand side of the Analysis environment. If the toolbar on the right is not displayed,
open it by clicking on the following icon:
Transfer Analysis Instructions The option is available only if the sample has been
analyzed.
The analysis profile and its parameters used for

peak detection and the reference marker table used
for size and concentration determination, if present
from the sample, will be transferred to the Analysis
tab of the toolbar.
Transfer Peak Calling Instruction The option is available only if peak calling has been
performed on the sample.
The peak calling instruction that has been used with

this sample for peak calling will be transferred to
the Peak Calling tab of the toolbar

Transfer Distribution Profile For DNA mode only. The option is available only if
distribution analysis has been performed on the
sample.
The distribution analysis profile that has been used

with this sample for distribution analysis will be
transferred to the Distribution tab of the toolbar.
Note: It is not possible to perform peak calling and distribution analysis in the same experiment. Thus, either
a peak calling instruction or a distribution profile is applied to a sample, but never both.
Note: Only users with the assigned user role Advanced User can use these options. However, the
parameters used with the sample can also be viewed in the Properties tab.
Reanalysis of multiple experiments
QIAxcel ScreenGel provides the possibility to analyze multiple experiments in the same way, without
needing to open each experiment manually.
This section describes how to perform so called batch processing of experiments.
To perform batch processing of experiments proceed as follows:
1. In the Analysis environment, select Batch experiment processing in the File menu. The Batch Processing
dialog will appear.
2. At the top of the dialog, select the directory containing the experiments to analyze. Click and in the
appearing dialog, navigate to and highlight the relevant directory. Click OK. The directory path should
appear in the upper text field and the experiments contained in that folder should be listed in the lower
text field.
3. Use the radio buttons below the directory path to indicate if all experiments in this folder and its
subdirectories should be processed, or if only selected experiments should be processed. If the second
option is chosen, select the experiments to process. Use the Shift or Ctrl key to select multiple
experiments. Ctrl+A selects all entries.
4. Select the profiles to be applied to the selected experiments.
If a new analysis should be performed for the experiments, select the corresponding analysis profile from
the drop-down list. For more details about the analysis of samples, see Peak detection. Details about how
to define a new analysis profile are available in Modifying an analysis profile. If no analysis profile is
selected, no new peak detection will be performed.
If a reference maker should be applied during analysis of the experiments, select the corresponding
reference marker from the drop-down list. For details about the application of a reference marker, see Size
and concentration determination. Details about how to define a new reference marker are available in
Creating a reference marker. A reference marker can only be applied during analysis. Therefore, if a
reference marker was chosen, batch processing can only be started if an analysis profile is also selected.
Note: Ensure that all selected experiments are run with the same alignment marker. Otherwise, the reference
marker cannot be used for certain experiments.

If a new peak calling should be performed for the experiments, select the corresponding peak calling
profile from the drop-down list. For details about peak calling, see Peak Calling. Details about how to
define a new peak calling profile are available in Creating a new peak calling instruction. If no peak
calling profile is selected, no peak calling will be performed.
If the results of the batch processing should be stored in a report, select the corresponding report profile
from the drop-down list. The report/export will be written to the default report/export output path. For
details about the report and export functionality, see Report/Export. Details about how to define a new
report profile are available in Modifying a report/export profile. If no report profile is selected, no report
will be created.
Note: If the Use Images as Displayed option is selected in a report/export profile, it will not be listed in the
Report/Export Profile drop-down list. This option is not available for batch processing.
5. Check the box at the bottom of the dialog if the processed experiments should be overwritten with the
results from the batch processing.
Note: Data in processed experiments may be lost if overwritten by results from the batch processing.
Note: If an experiment to be processed is open in the QIAxcel ScreenGel Software and the Save changes
back to experiments option is checked, the results will not be written to the open experiment. When
checking this option, ensure that all affected experiments are closed.
Note: If problems are encountered during processing, a warning message will appear at the end listing any
issues that occurred (e.g., the analysis parameters do not fit the data).

Analyzing and reporting five experiments with size determination and peak calling.
Customizing experiments
Experiments are created automatically from every process. Additionally, the user can create and modify
experiments. This allows the user to compare samples from different experiments, and even different
processes.
Note: Creating and modifying customized experiments requires the user role Advanced User.
A customized experiment may contain single rows or groups of rows as well as plates. However, within the
experiment all rows will be still grouped in plate(s). Every time a row or plate is added to an experiment
you get a copy of it. This means that the source experiment, from which the row/plate originates, will
remain unaffected by all changes within the target experiment.

Note: You can modify the composition of customized experiments only. The composition of an experiment,
which is the automatic result of a process, cannot be modified (see the image below).
Run results are marked with a padlock symbol. Custom

experiments are not marked.
For general information about handling experiments and the Experiment Explorer, see the Handling samples
and experiments section.
Creating a new experiment
To create a new customized experiment:
1. Click at the top of the Experiment Explorer.
2. Enter a unique name for the new experiment into the edit field of the dialog that appears and click OK.
Important: The experiment name cannot be changed later.
3. A new empty experiment will be created and displayed in the Experiment Explorer as the last experiment,
at the bottom.
Use the scrollbar of the Experiment Explorer if the new experiment is outside the view. The new experiment
will be activated automatically. If the previously active experiment was modified, the system asks you
whether to save the changes or not. For more details about activating and deactivating, see the Activating
an experiment section.
Refer to the Modifying an experiment section for information on how to collect samples for the new
experiment.

Note: The composition of this experiment can be modified at any time, in comparison to experiments
automatically generated by a process.
Note: New experiments can be created by users with the assigned user role Advanced User only.
Modifying an experiment
If a customized experiment should be modified, make sure that it is activated. For more details about
activating an experiment, see the Activating an experiment section.
Note: Only the composition of customized experiments can be modified. The composition of an experiment
that is the automatic result of a process cannot be modified, and therefore the context menu options
described below are disabled.
To modify an experiment:
1. Load the source experiment that contains the samples. For further details on loading, see the Loading
samples section.
2. Create or activate the experiment that is to be customized in the Experiment Explorer.
3. Expand the source experiment so that the required plates and rows are visible. The experiment can be
expanded without activating. For more details about expanding, see the Expanding and collapsing
section.
4. Modify the experiment as required:
To add a plate to the active experiment, right-click the plate to add and select the context menu option
Copy Plate to Active Experiment. A copy of the plate will be created and added to the active experiment
at the bottom.

Adding a plate to the active experiment.
Note: The complete plate will be copied to the experiment, but the original plate stays unchanged. Any
further modification of this plate in the active experiment does not affect the original plate.
To remove a plate from the active experiment, click the Close button of the plate. The plate will
disappear from the experiment.
Removing a plate from the active experiment.

Note: This plate will be removed only from the active experiment, but the original plate remains unchanged.
Adding a row is similar to adding a plate. Place the mouse cursor over the row to add to the active
experiment and select the menu item Copy to Active Experiment. To preserve the context of the row, a
copy of its plate will be created and added to the active experiment containing a copy of the selected
row. If you add another row from the same plate to the active experiment, a copy of the row will be
created and added to the copy of the plate inside the active experiment. Multiple rows of the same plate
can be added in a similar way, but by simultaneously holding the Shift or Ctrl key during selection.
Adding a row to the active experiment.
Note: A row can be located in the experiment only once.
Note: Individual samples cannot be added to the active experiment. Add the complete row instead, but
visualize the required samples only.
To remove a row from the active experiment, right-click the row letter and select the option Remove Row
from the context menu. The row will be removed from the active experiment. If the plate contains only one
row, you cannot remove it; instead, please remove the plate.

Removing a row from the custom experiment.
Report/Export
The Analysis environment provides a flexible and powerful tool for reporting (RTF or PDF format) and data
export (XML format).
For convenient reuse, corresponding report and export configurations can be stored together in report/
export profiles. Thus, both reporting and data export may be integrated to form a fully automated process
by including a report/export profile into a process profile.
You can specify which information has to be included in the report and export individually. The report and
export files can be customized to suit your needs.
Each report contains of two main sections:
The overview section for information about all samples, such as a gel overview
The sample details section for detailed information about each sample

In the sample details section, the information related to each sample is reported for each sample grouped in
the following subsections:
Sample Header
Sample Graphics
Result Table
Run Parameter
Analysis
Reference Marker
The order of the samples is the same as in the view.
For further details on customizing reports and export, see the Modifying a report/export profile section.
Generating a report
The basic procedure of manually generating a report in the Analysis environment is as follows:
1. Load the samples using the Experiment Explorer.

For further details on loading sample data, see section Loading sample data.
2. Inspect the samples before reporting.

See the Viewing sample data section for more details on data inspection.
For this step, the Gel view or the Electropherogram overview are especially useful.
3. Select the samples you want to report.

For further details on selecting samples, see section Selecting samples for analysis or report
4. Select report settings and start reporting.
On the right-hand side of the Analysis environment, the report toolbar can be found.
Select the Report tab of the toolbar.
Select a predefined report/export profile. The report settings of the selected profile are shown below the
drop-down list. For details, refer to the Report options section.
Make sure that at least one of the report formats PDF or RTF is selected. Additionally, ensure that at least
one of the options (Overview or Sample Details) is selected. If not, select another predefined report/export
profile. (Users assigned the user roles Advanced User or Basic User may modify the settings as they wish.)
Specify the directory where the report files will be saved (refer to section Modifying a report/export profile
for information on how to specify the report directory).
Click the Start Report/Export at the bottom of the Report tab to start reporting.

Note: The button Start Report/Export is disabled if no samples are selected in the view (see Step 3).
The report files will be generated automatically and stored in the specified directory.
If you have selected the Print report option the report will be printed on the default printer.
Note: Ensure that you have defined a default printer on your system.
5. Inspect the report files.
If the options Display Report and PDF were selected, the generated report will be opened automatically in
the default PDF reader.
Report options
The report/export settings are divided into two groups:
Report Options; contains the report settings
Export Options; contains the export settings
Note: You can collapse and expand each group by clicking and to the left of the group name.
Report Options
Report options.

The options are described below:
Directory Select the directory in which the generated report file should be stored by
clicking . In the dialog that appears, navigate to the correct directory and
click OK.
Save to origin Check this option to save the report in the same directory as the experiment. If this
experiment directory option is checked, any selected path in Directory will be ignored.
PDF A file in PDF format will be generated.
RTF A file in RTF format will be generated. You can select both formats.
Display Report If you select this option and the format option PDF is selected, the generated
report will be displayed automatically using the default PDF reader.
Print Report If you select this option the generated report file(s) will automatically be sent to the
default printer.
Note: Ensure that you have a default printer on your system.
Use Images as Use this option to obtain images that look similar to the presentation in the
Displayed QIAxcel ScreenGel Software regarding alignment, scales, labels, zoom, etc.
Note: This option is available in the analysis environment only, it may not be used
in a process profile.
Overview The report contains of an overview section.
Sample Details The report contains of a sample section.
Note: If one of the check boxes PDF or RTF is checked, the report/export profile is valid only if either the
Overview or Sample Details check box is selected additionally.
Overview section
If the Overview option is selected, the following information is included automatically to the overview
section of the report:
Report Date Date and time of report generation.

Experiment Name Name of the experiment the sample data belong to.
Cartridge ID ID(s) of the cartridge(s) that the samples were processed with.
Cartridge Expiration This information is automatically included if the cartridge has exceeded its expiration
Status date.
Calibration Status Calibration status of the cartridge(s) at process time.
Instrument ID Serial number of the instrument(s) used to process the samples.
Data Acquisition Only in case of an incomplete experiment.
Status
Gives information about planned and performed runs (e.g., 2 out of 8 runs
performed successfully).

Corrupt Experiment Only in case of an incomplete experiment, which was accepted by a user.
Accepted by
Name of the user who has accepted the experiment.
Corrupt Experiment Only in case of an incomplete experiment, which was accepted by a user.
Accepted on:
Date and time when the experiment was accepted.
Select the following optional information that you want to include into the overview section:
Optional overview information.
Special options for Peak Calling Result

Table.
Special options for Gel Overview. Special options for Electropherogram

Overview.

The optional fields are described next.
Note: If a result table option but no result table column is selected, the check box is marked yellow, and the
report/export profile is invalid.
Experiment Plate Experiment plate comment.

Comment
Reported by The ID of the user who generated the report/export.
Experiment Path The path where the experiment is stored.
Sample List All samples of a plate are listed with position, sample information and comment. If
the experiment contains samples from different plates, a sample list is included for
each plate.
Lot Information The entered lot numbers will be included.
Distribution Analysis Use this option for a distribution analysis in DNA mode to include the distribution
Result Table analysis result overview table. Each row in the table represents a sample.
Note: This option is available only if distribution analysis features are active.
Additional options to select are:
Show Profile Include the parameters of the distribution profile that was
Properties applied to the samples.
Sample Information Include the Sample Information column.
Total Concentration Include the column Total Concentration of the sample.
Total Molarity Include the column Total Molarity of the sample.
Sample Quality Include the Sample Quality column. This is the overall
quality assessment of the sample, generated in the
distribution analysis.
AoI Concentration Include the Concentration column for each area of interest.
AoI Molarity Include the Molarity column for each area of interest.
AoI Height Include the Height column for each area of interest.
AoI Height Check Include the Height Check column for each area of interest.
This is the quality assessment of the height of the area of
interest.
Ratio Include the Ratio column for each defined ratio. Based on
the selected calculation method, the column will show
molarity or concentration ratio.
Ratio Quality Include the Ratio Quality column for each defined ratio.
This is the quality assessment of the ratio.

Note: If a report includes too many areas of interest or ratios, the table is split
between two areas of interest or ratios. Sample information, total concentration,
total molarity and sample quality columns appear only in the first table. The
remaining tables are marked with "(continued)" in the header.
Note: If samples are selected to which different distribution profiles were applied, a
new table is generated for each distribution profile. Furthermore, if samples from
different plates are selected, a new table is generated for each plate.
Note: Cells with the value "Review" are highlighted in the report.
Peak Calling Result The peak calling result overview table will be included. Each row in the table
Table represents a sample. Additional options can be selected (see picture above).
Note: This option is available only if peak calling features are active.
Peak Calling Select this option to include the peak calling instruction
Instruction Table table to the peak calling result overview table.
Sample Information Select this option to include the Sample Information

column in the peak calling result overview table.
Found Select this option to include the Found column for each
peak of interest to the peak calling result overview table.
Size Select this option to include the Size column for each
peak of interest in the peak calling result overview table.
Concentration Select this option to include the Concentration column for

each peak of interest in the peak calling result overview
table.
Molarity Select this option to include the Molarity column for each
peak of interest in the peak calling result overview table.
Note: Calculated columns (such as Ratio, RIS) are automatically included, if they are
part of the applied peak calling instruction.
Note: If there are too many peaks of interest, the table is split between two peaks of
interest, The sample info and the calculated columns appear only in the first table,
the following tables are marked with "(continued)" in the header.
Note: If samples to which different peak calling instructions were applied are
selected, a new table starts for each peak calling instruction. Additionally, if
samples from different plates are selected, a new table starts for each plate.
Overall Result Table Select this option to include a table that presents size and/or concentration and/or
molarity results from all samples of a plate. A sub-table is included in the overall
table for each selected sample. Sample position on the plate and, if available,
sample information appear as the header of each sub-table. Each sub-table has as
columns the result values that were selected for reporting. Each row then lists a
detected peak and the corresponding results (size and/or concentration and/or
molarity).
Note: If samples from different plates are selected, a new table starts for each plate.

Overall Smear Result For a smear or gDNA analysis in DNA mode, use this option to include an overview
Table smear result table, including selected smear result properties.
If samples from different plates are selected, a new table starts for each plate. Each
row in the table represents a sample.
Select each table column to specify the result values to display: Median Size, Conc.
Area of Interest, Mol. Area of Interest, % NA Area of Interest, or % Conc. Area of
Interest.
Note: The columns of the Smear Result Table can be selected and reordered as
described for Result Table (below).
Select the options Total Concentration and Total Molarity to include the values for
total concentration or total molarity of the sample.
Gel Image Overview Select this option to include the gel image of all selected samples.
Click the Image options button to specify the appearance of the gel image
overview. Image options are described below.
Note: The Image options button is disabled if the Use Images as Displayed option is
selected.
Note: The gel image in the report will have the left-hand y-axis on both sides, also if
the Use Images as Displayed option is selected.
Unit of the If you select Size, the y-axis will show a size scale based
y-axis on the reference marker on both sides of the gel image,
also if the Use Images as Displayed option is selected. The
lanes in the gel image will be aligned according to the
alignment markers.
Note: The size scale can be created only if all selected

samples have been run with the same alignment marker,
have been analyzed with the same reference marker table,
and the alignment markers have been correctly identified.
Otherwise, a corresponding message will appear.
If you select Rel. Time, the y-axis will show relative

migration time. The lanes in the gel image will be aligned
according to the alignment markers.
Note: The relative time scale can be created only if all

selected samples have been run with the same alignment
marker, have been analyzed, and the alignment markers
have been correctly identified. Otherwise, the lanes
cannot not be aligned and the y-axis will display a
corresponding message.
If you select Abs. Time [min], the lanes will not be aligned
and the y-axis will show an absolute time scale.

Zoom to Alignment Select this option to scale the lanes so that the lanes start
Marker with the lower alignment marker band and end with the
upper alignment marker band (crop data outside of the
alignment markers).
Note: This is possible only if all samples are analyzed.

Individual Scaling Select this option to auto-scale the contrast for each gel
lane individually.
Show sample Select this option to include the sample information in

information each lane.
Show plate ID Select this option to display the plate ID, the repeat
number, and the entry number of each lane.
Show method Select this option to display the applied method above the
sample lane.
Gel Layout Use this option to determine the gel layout.
Select Standard Layout to order the lanes from left to right,

as they are ordered in the view.
Select Horizontal plate layout to order the lanes starting

with A1 at the upper left and ending with H12 at the
lower right.
Select Vertical plate layout to order the lanes starting with

H1 at the upper left and ending with A12 at the lower
right.
Select Reverse vertical plate layout for the vertical plate

layout but starting with A1 at the upper left and ending
with H12 at the lower right.
Select Split plate layout to split the vertical plate layout.

The left portion will start with H1 at the upper left and end
with A6 at the lower right. The right portion will start with
H7 at the upper left and end with A12 at the lower right.
Note: Positions for samples not selected remain empty.

Lanes per Row Use this option to specify the number of lanes per row: 4,
6, 8, 12, 16, 24, 32, 36, or 48.
Note: This option is available only if Standard layout is

selected in the Gel Layout option.
Rows per Page Use this option to specify the number of rows to be
included on one report page (a page split is introduced
after the specified number of rows).
Note: This option is not available if Standard layout is


Analysis details Select Highlight alignment markers to highlight in green
the bands of the alignment marker peaks.
Electropherogram Select this option to include an electropherogram overview of all selected samples.
Overview The order is the same as in the view. One gallery overview page with no more than
12 electropherograms will always be printed on one report page.
Click on the Image options button to specify the appearance of the reported
electropherogram overview. Image options are described below.
selected.
Unit of If you select Size, the x-axis will show a size scale based
x-axis on the reference marker. The electropherograms will be
aligned according to the alignment markers.

have been analyzed with the same reference marker
table, and the alignment markers have been correctly
identified. Otherwise, the x-axis will display a
If you select Rel. Time, the x-axis will show relative

migration time. The electropherograms will be aligned

marker, have been analyzed, and the alignment markers
have been correctly identified. Otherwise, the
electropherograms will not be aligned and the x-axis will
display a corresponding message.
If you select Abs. Time [min], the electropherograms will

not be aligned and the x-axis will show an absolute time
scale.
Zoom to Alignment Select this option to scale the electropherograms so that
Marker the electropherograms start with the lower alignment
maker peak and end with the upper alignment marker
peak (crop data outside of the alignment markers).

Individual Scaling Select this option to auto-scale the y-axis for each
electropherogram individually.
Show sample position Select this option to display he sample position at the top
of each electropherogram.

Show sample Select this option to display the sample information at the
information top of each electropherogram.
Show plate ID Select this option to display the plate ID at the top of the
electropherogram.
Show method Select this option to display the applied method at the top
of each electropherogram.
Show analysis details Select this option to show analysis details for the
analyzed samples.
Select Mark detected peaks to display the apex markers

of detected peaks.
Note: In DNA mode, a second option Show median of

markers with the median size of detected smear peaks.
Select Show suspend integration intervals to display the

suspend integration intervals.
Electropherogram Use this option to include the superposition electropherogram of all selected samples
Superposition View which have the superimposed flag set.
Note: The superposition view is restricted to 12 samples. In process environment and

in batch processing, the superposition is created only if the experiment contains 12
samples or less.
Note: Use the Use Images as Displayed option to report the electropherogram
superposition as displayed.
Click the Image options button to specify the appearance of the reported
electropherogram superposition. Image options are described below.
selected.
Unit of x-axis If you select Size, the x-axis will show a size scale based
on the reference marker. The electropherograms will be
Note: The size scale can be created only if all

superimposed samples have been run with the same
alignment marker, have been analyzed with the same
reference marker table, and the alignment markers have
been correctly identified. Otherwise, the x-axis will show
a message, instead.

migration time. The electropherograms will be aligned

superimposed samples have been run with the same
alignment marker, have been analyzed, and the
alignment markers have been correctly identified.
Otherwise, the electropherograms will not be aligned and
the x-axis will show a message, instead.
If you select Abs. Time [min], the electropherograms will

not be aligned and the x-axis will show an absolute time
scale.
Zoom to Alignment Select this option to scale the electropherograms, so that
maker peak, and end with the upper alignment marker
peak, if available (crop data outside of the alignment
markers).

Show Electrical Select this option to include a diagram of the
Current Curve superimposed electrical current measured during data
acquisition. The electrical current curve will appear below
the electropherogram superposition, aligned with the x-
axis.
Show size marker If this option is selected, and if exactly one size marker is
peak labels among the superimposed samples, the peak labels will be
displayed for the detected peaks of the marker sample.
Select the units for the peak labels in the drop-down list.
Note: In RNA mode, if you want the 28S/18S ratio or the RIS to be included in the report, select the
overview option Peak Calling Result Table (refer to Analyze RNA samples for information on how to analyze
RNA samples).
Sample details section

The following information is included automatically for each sample:
Information Description Report section

Experiment Name Name of the experiment the sample data Sample header
belong to.
Plate ID ID of the plate the sample belongs to. Sample header
Position Sample position on the plate. Sample header

Run Number If the same sample was processed multiple Sample header
times, this number identifies the run that
produced the sample data (for detailed
information, refer to Run parameters and
result structure).
Run Entry Number The run entry number of the plate (for detailed Sample header
information, refer to Run parameters and
result structure).
Run Date Date and time the process was started. Run
Instrument ID Serial number of the instrument the sample Run

was processed with.

Select the following optional information that you want to include in the sample section:
Optional sample details.
Note: If a result table option but no result table column is selected, the check box is marked yellow, and the
report/export profile is invalid.
The optional fields are described below:
Start Results on New If you select this option, the results for each sample will start on a new page.
Page
Experiment Plate If you select this option, the experiment plate comment is included in the Sample
Comment Header section.
Run Information If you select this option, the following information is included in the Run section of
the sample:
Rise time The parameter for the applied Bessel filter (see also
Settings).
Applied injection time The applied sample injection time.
Note: This time can differ from the methods sample

injection time if there was another sample injection time
specified in the process profiles run parameters.(see
Selecting run parameters).
Applied separation The applied separation time during method run.
time
Note: This time can differ from the methods separation
time if the user adjusted the separation time during run.

Processed by The ID of the user who processed the sample.
Method Information If you select this option, the following information is included in the Run section:
Applied method Name of the method the sample was processed with.
Method injection time Sample injection time as it was defined in the method.
Method injection Sample injection voltage as it was defined in the method.

voltage
Method separation Separation time as it was defined in the method.

time
Method separation Separation voltage as it was defined in the method.

voltage
Cartridge If you select this option, the following information will be included in the Run section:
Information
Cartridge ID ID of the cartridge the sample was processed with.
Cartridge Calibration Calibration status of the cartridge at process time: "OK",

Status "Not calibrated", or "Conditional OK." For information on
calibration status, refer to section Running the calibration
wizard.
Cartridge Expiry Date The expiration date of the cartridge that was used for
sample processing.
Sample Information The sample information is included to the Sample Header section.
Sample Comment The sample comment is included to the Sample Header section.
Analysis Parameter The analysis parameters applied to the sample will be included in the report section
Analysis.
Reference Marker The reference marker table used during analysis will be included.
Table
Electropherogram Use this option to include the electropherogram.
Single View
Select Use Images as Displayed to print the electropherogram as displayed.
Click the Image options button to specify the appearance of the reported single
electropherograms. Image options are described below.
Note: If Use Images as Displayed is selected, the gel lane and the electrical current
are combined with the electropherogram if they are visible in the view.
selected.

Unit of x-axis If you select Size, the x-axis will show a size scale based
on the reference marker.
Note: The size scale can be created only if the sample

has been analyzed with a reference marker table, and the
Otherwise, the x-axis will display a corresponding
message.

migration time.
Note: The relative time scale can be created only if the

sample has been analyzed, and the alignment markers
have been correctly identified. Otherwise, the x-axis will
If you select Abs. Time [min], the x-axis will show an

absolute time scale.
Zoom to Alignment Select this option to scale the electropherograms so that
maker peak and end with the upper alignment marker
peak (crop data outside of the alignment markers).

Show Gel Lane Select this option to display the gel representation below
the electropherogram, aligned with the x-axis.
Show Electrical Select this option to display a diagram of the electrical
Current current measured during data acquisition below the
electropherogram or below the gel lane.
Select Show analysis details to enable the following configuration options:
Mark detected peaks Select this option to display the apex markers for detected
peaks.


adjacent label are displayed. Hover the mouse cursor
over the peak apex to get a tool tip with the peak label.
Select the label units: size, absolute or relative migration

time.

Note: The label can be displayed as Size only if the
sample was analyzed with a reference marker (for details
refer to Size and Concentration determination). Otherwise,
"n/a" is displayed.

marker with the median size of detected smear peaks.
You can switch the corresponding label on and off.
Select the option Mark peak start and end in order to

mark the start and end points of detected peaks.
Show areas of interest For DNA mode only. If the sample was analyzed with a
DNA smear analysis profile, select Show areas of interest
to display the areas of interest of detected smear peaks.
integration interval intervals.
Show threshold Select this option to display the peak threshold.
Show baseline Select this option to display the baseline.
Gel Single View Use this option to report individual gel lanes for all selected samples.
Click the Image options button to specify the appearance of the reported single gel
images. Image options are described below.
selected.
Unit of y-Axis If you select Size, the axis will show a size scale based
on the sample peaks, if the sample has been analyzed
with a reference marker table and the alignment markers
have been correctly identified. Otherwise, the axis will
If you select Rel. Time, the axis will show relative

migration time, if the sample has been analyzed and the
Otherwise, the axis will display a corresponding
message.
If you select Abs. Time [min], the axis will show an

Zoom to Alignment Select this option to scale the lanes so that the lanes start
Marker with the lower alignment maker band and end with the
upper alignment marker band (crop data outside of the
alignment markers).

lane individually.
Analysis details Select Highlight alignment markers to highlight in green
Lot Information Select this option to include the entered lot numbers.
Result Table If you select this option, the peak result table will be included in the report.
Additional options appear to configure the result table (see below).
Peak Calling Result Select this option to include the peak calling result table in every sample section.
Table Additional options can be selected.
Note: This option is available only if peak calling features are active.
Sample Information Select this option to include the Sample Information

column in the peak calling result overview table.
Found Select this option to include the Found column for each
peak of interest to the peak calling result overview table.
Size For DNA and RNA mode only. Select this option to
include the Size column for each peak of interest in the
peak calling result overview table.
Concentration For DNA and RNA mode only. Select this option to
include the Concentration column for each peak of interest
in the peak calling result overview table.
Molarity For DNA and RNA mode only. Select this option to
include the Molarity column for each peak of interest in
the peak calling result overview table.
Note: Calculated columns (such as Ratio, RIS) are automatically included if they are
part of the applied peak calling instruction.
Note: If a report includes too many peaks of interest, the table is split between two
peaks of interest. Sample information and the calculated columns appear only in the
first table. The remaining tables are marked with "(continued)" in the header.
Smear Result Table For a smear or gDNA analysis in DNA mode, use this option to include a smear
result table. The following columns can be selected: Median Size, Conc. Area of
Interest, Mol. Area of Interest, Start Area of Interest, End Area of Interest, % Conc.
Area of Interest, NA Area of Interest, and % NA Area of Interest. Refer to Smear
result columns for further details.
Note: The columns of the Smear Result Table can be selected and reordered as
described for the Result Table (see below).
Select the options Total Concentration and Total Molarity to include the values for
total concentration or total molarity of the sample.
Distribution Result Use this option for a distribution analysis in DNA mode to include the distribution
Table analysis result table for a sample.

Note: This option is available only if distribution analysis features are active.
Additional options to select are:
Show Profile Include the parameters of the distribution profile that was
Properties applied to the sample.
Sample Information Include the Sample Information column.
Total Concentration Include the column Total Concentration of the sample.
Total Molarity Include the column Total Molarity of the sample.

Sample Quality Include the Sample Quality column. This is the overall
quality assessment of the sample generated in the
distribution analysis.
AoI Concentration Include the Concentration column for each area of interest.
AoI Molarity Include the Molarity column for each area of interest.
AoI Height Include the Height column for each area of interest.
AoI Height Check Include the Height Check column for each area of interest.
This is the quality assessment of the height of the area of
interest.
Ratio Include the Ratio column for each defined ratio. Based on
the selected calculation method, the column will show
molarity or concentration ratio.
Ratio Quality Include the Ratio Quality column for each defined ratio.
This is the quality assessment of the ratio.
Note: If a report includes too many areas of interest or ratios, the table is split
between two areas of interest or ratios. Sample information, total concentration,
total molarity and sample quality columns appear only in the first table. The
remaining tables are marked with "(continued)" in the header.
Note: In RNA mode, if you want the 28S/18S ratio or the RIS to be included in the report, select the
overview option Peak Calling Result Table (refer to Analysis of RNA samples for further information).

Select the following optional information that you want to include in the peak result table:
Result table options in DNA mode.
Note: If the Result Table option is selected, but no result table column is selected, the Result Table check box
is marked yellow, and the report/export profile is invalid.

The peak result table options are described below:
Size Adds the result table column Size [bp] or Size [nt] for DNA or RNA mode,
respectively.
Concentration Adds the result table column Conc. [ng/µl]. If you select this option, the total
concentration is added automatically as last value of the column.
Molarity Adds the result table column Mol. [nmol/l].
Height Percentage Adds the result table column Height %.
Normalized Area Adds the result table column NA.
Normalized Area Adds the result table column NA %.

Percentage
Signal to Noise Adds the result table column S/N (Signal-to-noise ratio).
FWHM Adds the result table column FWHM [sec] (full width at half maximum).
Resolution Adds the result table column Res.
Ratio Normalized Area Adds the result table column Ratio NA.
Time Adds the result table column Time.
Rel.Time Adds the result table column Rel. Time.
Start Adds the result table column Start.
Stop Adds the result table column Stop.
Height Adds the result table column Height.
Area Adds the result table column Area.
Note: Refer to section Peak result columns for more information about the columns.
Note: You can specify the field order of the result table in the report by drag and drop. Left-click on a
column name and drag it to the new position.

Exporting data
The basic procedure of exporting data in the Analysis environment is as follows:
1. Load the samples using the Experiment Explorer.

For more details about loading sample data, see section Loading sample data.
2. Inspect the samples before exporting.

See the Viewing sample data section for more details on data inspection.
For this step, the Gel view or the Electropherogram overview are especially useful.
3. Select the samples you want to export.

For more details about selecting samples, see section Selecting samples for analysis or report
4. Select export settings and start exporting.
On the right side of the analysis environment, the report toolbar can be found.
Select the Report tab of the toolbar.
Select a predefined report/export profile. The export settings of the selected profile are shown below the
report settings. For details, refer to the Export options section.
Make sure that at least one of the export options is selected. If not, select another predefined report/export
profile. (Users assigned the user roles Advanced User or Basic User may modify the settings as they wish.)
Specify the directory in which the export files will be saved (refer to section Export options for information
on how to specify the export directory).
Click the Start Report/Export at the bottom of the Report tab to start exporting.
Note: The button Start Report/Export is disabled if no samples are selected in the view (see Step 3).
The export files will be generated automatically and stored in the specified directory.

Export options
The report/export settings are divided into two groups:
Report Options containing the report settings
Export Options containing the export settings
Note: You can collapse and expand each group by clicking and to the left of the group name.
Collapse the report options or scroll down to see the export options.
Export Options
Export Options.
Additional output formats.

The options are described below:
Directory
Select the directory to which the export files will be saved by clicking . In the
dialog that appears, navigate to the correct directory and click OK.
Save to origin Check this box to save the report in the same directory as the experiment. If this
experiment option is selected, any selected path in Directory will be ignored.
directory
XML Export If you select this option, an export file in XML format will be generated. This file
contains all general experiment and sample details of the selected samples,
except electropherogram raw data. If the samples are analyzed, it contains the
analysis results.
An additional option to select additional output formats appears. The software

provides two formats. You can select all of them.
BIN_CSV_Export Use this option to export the peak calling result table
in .csv format (similar to the file format that was
exported by the BioCalculator 3.2 Software).
DistributionAnalysis_CSV_ Use this option to export the distribution analysis

Export overview result table in .csv format.
PeakCalling_CSV Use this option to export the peak calling result table
Export with all selected peak properties in .csv format.
ResultTable_csv_table Use this option to export the analysis results in .csv

format (similar to the file format that was exported by
the BioCalculator 3.2 Software).
ScreenGel_1.0 Use this option to convert the export file to the .xml
export format of the QIAxcel ScreenGel Software
version 1.0.
SmearResultTable_CSV_Ex Use this option to export the smear result overview

port table in .csv format.
Note: You can customize your own output formats. Define xslt scripts based on the
.xml export file and store them in the %DATA_DIR%
\ReportExportProfile\XSLT_Export directory. Script processing (e.g., VB- or Java-
Script) within a XSLT style sheet is supported. In XSLT style sheets, the configured
export directory is available as the parameter exportPath.
Note: To open generated .csv files in Excel, use the New from text option and
select Unicode (UTF-8) as the file origin format. Fields are delimited by commas
(,). Use General as the column data format. In the advanced options select period
(.) as the decimal separator in numbers and make sure not to use a thousands
separator. If the values are not listed in columns, highlight all cells, then use the
Text to Columns function in Excel and select the correct delimiters. This option does
not allow selecting the Unicode (UTF-8) format, which may result in unwanted
characters in the column headers.

XML Raw Data Export If you select this option, electropherogram raw data of the selected files will be
exported in XML format.
An additional option to select additional output formats appears. The software

provides one format.
RawData_CSV_Export Use this option to export the electropherogram raw

data in .csv format (similar to the file format which
was exported by the BioCalculator 3.2 Software).
Note: You can customize your own output formats. Define xslt scripts based on the
xml raw data export file and store them in the %DATA_DIR%
\ReportExportProfile\XSLT_RawExport directory. Script processing (e.g., VB- or
Java-Script) within a XSLT style sheet is supported. In XSLT style sheets, the
configured export directory is available as the parameter exportPath.

The image options are described below:
Use Images as Use this option to obtain images that look similar to the presentation in the
Displayed QIAxcel ScreenGel Software regarding alignment, scales, labels, zoom, etc.
Note: This option is available in the analysis environment only, it may not be used
in a process profile.
Gel Image Use this option to export the gel image of all selected samples.
Overview
Click on the Image options button to specify the appearance of the exported gel
image overview. Image options are described below.
Note: The Image options button is disabled if the Use Images as Displayed option
is selected.
Unit of If you select Size, the y-axis will show a size scale
y-axis based on the reference marker on both sides of the gel
image, also if the Use Images as Displayed option is
selected. The lanes in the gel image will be aligned

have been analyzed with the same reference marker
table, and the alignment markers have been correctly
identified. Otherwise, a corresponding message will
appear.
If you select Rel. Time, the y-axis will show relative

migration time. The lanes in the gel image will be

marker, have been analyzed, and the alignment
markers have been correctly identified. Otherwise, the
lanes cannot not be aligned and the y-axis will show a
If you select Abs. Time [min], the lanes will not be

aligned and the y-axis will show an absolute time scale.
Zoom to Alignment Select this option to scale the lanes, so that the lanes
Marker start with the lower alignment maker band, and end
with the upper alignment marker band, if available
(crop data outside of the alignment markers).

Individual scaling Select this option to auto-scale the contrast for each gel
lane individually.

Show sample Select this option to include the sample information in
information each lane.
Show plate ID Select this option to display the plate ID, the repeat
number, and the entry number of each lane.
Show method Select this option to display the applied method above
the sample lane.
Gel Layout Select this option to determine the gel layout.
Select Standard Layout to order the lanes from left to

right, as they are ordered in the view.
Select Horizontal plate layout to order the lanes starting

with A1 at the upper left and ending with H12 at the
lower right.
Select Vertical plate layout to order the lanes starting

with H1 at the upper left and ending with A12 at the
lower right.
Select Reverse vertical plate layout for the vertical plate

layout but starting with A1 at the upper left and ending
with H12 at the lower right.
Select Split plate layout to split the vertical plate layout.

The left portion will start with H1 at the upper left and
end with A6 at the lower right. The right portion will
start with H7 at the upper left and end with A12 at the
lower right.
Note: Positions for samples not selected remain empty.

Lanes per Row Use this option to specify the number of lanes per row:
4, 6, 8, 12, 16, 24, 32, 36, or 48.
Note: This option is available only if Standard layout is

Rows per File Use this option to specify the number of rows to be
included in one file (the image is split into several files
according to the specified number of rows).
Note: This option is not available if Standard layout is

Highlight alignment Select this option to highlight in green the bands of the
markers alignment marker peaks.

Electropherogram Overview Select this option to export the electropherogram overview for all selected
samples. The order is the same as in the view. One gallery overview page (at
most 12 electropherograms) will always be exported to one file.
Click on the Image options button to specify the appearance of the exported
electropherogram overview. Image options are described below.
Note: The Image options button is disabled if the Use Images as Displayed
option is selected.
Unit of x-axis If you select Size, the x-axis will show a size scale
based on the reference marker. The
electropherograms will be aligned according to the
alignment markers.

selected samples have been run with the same
alignment marker, have been analyzed with the
same reference marker table, and the alignment
markers have been correctly identified. Otherwise,
the x-axis will show a corresponding message.

migration time. The electropherograms will be
Note: The relative time scale can be created only if

all selected samples have been run with the same
alignment marker, have been analyzed, and the
Otherwise, the electropherograms will not be
aligned and the x-axis will show a corresponding
message.
If you select Abs. Time [min], the electropherograms

will not be aligned and the x-axis will show an
Zoom to Alignment Select this option to scale the electropherograms so
Marker that the electropherograms start with the lower
alignment maker peak, and end with the upper
alignment marker peak (crop data outside of the
alignment markers).
Note: This is possible only if all samples are

analyzed.

Show sample position Select this option to show the sample position at
the top of each electropherogram.
Show sample Select this option to show the sample information at
information the top of each electropherogram.
Show plate ID Select this option to show the plate ID at the top of
the electropherogram.
Show method Select this option to show the applied method at
the top of each electropherogram.
Show analysis details Select this option to show analysis details for the
analyzed samples.
Select Mark detected peaks to show the apex

markers of detected peaks.
Note: In DNA mode, a second option Show median

of size is available. If the sample was analyzed
with a DNA smear analysis profile, select this
option to display the markers with the median size
of detected smear peaks.
Select Show suspend integration intervals to display

the suspend integration intervals.
Electropherogram Use this option to export a superposition view of all selected samples which
Superposition View have the "superimposed" flag set.
Note: The superposition view is restricted to 12 samples. In process

environment and in batch processing, the superposition is created only if the
experiment contains 12 samples or less.
Note: Use the Use Images as Displayed option to export the electropherogram
superposition as displayed.
Click the Image options button to specify the appearance of the reported
electropherogram superposition. Image options are described below.
option is selected.
based on the reference marker. The
electropherograms will be aligned according to the
alignment markers.

superimposed samples have been run with the
same alignment marker, have been analyzed with
the same reference marker table, and the alignment
the x-axis will show a message, instead.

migration time. The electropherograms will be

all superimposed samples have been run with the
same alignment marker, have been analyzed, and
the alignment markers have been correctly
identified. Otherwise, the electropherograms will
not be aligned and the x-axis will show a message,
instead.
If you select Abs. Time [min], the electropherograms

will not be aligned and the x-axis will show an
Zoom to Alignment Select this option to scale the electropherograms,
Marker so that the electropherograms start with the lower
alignment marker peak, if available (crop data
outside of the alignment markers).

analyzed.
Show Electrical Select this option to include a diagram of the
Current Curve superimposed electrical current measured during
data acquisition. The electrical current curve will
appear below the electropherogram superposition,
aligned with the x-axis.
Show size marker If this option is selected, and if exactly one size
peak labels marker is among the superimposed samples, the
peak labels will be displayed for the detected
peaks of the marker sample. Select the units for the
peak labels in the drop-down list.
Single Electropherograms Select this option to export the electropherograms for all selected samples in
separate files.
Use the Use Images as Displayed option to export the electropherogram as

displayed.
single electropherograms. Image options are described below.
Note: If the Use Images as Displayed option is selected, the gel lane and the
electrical current are combined with the electropherogram if these are visible
in the view.
option is selected.

based on the reference marker.
Note: The size scale can be created only if the

sample has been analyzed with a reference marker
table, and the alignment markers have been
correctly identified. Otherwise, the x-axis will show
a corresponding message.

migration time.

the sample has been analyzed and the alignment
the x-axis will show a corresponding message.
If you select Abs. Time [min], the x-axis will show

an absolute time scale.
Zoom to Alignment Select this option to scale the electropherograms,
Marker so that the electropherograms start with the lower
alignment marker peak, if available (crop data

analyzed.
Show Gel Lane Select this option to export the gel lane combined
with the electropherogram (the gel lane is below
the electropherogram).
Show Electrical Select this option to export the electrical current

Current curve below the electropherogram or below the gel
lane.
Select Show analysis details to enable the following options for analyzed
samples:
Mark detected peaks Select this option to display the apex markers for
detected peaks.


adjacent label are displayed. Hover the mouse
cursor over the peak apex to get a tool tip with the
peak label.

Select the label units: size, absolute or relative
migration time.
Note: The label can be displayed as Size only, if

the sample was analyzed with a reference marker
(for details refer to Size and Concentration
determination). Otherwise, "n/a" is displayed.
Note: In DNA mode, a second option Mark median

of size is available. If the sample was analyzed
with a DNA smear analysis profile, select this
option to display the marker with the median size
of detected smear peaks. You can switch the
corresponding label on and off.
Select the option Mark peak start and end to mark

the starting and ending points of detected peaks.
Show areas of interest For DNA mode only. If the sample was analyzed
with a DNA smear analysis profile, select Show
areas of interest to display the areas of interest of
detected smear peaks.
integration interval intervals.
Show threshold Select this option to display the peak threshold.
Show baseline Select this option to display the baseline.
Single Gel Images Use this option to individually export the gel lanes for all selected samples.
single gel images. Image options are described below.
Note: The Image options button is disabled if the Use Images as Displayed option
is selected.
Unit of y-axis If you select Size, the axis shows a size scale based on
the sample peaks, if the sample has been analyzed with
a reference marker table and the alignment markers
have been correctly identified. Otherwise, the axis will
show relative migration time, if possible.
If you select Rel. Time, the axis will show relative

migration time, if the sample has been analyzed and
the alignment markers have been correctly identified.
Otherwise, the axis will show an absolute time scale.
If you select Abs. Time [min], the axis will show an


Note: This option is not available if the Use Images as
Displayed option is selected.
Zoom to Alignment Select this option to scale the lanes so that the lanes
Marker start with the lower alignment maker band, and end
with the upper alignment marker band (crop data
lane individually.
Analysis details If you select Show detected peaks and if the sample was
analyzed, the y-axis will be labeled with the apex for
detected peaks.
Note: In DNA mode, a second option Show median of

size is available. If the sample was analyzed with a
DNA smear analysis profile, select this option to display
the median size for detected smear peaks.
Select Highlight alignment markers to highlight in green

The image export settings are described below. They appear if at least one image type is selected for
export.
File Type Select the file type for the image files.
Resolution Select the resolution for the image files; the available resolutions are: 75 dpi (dots
per inch), 150 dpi, 300 dpi, and 600 dpi. For small bands, use 150 dpi.
Modifying a report/export profile
Note: Only users with the Advanced User or Basic User role can modify report/export options.
To modify a report/export profile proceed as follows:
1. Open the Report tab.
Select the Report tab.
2. Select the report/export profile you want to modify.
Select the report/export profile in the Report/Export Profile drop-down list.
3. Change the profile options according to your needs.

See the Report options and Export options sections for detailed information.
Note: The system notifies modifications on the profile by displaying a "*" at the beginning of the profile
name.
4. Save the modified report/export profile.
Click the Save as button. Click OK in the Save Profile dialog which appears.
Saving a report/export profile.
Note: If you want to use the modified report/export options only once, just click Start Report/Export without
saving the modifications. However, your changes will lost when you select another report/export profile.
Note: Report profiles provided by QIAGEN cannot be modified. However, to save your modifications enter
a new unique profile name in the Save Profile dialog. A new profile will be created containing your
modifications. This is possible for users with the Advanced User role only.
Creating a new report/export profile
Note: Only users with the Advanced User role can create a new report/export profile.
To create a new report/export profile proceed as follows:
1. Open the Report tab.
Select the Report tab.
2. Select a report/export profile.
Select the profile from the Report/Export Profile drop-down list. The selected profile serves as a template for
the creation of the new profile.
Note: Select NewReport/ExportProfile to create a report/export profile from scratch. The system will show
*NewReport/ExportProfile after selection.
3. Set the profile options according to your needs. See the Report options and Export options sections for
detailed information about report/export options.
Note: The system notifies modifications on the profile by displaying a "*" at the beginning of the profile
name.

4. Save the modified report/export profile under a new name.
Click the Save as button and enter a new unique profile name in the Save Profile dialog that appears.
Saving a report/export profile.
Service
The Service environment provides functionality for cartridge calibration as well as troubleshooting and
maintenance tools for the QIAxcel Advanced instrument.
On the left side of the Service environment, a Status Information panel is displayed (See Status Information
panel).
Service environment with active System Check screen. The Status Information panel is shown to the left of
the screen.

Note: The Terminal and Logs screens of the Service environment may be accessed by service personnel only
and are not described in this manual.
Calibrating a cartridge
Every new cartridge requires intensity calibration prior to sample analysis. The intensities of each capillary
are normalized and a factor is applied for every subsequent run. This corrects for natural intensity reading
variations between each capillary in the cartridge. The data for each cartridge intensity calibration are
stored in a single file named <cartridge-id>_<instrument-id>.xcc. This file is saved in the directory %
DATA_DIR%\CartridgeCalibrationData\.
Note: To inspect calibration data, switch to the analysis environment and click the Load experiment button
of the Experiment Explorer. In the file dialog that appears, select the path ending with "[Calibration results
]."
Note: If for any reason a different computer is used to the one containing the calibration file, the file should
be transferred to the new computer. Otherwise, recalibration of the cartridge is required.

Running the calibration wizard
Intensity calibration of the cartridge is performed in the Calibration screen of the Service environment:
1. Load QX Intensity Calibration Marker onto the buffer tray position MARKER2 as detailed in step 7 of
Preparing the buffer tray.
2. Launch the calibration run by clicking the Start calibration button.
Note: The total run time for the calibration routine is about 16 minutes.
3. Confirm that the QX Intensity Calibration Marker is loaded. Optionally, enter the lot ID. Start the
calibration by clicking the OK button.
Confirmation dialog.
If the QX Intensity Calibration Marker is not loaded correctly, cancel the dialog. Load it again and repeat
step 1.
4. Once the calibration is complete, the calibration results are displayed next to the gel/electropherogram
view. The result table shows the area, calibration factor, and the result ("Passed" or "Failed") for each
channel.

Calibration results.
Note: A successfully calibrated cartridge should have a normalized area in a range as described in the
respective kit handbooks.
Note: If one or more channels fail, the calibration process should be repeated. If the issue persists, please
contact QIAGEN Technical Services or refer to the Troubleshooting section in the handbook supplied with
the QIAxcel Kit you are using.
5. Accept the calibration result. The cartridge is now calibrated.
Note: Discard the calibration result if one or more channels fail.
Note: A user with user role Advanced User can accept calibration results even if one or more channels
failed. In this case, the calibration status will be "Conditional OK." Only users with the user role Advanced
User can perform processes using cartridges with calibration status "Conditional OK."

Recalibrating a cartridge
To recalibrate a cartridge, repeat the procedure detailed in Running the calibration wizard. The calibration
results of previous calibration procedures are discarded when recalibrating a cartridge.
Note: It is possible to calibrate a cartridge that has no calibration runs left. In this case, three regular runs
are used instead of one calibration run.
System check
The System Check screen of the Service environment provides several procedures for detecting problems with
the QIAxcel Advanced instrument:
Complete Check
The complete check performs all the system checks listed below.
Detector Test
The detector test checks the raw count of all 12 channels.
Filter Check
The filter check detects blockage of the purge filter.
Movement Check
The movement test verifies that the sample tray can be moved properly and that the position sensors work
as expected.
Leakage Test
The leakage test checks for N2 leakage.
Note: The test results are stored to the directory %DATA_DIR%\SystemTest\.
Note: The troubleshooting folder functionality is described in the Troubleshooting folder section.
Complete check
A Complete Check performs all available system checks: Detector Test, Filter Check, Movement Check and
Leakage Test.

Complete check.
Note: The complete check takes approximately 4.5 hours.

Detector test
The Detector Test verifies that the detectors of all 12 channels of the QIAxcel Advanced instrument work as
expected. It may be performed when one or more channels in a new cartridge do not provide data signals
and the baseline is flat.
Perform the Detector Test by following the instructions shown on the screen. The test takes only several
seconds. At the end of the test, the acquired data is shown, and the results are stored.
Note: If not instructed otherwise, perform this test with a cartridge inserted and latched.
Detector test finished.

Filter check
In rare instances, the purge filter that sits inside the QIAxcel Advanced instrument may become blocked with
gel carryover. This blockage can be diagnosed using the Filter Check. It takes about two minutes. At the
end of the check, the filter status (passes or failed) is shown and the results are stored.
Note: A cleaning tissue, for example Kimwipe, is needed for this check.
The Filter Check is performed by following the instructions shown in the wizard:

Movement check
The Movement Check verifies that the tray motors and tray sensors work as expected. This test is fully
automated and requires no user interaction except cartridge removing. It takes several seconds. At the end
of the test, a test summary (passed or failed) is shown and the results are stored.

Leakage test
The Leakage Test checks for leakages in the N2 tubing of the QIAxcel Advanced instrument. This fully
automated test takes approximately 240 minutes. After the test, the leakage rate is calculated if a leakage
is detected and the results of the test are stored.

Maintenance
The Maintenance screen of the Service environment provides several maintenance and troubleshooting
procedures for the QIAxcel Advanced instrument and cartridges:
Motor teaching (for service personnel only; not described here)
Purge
Long purge
Empty N2 bottle
Set instrument ID
Troubleshooting folder
Purge
The Purge method allows the user to remove air bubbles from the gel cartridge and clean the capillaries.
The process is fully automated and takes less than a minute.

Long purge
The Long Purge method allows the user to remove air bubbles from the gel cartridge and clean the
capillaries extensively. The process is fully automated and takes about 3 minutes.

Empty N2 bottle
To remove a pressurized N2 cylinder, you must release the remaining pressure first. The Empty N2 Bottle
function purges the nitrogen, which takes about a minute.
Note: You must first remove the QIAxcel gel cartridge before performing this action.
Important: Repeat this operation until no hissing sound can be heard at the end of the purge operation.

Setting the instrument ID
Setting the QIAxcel instrument ID (serial number) is possible only if the instrument is connected and the
instrument ID has not been set. The instrument ID can be found on a label at the rear side of the instrument
housing.
The instrument ID is required to identify each instrument and check that a cartridge is calibrated on a certain
instrument (see Calibrating a cartridge).
Important: Make sure you have entered the correct instrument ID before clicking the Apply button. Once set,
the instrument ID cannot be changed again, except by a QIAGEN service personnel.
Troubleshooting folder and log files
The Troubleshooting folder function allows export of log files and test results produced within a specified
time period.
To export log files or test results, proceed as follows:
1. Switch to the Service environment.
2. Select the Maintenance or System Check screen.

3. Click the Troubleshooting folder, which is located at the bottom of the screen. It opens the following
dialog:
Select information to be exported.
4. Select the time period in which the test results were produced or a problem occurred. In most cases, this
is Start Date: yesterday, and End Date: today.
5. In the Results column, select the test results to be exported.
6. In the Logging Information column, select all log file types.
7. Click OK. The exported files are stored under the Troubleshooting directory defined in the Settings.
8. To navigate to the Troubleshooting directory, select the Open Data Directory->Troubleshooting option
from the File menu .

Open Data Directory function.
9. Select the just created file Troubleshooting_..._.zip.
Refer to the Settings section for information about log file levels.

Configuration
Application settings, users and profiles are managed in the Configuration environment:
Configuration environment with active Settings screen.
Settings
The Configuration environment of the QIAxcel ScreenGel Software provides several settings options as
described below.
Note: Global settings options are read only for users with the assigned role Routine User or Basic User.
Refer to the User roles section for more information.
Use global settings The global settings option is used to share both general settings and profiles
among several users.
Use private settings When using private settings, both the general settings and the created profiles of
the user are private.
Note: The private settings option can be activated only if the user has the right to
maintain private settings (see User management).

The settings are grouped according to functionality. The following table gives an overview of the sections:
21 CFR Part 11 Controls functionality required by 21 CFR Part 11 (FDA guidelines on electronic
Support records). Select this option to enable auto-lock and to limit the number of failed logins.
Option Description
AutoLock The system automatically locks the QIAxcel ScreenGel
Software after the specified period of idle time, except when
a process is running. To unlock, the user must login again.
Refer to the User authentication section for more information
about how to unlock.
Note: Idle time means time without user action or instrument

action.
Maximum number After the specified number of failed logins, the system
of failed logins automatically locks the user account. It can be unlocked by
the administrator only.
Log files The QIAxcel ScreenGel Software writes all log messages to one main log file. In
addition, separate log files can be created for individual log message types (IVD,
Instrument, etc) and for errors. The language of all log files is English. An exception is
the separate IVD log file (audit trail). If the software language is other than English, the
file exists twice, one in English, and one in the selected language.
Start with the levels as shown in the following image.
The size of a log file is limited; this size is configured by the Maximum log file length.
To always have the latest log files available, a new file will be created when the
maximum size has been reached. The number of log files to be kept is configured by
the Maximum log files per type. When, for a particular log file type, the maximum
number of files has been reached, the oldest file of that type will be deleted.

The verbosity increases from Critical to Verbose. When Critical is selected, only critical
log messages are written to the log file. When Verbose is selected, all log messages
are written to the log file.
Note: The Verbose level can decrease the performance of the QIAxcel ScreenGel
Software. Keep the information as short as possible for each log and file type. Start
with the levels as shown in the image above.
The main log file gives an overview of the last actions in the software. The verbosity of
the main log file is set in the Main Log Level column of the above table. This describes
how much information of a log type will be added to the main log file.
The verbosity of the individual log files is set in the Log File Level column. Increase the
log level for special types of error tracking.
The error log file gives an overview of the last errors. The verbosity of the error log file
is set in the Error Log Level column of the table shown above. This describes how much
information of a log type will be added to the error log file. Typically, only the
verbosities Error and None are used for the error log file.
Log Type Description

IVD Audit trail. If this is also included in the main log file, it
helps to understand the last actions.
Instrument In case of communication problems, it can be useful to

increase the Log File Level to Verbose for a certain time span
and to reproduce the situation. With these settings, the
Instrument log file reaches the maximum log file length very
soon (after one run). Therefore, disconnect from the
instrument just after the situation occurred, export the log
files, and return to verbosity Warning. Use verbosity Error in
the columns Main Log Level and Error Log Level to keep the
overview character of the main log file and the error log
file.
User Traces the user management actions.
View Information from the graphical user interface of the software.
Presentation Information from the graphical user interface of the software.
Service Information from the software logic.
Persistence Information about loading and saving. Increase verbosity of

the Log File Level if there are problems with loading and
saving experiments or profiles.
Other All other information.
Refer to the Troubleshooting folder and log files section for information how to export
log files.
Generate plate ID When enabled, defines how automatically generated plate IDs are constructed.

The following options define construction of the plate ID.
Option Description
Cartridge ID If this option is selected, the generated plate ID will contain
the Cartridge ID at the start.
Date If this option is selected, the generated plate ID will contain

the date of the data acquisition. If Cartridge ID is included,
the date will be placed next to the Cartridge ID.
Time or Counter Specifies how the uniqueness of the plate ID is achieved:

with the time of the process start (including hours, minutes,
and seconds) or with the counter incremented for the next
plate ID generation.
Note: If the plate ID is edited during process setup after

automatic generation, the time will not reflect the exact
process start time, but will reflect the time the plate ID was
generated during process setup.
The Example field shows what the generated plate ID may look like.
Sample Selection Specifies which optional information can be entered at the Sample Selection screen of
the process wizard.
Option Description
Enable input Select this option only, if you want to provide lot IDs for Buffers.
fields for If this option is not selected, you cannot provide lot IDs for
Buffer lot IDs Buffers during process setup.
Enable input Select this option only, if you want to provide lot IDs for Markers
fields for . If this option is not selected, you cannot provide lot IDs for
Marker lot Markers during process setup.
IDs
Provide Select this option, if you usually provide sample information.
Sample Even if this option is not selected, you can provide sample
Information information, but have to select the Provide Sample Information
option at the Sample Selection screen of the process wizard
manually.
Prevent Select this option if you want sample information from imported
modification rack files to be "read only."
of imported
sample
information

Instrument
Option Description
Latch cartridge If this option is selected, the system latches the cartridge
automatically automatically after a cartridge is inserted and the cartridge
door is closed.
Perform calibration If this option is selected, the system performs cartridge

automatically calibration automatically, if the inserted cartridge has not yet
been calibrated.
COM Channel Specifies the COM channel the QIAxcel Advanced instrument
is connected to. After login, the system automatically tries to
connect to the QIAxcel Advanced instrument using the
specified COM port.
Rise Time The rise time is a parameter of the Bessel filter applied to the raw data during
acquisition. This parameter should not be changed unless you know the function of the
Bessel filter and the effects of changes to the rise time parameter.
Directories Specifies the directories for acquired raw data and all other application data.
The base directory for the directories listed below is initially (i.e., after the QIAxcel
ScreenGel installation) the Application Data directory which is specified during the
Installation of the ScreenGel Software. All these directories are configurable.
The following directories can be specified:
Directory Description
name
Export Default export directory. This is the default directory in which
export files are generated, unless a different directory is
chosen in the export profile.
Report Default report directory. This is the default directory in which
report files are generated, unless a different directory is
chosen in the report profile.
Header & Directory for report header and footer. During report
footer generation the system looks here to find a header and footer
to be included in the report.
Sample Default directory for importing or exporting sample information
information (see Running procedure or Running a process with advanced
options, respectively). An example import rack file can be
found in the default directory %DATA_DIR%\SampleInfo.
Troubleshooti Directory where files created by the Troubleshooting folder are
ng stored.

Experiment Directory that contains 3 sub-directories: DNA and RNA. The
experiment data files (both acquired as a process run result or
combined in the Analysis environment) are saved by default in
these sub-directories (according to the application mode),
unless a different directory was chosen in the process profile.
Local During a process, the experiment is saved in this directory. It
Experiment is hard-coded to %DATA_DIR%\LocalExperiment. After the
process has finished, the experiment is moved to the
experiment path defined in the process profile. Only if this
transfer fails (e.g., if it is a remote drive, and someone has
tripped over the network cable), the experiment can still be
found in the Local Experiment directory.
ExportTransfo This directory contains XSLT scripts for transforming export
rmationScript XML files. XSLT is a declarative language that enables
s transformation of the export XML file into a different format, for
example, another XML, HTML, or plain text. Some example
XSLT files can be found in the default directory %DATA_DIR%
\ReportExportProfile\XSLT_Export, for creating files in .csv
format from the export.
ExportRawTra This directory contains XSLT scripts for transforming raw data
nsformationSc export XML files. An example XSLT file can be found in the
ripts default directory %DATA_DIR%
\ReportExportProfile\XSLT_RawExport, for creating a file in .
csv format from the raw data export.
Note: The directories above can be opened in the Windows Explorer directly from QIAxcel ScreenGel
Software through the menu item File/Open Data Directory.
Most settings changes take immediate effect after clicking OK. The following table lists settings that require
additional actions:
Generate plate ID section Active after next login.
Instrument-COM channel Active after reconnection with instrument.
Note: After clicking OK, the system asks you to reconnect to the
new COM channel.
Directories Next login.

Changing the language
To view the languages supported by the software or to change the language:
1. In the File menu select the Language option.
2. Select the language in the drop-down box.
3. Close and restart the software.
Profile management
Several dialog boxes of the QIAxcel ScreenGel Software allow the creation of new profiles, for example
analysis profiles, size marker tables, and reference marker tables. The Profile Manager lists all profiles
grouped by type. Profile details can be printed and profiles can be deleted using the Profile Manager.
Note: Profiles that are marked with a padlock symbol are default profiles provided by QIAGEN. These
profiles cannot be deleted.

User management
Administrators have access to the User Manager tab, in which user accounts can be modified:
The User Manager.
Editing user accounts

To edit an existing user account:
1. Select the user account to be modified.
2. The details are displayed in the section at the bottom of the dialog.
3. Modify the parameters as required.
4. Click the Apply button.
Note: In the User Manager, the user name, role, password, and authorizations of existing user accounts can
be changed. The user ID (login name) is the unique identifier of a user and cannot be changed.
Adding users
To add a new user:
1. Click the Add button.
2. Specify a user ID not already in use, a user role, and a password. For details about user roles, refer to
the User roles section.
3. Set the allowed run modes and user options.

Note: You can create several user accounts for one person by giving the accounts different user IDs. This
may be useful to distinguish different roles.
Deactivating user accounts

User accounts cannot be deleted, but they can be deactivated if users no longer work with QIAxcel
ScreenGel Software data.
To deactivate a user account:
1. Select the user account to be deactivated from the list of users.
2. Uncheck the Activated option in the user settings. Deactivated users cannot log in anymore.
Note: Only activated users are shown in the user table. To show deactivated users, check the Show
deactivated user accounts checkbox below the user table.
User options
Allow private Allows the user to maintain private settings.

settings
May skip On the Run Check page of the process wizard, the user may skip the confirmation of
confirmation of check messages.
run checks
May revise Enables the user to Revise sample information in the Experiment Explorer.
sample
information after
run
May accept If an experiment has run incompletely, the user can mark it as complete in the Experiment
incomplete Explorer, overriding all warnings.
experiments

The following maintenance procedures must be carried out to ensure reliable operation of the QIAxcel
Advanced:
Following these procedures ensures that the QIAxcel Advanced is free of dust and liquid spills.
Important: Disconnect the line power cord from the power outlet before servicing.
Servicing
The QIAxcel Advanced is supplied with a warranty that lasts for 1 year, starting from the date of shipment.
The warranty includes all repairs due to mechanical breakdown. Application development, software
upgrades, accessories, and disposable items are not included in the warranty.
QIAGEN offers comprehensive Service Support Agreements, including Warranty Extensions, Full Cover
Support Agreements, and instrument/application training, including on-site installation. Service Support
Agreements maximize productivity and ensure high performance from your instrument. In addition, service
histories are fully documented and all parts are certified and guaranteed.
Contact your local QIAGEN Field Service Specialist or your local distributor for more information about
flexible Service Support Agreements from QIAGEN.

Cleaning agents
CAUTION
Damage to the instrument [C2]
Do not use bleach, solvents, or reagents containing acids, alkalis, or abrasives to

clean the QIAxcel Advanced.
WARNING
Risk of electric shock [W11]
Do not open any panels on the QIAxcel Advanced other than described in this user
manual.
Risk of personal injury and material damage
Only perform maintenance that is specifically described in this user manual.

Wipe the instrument with a damp cloth only.
The sample plate holder inside the instrument should be cleaned occasionally using a moist, soft cloth.
Wash the buffer tray in warm water using a mild detergent, rinse thoroughly with deionized water or
reverse-osmosis water, and let it dry before filling with fresh buffer. The buffer tray should be cleaned before
using a new QIAxcel gel cartridge.

This section makes you familiar with the activities which may be required to maintain the QIAxcel Advanced
or correct a failure.
Fuse replacement and cleaning
1. Switch off the QIAxcel Advanced using the main power switch.
2. Unplug the power cord from the power outlet and from the rear of the instrument.
3. Use a small flat-bladed screwdriver to remove the fuse-carrier assembly located above the area where the
cord connector enters into the inlet.
Replacing the fuse.

4. Replace the fuse.
Replace only with time-delay 4 A (250 V) fuses, marked “T4A250V” cat. no. 9241178. If replacement
fuses are not available, contact QIAGEN Technical Services.
5. Re-insert the fuse-carrier assembly and plug in the power cord.
6. Turn on the power and check the instrument for normal operation, i.e., check that the status changes in
the status panel (see section Operating the QIAxcel Advanced). If the instrument does not function
normally, or continues to blow fuses, unplug the system and contact QIAGEN Technical Services.

N2 cylinder replacement
N2 cylinders should be changed when one or both low pressure warnings are shown in the Status
Information panel.
Remove the old N2 cylinder:
Note: To remove a pressurized N2 cylinder, empty the N2 bottle first (see Empty N2 bottle).
1. Open the sample door and remove the buffer tray.

2. Gently pull up on the N2 cylinder port. Do not pull past the detent hole.
3. Turn the cylinder counter-clockwise to allow the remaining N2 to gradually leak out.
Note: Dispose of empty N2 cylinders as recyclable steel material according to your local regulations.
Insert a new N2 cylinder:
4. Screw a new, unpunctured N2 cylinder into the cylinder port in a clockwise direction.
Important: Only use N2 cylinders provided by QIAGEN (cat. no. 929705).
5. Turn until the needle inside the port punctures the N2 cylinder. Do not over-tighten: the cylinder should
only be finger tight.
6. Gently push down on the N2 cylinder until it is in the stowed (down) position.
Alternate N2 supply
The QIAxcel Advanced external N2 port (located at the rear of the instrument) can be supplied with clean,
noncondensing compressed nitrogen. This external N2 source can be used instead of the internal N2
cylinder. The regulated N2 minimum input pressure must be 50 psi (345 kPa) and the maximum input
pressure should not exceed 75 psi (517 kPa).
To connect an external N2 source, use the supplied urethane tubing (2 mm inner diameter x 3.18 outer
diameter) rated for 150 psi. Additional tubing can be purchased separately (cat. no. 9018435).
Connect the urethane tubing from the output of the external N2 source to the QIAxcel Advanced by firmly
inserting the tubing into the fitting located on the rear panel of the instrument.
Turn on the external N2 source pressure, and set the input pressure to 50–75 psi (345–517 kPa).

Blocked purge filter
Before a new sample run, fresh gel is purged from the gel reservoir of the cartridge into the capillaries by
applying pressure through the purge line and purge port of the instrument. In rare cases when the QIAxcel
gel cartridge was not stored in an upright position and equilibration conditions were not maintained, gel
may run into the purge line of the instrument. A purge filter that is placed in the instrument prevents gel from
running into the instrument's pressure valves. Gel in the filter or purge line will dry and thus block the filter
or purge line.
To diagnose a blocked purge filter or purge line, the Filter Check with the QIAxcel ScreenGel Software can
be performed. If the filter is blocked, a replacement of the purge filter is required. In very rare cases the
purge line needs to be rinsed with water to resolve gel debris blocking the purge line tubing.
Note: Replacement of the purge filter and cleaning of the purge line is only required when the filter test
failed and tubing is clogged.
Note: It is not required to replace the purge filter or cleaning the purge line as a preventive maintenance.
Performing a Filter Check

1. Switch on the QIAxcel Advanced.
2. Launch the QIAxcel ScreenGel Software .
3. Go to the System Check tab in the service environment and perform the guided Filter Check (see Filter
check).
4. If Filter Check fails, replace the filter and test again.

Replacement of purge filter
1. Open the service door.
2. Remove the purge filter.
Note: Do not pull on the tubing.
3. Place a new purge filter and attach tightly to the connectors.

4. Perform the Filter Check again.
Note: If the Filter Check fails again, contact QIAGEN Technical Services.
Additional filters can be ordered from QIAGEN.
9021980 Set, Purge Filters (10), QX; please contact QIAGEN Technical Services.

Troubleshooting
This section provides information about what to do if an error occurs when using the QIAxcel Advanced
and QIAxcel ScreenGel.
If you need to contact QIAGEN Technical Services about an error, note down the steps leading to the error
and the information from any dialog that appear. This will help the QIAGEN Technical Service Specialist to
resolve the error.
Refer to the Troubleshooting folder and log files section for detailed information on how to retrieve log files
and system test results.
System setup
Comments and suggestions
Instrument does not turn on
a) Power cord not connected Check the power connection.
b) Fuse blown Replace the fuse.

Computer software cannot communicate with system
a) RS232 cable is not connected Check the connection of the RS232 cable. To retry the
between PC and system
connection to the instrument, click the icon in the software in
the Process environment.
b) Incorrect COM channel settings Check the COM channel setting (see section Settings). At the
bottom of the settings screen, click OK to confirm the changes.
Click Yes in the message shown to connect again to the newly
selected COM channel. If the icon is visible, the instrument

is ready to operate. If the problem persists, change the log level
of the instrument log to verbose (see section Settings for
information how to do this). Close the software, restart it, and
login. Wait until the message appears as "the instrument is not
available." Then collect the troubleshooting folder as described
in the section Troubleshooting folder and log files. Ensure to
check the boxes in the list at the right to include the logging
information. Send the file created to QIAGEN Technical Services.
c) Instrument software version does If switching between the QIAxcel ScreenGel and the
not match the software version BioCalculator Software, close the software, turn the QIAxcel
Advanced off at the power switch, wait 20 seconds and then turn
it on again before launching the other software. Ensure you have
opened only one of the software at a time.

d) Software cannot detect the COM Check the user permission for the registry entries that are
port. concerned the COM ports. The pertained registry entry is
typically named
H K E Y_LO C A L_M A C H IN E \S YS TE M \C o n tro lS e t0 0 1
\E n um \A C PI\PN P0 5 0 1 \X X X X X X \De v ice Param e te rs. Make
sure that user Everyone has at least read permission for this entry,
otherwise the COM port scan procedure (which is invoked at
start of the application) might fail if the QIAxcel ScreenGel is
being operated by a user who does not have administrator
permissions.
e) Firmware update is not successful The QIAxcel ScreenGel Software comes with an up-to-date
instrument software for instruments with serial number 30281 and
higher. If the update process could not be completed, the
QIAxcel Advanced instrument cannot connect to the QIAxcel
ScreenGel Software any longer. In this case, the software
provides an option to repeat the update process. Ensure that the
cable between the instrument and the computer is connected
correctly. Turn on the instrument. Restart the QIAxcel ScreenGel
Software and login. Wait until the icon changes to . In

this case, the instrument is ready to operate again. Otherwise, a
message appears that the instrument is not available. Click the
Troubleshoot button. In the next message, click Retry instrument
update. Wait for the Updating Instrument dialog. Wait a few
minutes until the update is complete and the message closes. If
the update is successful, the icon is visible and the
instrument is ready to operate. Otherwise, if the icon is

visible, change the log level of the instrument log to verbose (see
section Settings for information how to do this) and repeat the
steps to update the instrument again. Then collect the
troubleshooting folder as described in the section
Troubleshooting folder and log files. Ensure to check the boxes in
the list at the right to include the logging information. Send the
file created to QIAGEN Technical Services.
No serial port in laptop computer
Some laptops do not have a serial Contact the PC manufacturer to request the correct serial port
port connector.
QIAxcel ScreenGel Software does not start
a) QIAxcel ScreenGel Software not Install the QIAxcel ScreenGel Software.
installed
b) Old version of Microsoft The QIAxcel ScreenGel Software operates with Windows 7 (32
Windows and 64 bit) and Windows 10 (64 bit) (see section Computer and
software for more details).

Operation
N2 cylinders do not last long
a) Air leak Double check the N2 cylinder to make sure it is tight.
b) Internal leak if N2 cylinder last Contact QIAGEN Technical Services.

only a couple of days
Samples tray does not move
a) Transport lock is in place Remove the transport lock.
b) Sample door is not closed Close the sample door.

Cannot insert cartridge into system
Cartridge installed backwards Make sure the cartridge front cover faces the front of the system
and check that the purge cap seal has been removed.
Cartridge cannot be latched
a) N2 pressure low Replace the N2 cylinder.
b) Cartridge door is open Close the cartridge door.
c) Cartridge smart key not inserted Insert the smart key.

Cannot run system
a) Sample door and/or cartridge Close the sample door and/or cartridge door.
door are open
b) Cartridge smart key not detected Insert the cartridge smart key
c) Pressure low Replace the N2 cylinder
QIAxcel ScreenGel Software is slow

a) Too many experiments open in Close some of the opened experiments and then restart the
experiment explorer QIAxcel ScreenGel Software. Try to keep the number of opened
experiments low.
b) Too many applications running Close all unnecessary applications.

concurrently.
Problems when files are/shall be located on the network folder

a) Network folder is not visible in the If the network folder is not visible in the software although it has
file dialog been mapped, e.g., by an administrator, try the following to
make the mapping visible for all Windows users. Delete the
existing mapping. Then use the net use command together with a
UNC name to map the network location. For example, in the
command prompt, type the following command and press Enter:
net use \\< computername >\< sharename > /user:< username
>

Ask your local IT for assistance, if required.

b) It takes too long to open a If you are using only one of the sub-folders of the network folder,
network folder map directly to the sub-folder instead of mapping the entire
network folder. Use the net use command as described above.
DNA applications
DNA peaks signal variation in channels
New cartridge requires Calibrate the cartridge (see section Calibrating a cartridge).
calibration
Slow peak migration time in channels
a) Air bubbles in gel Perform a purge or 3-minute purge (see Maintenance) to remove air bubbles,
cartridge capillaries or change the QX Separation Buffer.
b) Current too low due Increase the room temperature.

to low temperature
c) Current too low due Perform a purge or 3-minute purge to clean the capillary tips (see Maintenance
to partially dry ).
capillary tips
Weak signal of the QX Alignment Marker
Degraded/old QX Change the QX Alignment Marker.
Alignment Marker
No signal in channels
a) No samples injected Check the volume of sample (10 µl minimum).
b) Blocked capillary Purge the instrument to remove the blockage (see Maintenance). If this does
channel not work, replace the cartridge.
c) Broken capillary or Replace the cartridge.

optical fiber in
cartridge
d) Light source problem Check if all LEDs are illuminated. Contact QIAGEN Technical Services.
(LEDs off)
e) No purging of the Perform a Filter Check.

cartridge/purge filter
blocked

Loss of resolution in channels
a) Old gel in some Perform a purge or 3-minute purge to fill the channels with new gel, or repeat
channels or clogged the purge method several times to remove clogging (see Maintenance).
channels
b) Saturated signals Reduce the sample injection time or select a more suitable method.
c) Expired cartridge Use a new cartridge.

Broad or saturated DNA peak/band
a) DNA concentration Dilute the DNA solution in QX DNA Dilution Buffer.
too high Reduce the injection time.
Choose a method for high DNA concentration samples (e.g., 0H500 [see
Appendix B]).
b) Broken channel with Call QIAGEN Technical Services and replace cartridge.
high background
DNA signal too low
a) DNA concentration Increase the sample injection time.
too low Choose a method for low DNA concentration samples (e.g., 0L500 [see
Appendix B]).
b) Salt concentration too Desalt or dilute the DNA samples to reduce the salt concentration and
high in sample enhance DNA injection.
solution
Separation current (µA) too low
a) QX Separation Buffer Replace the QX Separation Buffer.
is contaminated
b) Blocked capillary Replace the QIAxcel gel cartridge.

channel
Separation current (µA) too high
a) QX Separation Buffer Replace the QX Separation Buffer.
contaminated
b) Salt concentration too Desalt or dilute the DNA samples in QX DNA Dilution Buffer.
high in sample
solution
Data squeezed together on gel image folder
a) Extra peaks before Repeat the analysis as described in Analysis of DNA samples. During the
the first peak or after procedure, follow the instructions to increase the Alignment Marker Threshold.
the last peak were
detected

b) Wrong peaks were Repeat the analysis as described in Analysis of DNA samples. During the
identified as the first procedure, follow the instructions to increase the Alignment Marker Threshold.
and last peaks for
alignment
c) Upper alignment Repeat the analysis as described in Analysis of DNA samples. During the
markers were missing procedure, follow the instructions to decrease the Alignment Marker Threshold.
or below the Replace the new markers for the next run.
threshold setting
d) Sample signals too Dilute the samples or use the H Methods (see Appendix B) for sample analysis.
strong and cause the
alignment below the
threshold setting
Data not aligned
a) Upper marker Change to a new alignment marker.
missing
b) Migration problem Purge and run the sample again.

due to air bubbles
c) Migration problem Increase the separation time.

due to low
temperature
d) Start Analysis button Click the Start Analysis button to perform analysis.
in the "Analysis"
environment not
clicked
e) Samples with different Remove samples with a different alignment marker from the view.
alignment markers
visualized
f) Alignment markers not Repeat the analysis as described in Analysis of DNA samples. During the
identified correctly procedure, follow the instructions to adapt the analysis parameters.
No size calling in the result table
a) The reference marker Repeat the analysis as described in Analysis of DNA samples. Select the right
is turned off marker table.
b) Peak detection failed Repeat the analysis as described in Analysis of DNA samples. During the
procedure, ensure that peaks are detected correctly, especially the alignment
marker peaks.
Wrong size calling
a) Wrong reference Repeat the analysis as described in Analysis of DNA samples. Select the right
marker table used marker table.

b) Reference marker Repeat the analysis as described in Analysis of DNA samples. Make sure that
table setting the correct alignment marker is set (refer to Checking alignment marker).
problems Make sure the number of peaks in the Rel. Time and size (bp) columns are
equal in the reference marker table.
No size scale in gel image
a) Data not aligned Remove samples with a different alignment marker from the view.
Repeat the analysis as described in Analysis of DNA samples. Make sure all
alignment marker peaks have been identified correctly.
b) Samples analyzed Repeat the analysis as described in Analysis of DNA samples using the same
with different reference marker table for all samples.
reference marker
tables
Required scale type not created
a) Samples not analyzed Click the Start Analysis button to perform the analysis.
b) Samples with different Remove samples with a different alignment marker from the view.
alignment markers
visible
c) No size determination Repeat the analysis as described in Analysis of DNA samples using the same
reference marker table for all samples.
Upper alignment markers resolved in double peaks

High salt sample Dilute the sample or change the parameter setting.
RNA applications
Alignment is off
a) The first peak is below the Repeat the analysis as described in Analysis of RNA samples.
threshold During the procedure, follow the instructions to decrease the
Alignment Marker Threshold.
Contamination, for example, by salt may result in aberrant

migration of individual lanes that may be too large for proper
alignment. Use less sample or perform an additional cleanup of
RNA samples that show delayed migration.
b) Degraded/old calibration marker Replace the calibration marker.

Required scale type not created
a) Samples not analyzed Click the Start Analysis button to perform the analysis.

b) Samples with different alignment Remove the samples with a different alignment marker from the
markers visible view.
c) No size determination Repeat the analysis as described in Analysis of RNA samples

using the same valid reference marker table for all samples.
The ratio of rRNA (28S/18S) is too low
Degraded RNA samples Change the RNA sample.
The signal of RNA sample is too low
a) Low RNA sample concentration Increase the sample volume up to 5 µl. Mix an equal volume of
RNA loading buffer to sample. For example, if 2 µl of RNA
sample was used, mix the RNA sample with 2 µl of RNA loading
buffer.
b) Degraded RNA samples Change the RNA samples.

Broad RNA peaks
a) Degraded RNA samples Change the RNA samples.
b) Incomplete RNA denaturation Repeat the RNA denaturation process.

process
c) Aged buffer Replace the separation buffer every 25 runs.
Only 18S RNA peak detected

Incomplete RNA denaturation process Repeat the RNA denaturation process.
RNA degradation will also result in disappearance of the 28S

peak first.
Calibration marker signal variation in channels
a) New cartridge requires Calibrate the cartridge (see section Calibrating a cartridge).
calibration
b) Cartridge intensity calibration is Calibrate the cartridge (see section Calibrating a cartridge).
incorrect
c) Degraded/old QX Calibration Change the QX Calibration Marker.

Marker
Delayed peak migration in some channels
a) Air bubbles in capillaries Use the Long purge to remove air bubbles
(see Maintenance).
b) Air bubbles in calibration marker Remove the air bubbles from the vials.
or RNA sample vials

Glossary
Term Description
Buffer tray The buffer tray is a removable plastic tray that sits in the buffer tray holder of the
QIAxcel Advanced and holds QX Separation and Wash Buffers and QX Intensity
and Alignment Markers.
Buffer tray holder The buffer tray holder is located inside the QIAxcel Advanced under the sample
door. The buffer tray, which holds QX Separation and Wash Buffers and QX Intensity
and Alignment Markers, is placed in the buffer tray holder prior to sample analysis.
Cartridge door The door that allows the QIAxcel gel cartridge to be loaded into the QIAxcel
Advanced. This door should remain closed during operation of the QIAxcel
Advanced.
Channel(s) Each QIAxcel gel cartridge has 12 channels (capillaries) through which the samples
for analysis pass.
Method A method is the collection of commands and parameters that are applied to an
individual sample run. A number of default methods are preinstalled.
Mineral oil For covering solutions and/or samples to prevent evaporation.
N2 door The N2 door, located to the right of the sample door, allows insertion and removal
of the N2 cylinder.
Position An area of a rack/plate that can contain something. Examples of positions include
the wells of a microplate or slots in the sample plate holder.
Power switch A button located at the back of the QIAxcel Advanced in the bottom-left corner. It
allows the user to switch the QIAxcel Advanced on and off.
Process Profile This defines settings for data acquisition. Defines all parameters for the
electrophoresis run.
Purge port The purge port is located inside the QIAxcel Advanced instrument and aligns with the
purge hole of the QIAxcel gel cartridge.
QX Alignment Allows sample migration time to be calibrated.

Marker
QX DNA or RNA Allows dilution of concentrated samples.

Dilution Buffer
QX DNA or RNA Enables separation of DNA or RNA molecules in the QIAxcel gel cartridge.
Separation Buffer
QX DNA or RNA Enables creation of a reference marker table allowing DNA/RNA size and/or
Size Marker concentration determination.

Term Description
QX DNA or RNA For washing the capillary tips to prevent cross-contamination.
Wash Buffer
QX Intensity Allows calibration of the signal intensity for each new gel cartridge.
Calibration Marker
Sample door The door that provides access to the sample plate holder and the buffer tray holder.
This door should remain closed during operation of the QIAxcel Advanced.
Sample plate holder The sample plate holder is located inside the QIAxcel Advanced under the sample
door. 96-well plates or sample strips containing the samples for analysis are placed
in the sample plate holder.
Service door The service door allows access to the purge filter and a manometer.
Smart key This key attached to the QIAxcel gel cartridge holds information about the cartridge
(i.e., cartridge identifier, calibration status, number of runs). The smart key should be
inserted into the smart key socket on the QIAxcel Advanced to enable sample
analysis.
Smart key socket The smart key socket allows the QIAxcel Advanced instrument to read and display
the information on the smart key.

Appendices
The appendices contain technical data, QIAxcel methods and accessories, descriptions of the data analysis
algorithms, and warranty terms.
Appendix A
Technical data
QIAGEN reserves the right to change specifications at any time.
Environmental conditions
Operating conditions
Power 100–240 V AC, 50–60 Hz, 360 VA
Fuse rating 4 A (250 V) time-delay fuse (for 100–240 V AC)
Overvoltage category II
Air temperature 15–30ºC (59–86ºF)
Relative humidity 10–75% (noncondensing)
Altitude Up to 2000 m (6500 ft.)
Place of operation For indoor use only
Pollution level 2
Environmental class 3K2 (IEC 60721-3-3)
Transportation conditions
Air temperature –25ºC to 60ºC (–13ºF to 140ºF) in manufacturer’s package
Relative humidity Max. 75% (noncondensing)
Storage conditions
Air temperature 15ºC to 30ºC (59ºF to 86ºF) in manufacturer’s package
Relative humidity Max. 75% (noncondensing)

Mechanical data and hardware features
Dimensions (door Width: 370 mm (14.57 in.)
closed) Height: 405 mm (15.94 in.)
Depth: 555 mm (21.85 in.)
Dimensions (doors Width: 370 mm (14.57 in.)

open) Height: 706 mm (27.80 in.)
Depth: 555 mm (21.85 in.)
Mass 27 kg (59.52 lb.)
Capacity Up to 96 samples per run
Software Default protocols are provided with the QIAxcel ScreenGel Software supplied
with the QIAxcel Advanced. Updated protocols are available from www.qiagen.
com/QIAxcelAdvanced.
Waste Electrical and Electronic Equipment (WEEE)

This section provides information about disposal of waste electrical and electronic equipment by users.
The crossed-out wheeled bin symbol (see below) indicates that this product must not be disposed of with
other waste; it must be taken to an approved treatment facility or to a designated collection point for
recycling, according to local laws and regulations.
The separate collection and recycling of waste electronic equipment at the time of disposal helps to
conserve natural resources and ensures that the product is recycled in a manner that protects human health
and the environment.
Recycling can be provided by QIAGEN upon request at additional cost. In the European Union, in
accordance with the specific WEEE recycling requirements and where a replacement product is being
supplied by QIAGEN, free recycling of its WEEE-marked electronic equipment is provided.
To recycle electronic equipment, contact your local QIAGEN sales office for the required return form. Once
the form is submitted, you will be contacted by QIAGEN either to request follow-up information for
scheduling collection of the electronic waste or to provide you with an individual quote.

FCC Declaration
The ’’United States Federal Communications Commission’’ (USFCC) (in 47 CRF 15. 105) declared that the
users of this product must be informed of the following facts and circumstances.
This device complies with part 15 of the FCC. Operation is subject to the following two conditions: (1) This
device may not cause harmful interference, and (2) this device must accept any interference received,
including interference that may cause undesired operation.
This Class B digital apparatus complies with Canadian ICES-003.
The following statement applies to the products covered in this manual, unless otherwise specified herein.
The statement for other products will appear in the accompanying documentation.
NOTE: This equipment has been tested and found to comply with the limits for a Class B digital device,
pursuant to part 15 of the FCC Rules. These limits are designed to provide reasonable protection against
harmful interference in a residential installation. This equipment generates, uses and can radiate radio
frequency energy and, if not installed and used in accordance with the instructions, may cause harmful
interference to radio communications. However, there is no guarantee that interference will not occur in a
particular installation. If this equipment does cause harmful interference to radio or television reception,
which can be determined by turning the equipment off and on, the user is encouraged to try to correct the
interference by one or more of the following measures:
Reorient or relocate the receiving antenna.
Increase the separation between the equipment and receiver.
Connect the equipment into an outlet on a circuit different from that to which the receiver is connected.
Consult the dealer or an experienced radio/ TV technician for help.
QIAGEN GmbH, Germany is not responsible for any radio television interference caused by unauthorized
modifications of this equipment or the substitution or attachment of connection cables and equipment other
than those specified by QIAGEN GmbH, Germany. The correction of interference caused by such
unauthorized modification, substitution or attachment will be the responsibility of the user.

Declaration of conformity
Name and address of the legal manufacturer
QIAGEN GmbH
QIAGEN Strasse 1
40724 Hilden
Germany
An up-to-date Declaration of Conformity can be requested from QIAGEN Technical Services.

Appendix B
QIAxcel Advanced methods
A number of default methods are available for each QIAxcel Kit. Note that only the methods available for
the particular cartridge type can be selected.
Note: If you require a custom method to be created, please contact QIAGEN Technical Services.
DNA/RNA methods
Each method name is an acronym, providing information on the specific QIAxcel Kit/QIAxcel gel cartridge
being used, the sample injection time and voltage, and the separation time and voltage, as described
below.
Description of method name acronyms.

Please find below a complete list of methods available for each QIAxcel gel cartridge type and information
regarding their associated fragment sizes and best resolution.
QIAxcel DNA High Resolution methods

The QIAxcel DNA High Resolution Gel Cartridge is designed for high-resolution (3–5 bp) genotyping, high-
resolution multiplex PCR, and AFLP/RFLP analysis of less than 20 fragments. The gel cartridge can separate
fragment sizes ranging from 15 bp to 10 kb. The resolution depends on the fragment size and the method
chosen to run the assay:
Guidelines for method selection using the QIAxcel DNA High Resolution Kit
Fragment size
100–500 bp 500 bp – 1 kb 1–5 kb 5–10 kb
Method Best resolution
0M400* 20 bp 100 bp 500 bp N/A
†
0L400
0H400‡
0M500* 10 bp 50 bp 200 bp N/A
0L500†
0H500‡
0M700* 3–5 bp N/A N/A N/A
†
0L700
0H700‡
0M800* 3–5 bp N/A N/A N/A
0L800†
0H800‡
0M1200* N/A N/A 500 bp – 1 kb 1– 1.5 kb
†
0L1200
0H1200‡
* We recommend the 0M400, 0M500, 0M700, 0M800, and 0M1200 methods for DNA concentrations of
10–100 ng/µl (e.g., PCR products amplified from genomic DNA with 30–40 cycles).
† We recommend the 0L400, 0L500, 0L700, 0L800, and 0L1200 methods for DNA concentrations of <10
ng/µl.
‡ We recommend the 0H400, 0H500, 0H700, 0H800, and 0L1200 methods for DNA concentrations of
>100 ng/µl (e.g., high-yield PCR products).
M Methods
We recommend the 0M400, 0M500, 0M700, 0M800, and 0L1200 methods for DNA concentrations of
10–100 ng/µl.

Sample
Sample injection injection Separation Separation
Method voltage (kV) time (s)* voltage (kV) time (s)
0M400 5 10 6 400
0M500 5 10 5 500
† 5 10 3 700
0M700
0M800 5 10 3 800
0M1200 5 10 3.5 1200
* Sample injection time can be adjusted (minimum 1 s; maximum 60 s). Reduce the injection time if the
signal is saturated, as indicated by peaks with flat tops. Increase sample injection time if the signal is
below the default setting of the threshold of 5%.
† We recommend using method 0M800 instead.
L Methods
We recommend the 0L400, 0L500, 0L700, 0L800, and 0M1200 methods for DNA concentrations of <10
ng/µl.
Sample
0L400 8 20 6 400
0L500 8 20 5 500
0L700† 8 20 3 700
0L800 8 20 3 800
OL1200 8 20 3.5 1200
† We recommend using method 0L800 instead.

H Methods
We recommend the 0H400, 0H500, 0H700, 0H800, and 0H1200 methods for DNA concentrations of
>100 ng/µl.
Sample
0H400 2 20 6 400
0H500 2 20 5 500
† 2 20 3 700
0H700
0H800 2 20 3 800
0H1200 2 20 3.5 1200
† We recommend using method 0H800 instead.
Note: Unpurified PCR products contain dNTPs and primers, which can contribute to the optical density (OD)
and cause over estimation of the DNA concentration.
QIAxcel DNA Screening methods

The QIAxcel DNA Screening Kit is designed for low-resolution (>20 bp) genotyping, low-resolution
multiplex PCR, single PCR screening, plasmid DNA digestion checking, plasmid and oligo DNA quantity
checking, and gDNA quality checking. The gel cartridge can separate the fragment size range from 15 bp
to 5 kb. The resolution depends on the fragment size and the method chosen to run the assay:

Guidelines for method selection using the QIAxcel DNA Screening Kit
Fragment size
<500 bp 500 bp – 1 kb 1–5 kb
Method Best resolution
AM320* 20 bp 100 bp 500 bp
†
AL320
AH320‡
AM420* 20 bp 100 bp 500 bp
†
AL420
AH420‡
APH600 Uncut plasmid DNA checking
APL600
AM900 gDNA quality checking
* The AM320 and AM420 methods are recommended for DNA concentrations 10–100 ng/µl (e.g., PCR
products [30–40 cycles] amplified from genomic DNA).
† The AL320 and AL420 methods are recommended for DNA concentrations <10 ng/µl.
‡ The AH320 and AH420 methods are recommended for DNA concentrations >100 ng/µl (e.g., high-yield
PCR products).
M Methods
The AM320 and AM420 methods are recommended for DNA concentrations 10–100 ng/µl, while method
APH600 is recommended for purified high-copy plasmid DNA (50–300 ng/µl) in elution buffer. Method
AM900 is recommended for a visual quality check of gDNA purified using silica-based methods.
Sample
Sample injection injection time Separation Separation time
Method voltage (kV) (s)* voltage (kV) (s)
AM320 5 10 6 320
AM420 5 10 5 420
APH600 1 5 6 600
AM900 2 40 3.5 900
L Methods
The AL320 and AL420 methods are recommended for DNA concentrations <10 ng/µl, while method
APL600 is recommended for purified low-copy plasmid DNA (<50 ng/µl) in elution buffer.

Sample
AL320 8 20 6 320
AL420 8 20 5 420
APL600 3 5 6 600
* Sample injection time can be adjusted from 5 to 40 seconds to obtain optimal signals. Reduce the
injection time if the signal is saturated, as indicated by peaks with flat tops. Increase sample injection time if
the signal is below the default setting of the threshold of 7%.
H Methods
The AL320 and AL420 methods are recommended for DNA concentrations >100 ng/µl.
Sample
AH320 2 20 6 320
AH420 2 20 5 420
Note: Unpurified PCR products contain dNTPs and primers, which can contribute to the optical density (OD)
and cause overestimation of the DNA concentration.
QIAxcel DNA Fast Analysis methods

The QIAxcel DNA Fast Analysis Gel Cartridge is designed for rapid analysis of PCR fragments. The gel
cartridge can separate fragments ranging from 15 bp to 3 kb in size.
Note: The QIAxcel DNA Fast Analysis Cartridge, QX DNA Size Marker 50 bp – 1.5 kb, and the
corresponding methods are not suited for concentration determination.

Methods for use with the QIAxcel DNA Fast Analysis Cartridge
Sample
DM80 15 8 15 80
DM80 v2.0† 15 8 15 80
DM150 10 10 10 150
DM190 10 15 10 190
* Sample injection time can be adjusted (minimum 1 s; maximum 40 s). To obtain optimal signals, we
recommend using a minimum of 5 s and a maximum of 15 s.
† DM80 v2.0 includes a longer purge time between runs and thus improves the background level.
QIAxcel RNA Quality Control methods

The QIAxcel RNA Quality Control Gel Cartridge is designed for quality control of total RNA, cRNA,
fragmented RNA, and single-stranded cDNA.
Method CM-F-RNA is recommended for use with fragmented RNA and fragmented DNA at a
concentration of 250–500 ng/µl.
Method CM-RNA is recommended for use with total RNA at a concentration of 300–1000 ng/µl or
cRNA at a concentration of 100–500 ng/µl.
Method CL-RNA is recommended for use with total RNA at a concentration of 50–300 ng/µl or cRNA at
a concentration of <100 ng/µl.
Note: Total RNA and cRNA concentrations >1 µg/µl should be diluted to 1 µg/µl in sterile DEPC water
before denaturing.
Sample
CM-F-RNA 7 20 3 600
CM-RNA 5 20 6 600
CL-RNA 8 20 6 600

Appendix C
QIAxcel accessories
Product Contents Cat. no.

QIAxcel Advanced Instrument Automated system for fast and fully 9001941
automated DNA fragment analysis or
qualitative and quantitative RNA analysis,
QIAxcel ScreenGel software, 1-year warranty
on parts and labor
QIAxcel Advanced Priority Package Capillary electrophoresis device: includes 9002124
Priority Package with computer, QIAxcel
ScreenGel Software, installation, training, 2-
year warranty on parts and labor, and 2
preventive maintenance visits
QIAxcel Advanced Priority Package Plus Capillary electrophoresis device: includes 9002125
Priority Package Plus with computer,
QIAxcel ScreenGel Software, installation,
training, 3-year warranty on parts and labor,
and 3 preventive maintenance visits
QIAxcel Kits
QIAxcel DNA High Resolution Kit (1200) QIAxcel DNA High Resolution Cartridge, 929002
Buffers, Mineral Oil, QX Intensity Calibration
Marker, 12-Tube Strips
QIAxcel DNA Screening Kit (2400) QIAxcel DNA Screening Cartridge, Buffers, 929004
Mineral Oil, QX Intensity Calibration
Marker, 12-Tube Strips
QIAxcel DNA Fast Analysis Kit (3000) QIAxcel DNA Fast Analysis Cartridge, 929008
Buffers, Mineral Oil, QX Intensity Calibration
Marker, QX DNA Size Marker 50 bp – 1.5
kb, QX Alignment Marker 15 bp/3 kb, 12-
Tube Strips
QIAxcel RNA QC Kit v2.0 (1200) For 100 runs of 12 samples: QIAxcel RNA 929104
Quality Control Cartridge, Buffers, Mineral
Oil, QX Intensity Calibration Marker, QX
RNA Alignment Marker, QX RNA Size
Marker 200-6000 nt, QX RNA Denaturation
Buffer, 12-Tube Strips
DNA size markers
QX DNA Size Marker pUC18/HaeIII (50 µl) DNA size marker with 9 fragments: 80–587 929550
bp
QX DNA Size Marker FX174/HaeIII (50 µl) DNA size marker with 11 fragments:72– 929551
1353 bp

QX DNA Size Marker 100 bp – 2.5 kb 50 µl DNA size marker with 14 fragments: 929559
(50 µl) 100 bp – 2.5 kb
QX DNA Size Marker 25–500 bp v2.0 50 µl DNA size marker with 17 fragments: 929560
25–500 bp
QX DNA Size Marker 50–800 bp v2.0 50 µl DNA size marker with 11 fragments: 929561
50–800 bp
QX DNA Size Marker 250 bp – 4 kb v2.0 50 µl DNA size marker with 11 fragments: 929562
250 bp – 4 kb
QX DNA Size Marker 250 bp – 8 kb v2.0 50 µl DNA size marker with 11 fragments: 929563
250 bp – 8 kb
Alignment markers
QX Alignment Marker 15 bp/600 bp (1.5 ml) Alignment marker with 15 bp and 600 bp 929530
fragments
QX Alignment Marker 15 bp/1 kb (1.5 ml) Alignment marker with 15 bp and 1 kb 929521
fragments
fragments
fragments
fragments
fragments
fragments
QX RNA Alignment Marker (1.5 ml) 1.5 ml RNA alignment marker 929510
Calibration marker
QX Intensity Calibration Marker (600 µl) 600 µl QX Intensity Calibration Marker 929500
Buffers
QX DNA Dilution Buffer (15 ml) 15 ml QX DNA Dilution Buffer 929601
QX RNA Dilution Buffer (15 ml) 15 ml QX RNA Dilution Buffer 929602
QX Separation Buffer (40 ml) 40 ml QX Separation Buffer 929603
QX FA Separation Buffer (40 ml) 40 ml QX Separation Buffer; for use with 929606
QIAxcel DNA Fast Analysis Cartridges
QX Wash Buffer (40 ml) 40 ml QX Wash Buffer 929604
QX Mineral Oil (50 ml) 50 ml QX Mineral Oil 929605

Accessories
QX Cartridge Stand QX Cartridge Stand 929701
QX Cartridge Stand Cover QX Cartridge Stand Cover 929707
QX Buffer Tray QX Buffer Tray 929702
QX 0.2 ml 12-Tube Strip (80) 80 x QX 0.2 ml 12-Tube Strips 929703
QX Multicolor 0.2 ml 12-Tube Strip (80) 80 x QX Multicolor 0.2 ml 12-Tube Strips 929704
QX Nitrogen Cylinder (6) 6 x QX Nitrogen Cylinder 929705
QX Cartridge Purge Tool QX Cartridge Purge Tool 9241169
For up-to-date licensing information and product-specific disclaimers, see the respective QIAGEN kit
handbook or user manual. QIAGEN kit handbooks and user manuals are available at www.qiagen.com or
can be requested from QIAGEN Technical Services or your local distributor.

Appendix D
DNA analysis algorithm description
Summary
The figure below shows a flow diagram of the algorithm. The first step of the data analysis is smoothing.
Then, an iterative approach is used to construct the baseline. The objective of this baseline construction is
to effectively remove the peaks but accurately follow any other disturbances, e.g. baseline drift and shifts,
in the electropherogram. The next step is the cluster detection. Clusters are defined as data subsets in the
electropherogram where there is a certain minimal difference in signal between the actual data and the
constructed baseline. In this step, no distinction is made between a single peak or multiple not baseline
separated peaks. The next step is to split clusters that contain more than one peak. Finally, the actual peak
detection is performed, in which peak apex, start point, end point and area are determined.

Smoothing
Smoothing is performed to increase the signal-to-noise ratio (S/N) of the data.
Smoothing is performed with a Savitzky-Golay filter using a second order polynomial. One exception is the
analysis of smear DNA samples. A weighted average filter is applied to smooth this type of data.
Baseline construction
The baseline construction is based on a moving median filter. The median of a dataset is defined as the
center point of a dataset sorted in ascending order. A moving median filter processes the input data by
replacing each data point by the median of a data subset centered around that datapoints.
If the original dataset is an electropherogram, the electrophoretic peaks will be sorted towards the high end
because they have a higher intensity than the noise peaks. This means that as long as the size of the moving
median filter (Filter Size) is at least twice the baseline peak width, datapoints of that peak will never reach
the center (median) of the data subset, and will therefore be removed.

Mathematically the construction of the baseline using a moving median filter can be described as follows:
in which B(i) represents the constructed baseline, E(i) the electropherogram, and r the filter rank.
An exception is the analysis of smear DNA and gDNA samples. The baseline for smear DNA analysis is
constructed by taking the straight line that results from interpolating between the average signal values of
ranges specified at the beginning and at the end of the electropherogram. The baseline for gDNA analysis
is constructed by taking a horizontal straight line that starts from the average signal values at the beginning
of the electropherogram.
Cluster detection
After the baseline construction, the actual peak detection is started. The first step of this process is called
cluster detection. Clusters are defined as regions, i.e. data subsets, in the electropherogram where there is
a significant difference between the raw data and the constructed baseline (see figure below). The
parameter used to find these regions is the Threshold. The threshold is an imaginary line parallel to the
constructed baseline, which marks the minimal height a peak must have (in reference to the constructed
baseline) to be detected.
The identified regions can contain either one peak (peaks 1 and 2) or multiple, not baseline separated,
peaks (peaks 3 and 4). In either case the region is called a cluster. Initially, the cluster start- and end points
are marked as the points where the raw datapoints and the Minimum Peakheight threshold line cross.

The iteration process
As pointed out before, the successful removal of peaks during the baseline construction is dependent on the
baseline filter size and peak width. In some cases it is not easy, or even impossible, to find a baseline filter
size for optimal removal of all peaks in the electropherogram. This is especially the case in
electropherograms with a wide variety of peak widths (requiring a large filter size on a very unstable
baseline (requiring a small filter size to accurately preserve these relative high frequency baseline
disturbances). The following Figure shows the effect of a too small filter size on the results of the baseline
construction.
In the first pass, peak 1 is removed, but in peaks 2 and 3, the constructed baseline starts following the
peak. Without any further modifications to the algorithm, this would result in inaccurate peak integration.
To solve this problem the algorithm was made iterative. This means that multiple passes through the
baseline construction and cluster detection are made, improving the baseline in each pass. The whole
iteration process is based on the fact that even though the baseline construction during the first pass was
not optimal, normally most of the clusters are still detected.
The principle of the iteration process is that the cluster information obtained in the previous pass is used to
optimize the baseline construction in the current pass. In every additional pass, similar to the first pass, a
moving median filter is used for the baseline construction. However, before determining the baseline, a
check is made for overlaps between the clusters detected in the previous pass and the current filter position.
If an overlap is detected, those points are deleted from the sorted data subset, leaving virtually only
datapoints corresponding to baseline points in the original electropherogram. The value for the baseline is
now determined by taking the median of this new shortened data subset.
The figure of pass 2 shows the new baseline calculated after two passes. The baseline under peak 2 is now
correct but the baseline under peak 3 is still incorrect. Note, however, that the cluster start- and end points
in peak 3 have shifted considerably closer to the correct position. A third pass therefore will remove a
larger part of the peak from the sorted data subset leading to an improved baseline as shown after pass 3.

Cluster splitting
During the cluster detection, clusters with one or several peaks are determined. In cluster splitting step splits
clusters with more than one peak into several clusters. This facilitates the peak detection in the next step.
The algorithm used is very similar to the cluster detection algorithm. Cluster splitting is performed by
iteratively increasing the threshold until clusters with more than one peak decompose to several clusters.
Note: During Smear Analysis the goal is to detect smear peaks. As these peaks are relatively broad, the
cluster splitting step is omitted during smear peak detection.
Peak detection
After the cluster splitting, each cluster contains exactly one peak. The apex of the peak is determined by
looking up the maximum data point in the cluster. Then, the exact start- and end points of the peak are
determined. Two criteria are used for this purpose; the first criterion locates the start- and end points of a
cluster at the first point (in both directions, starting from the center of the cluster) were the raw data and the
constructed baseline cross each other. The second criterion is used to detect cluster borders in case of
overlapping peaks (where the raw data and baseline do not cross). In this case the start- and end points of
a peak are located at the points where the absolute value of the first derivative remains below a certain
threshold for several datapoints. Starting at the center of the cluster, the actual start- and end points of a
cluster are found at the first points where one of these two criteria is met.
Note: During the peak detection, peaks that are too close to each other are merged (based on the M inimum
distance parameter). To ensure detection of overlapping peaks, make sure that the value of the M inimum
distance is less than the distance between two peaks. Lower the M inimum distance if necessary, especially
if your peaks are very sharp and closely resolved.
Note: During Smear and gDNA Analysis alignment marker peaks are detected as normal peaks and smear
peaks are detected as smear peaks. Each smear peak has an assigned Area of Interest. The borders of the
Area of Interest are initially set to the borders of the detected peak.

Appendix E
Liability clause
QIAGEN shall be released from all obligations under its warranty in the event repairs or modifications are
made by persons other than its own personnel, except in cases where the Company has given its written
consent to perform such repairs or modifications.
All materials replaced under this warranty will be warranted only for the duration of the original warranty
period, and in no case beyond the original expiration date of original warranty unless authorized in writing
by an officer of the Company. Read-out devices, interfacing devices and associated software will be
warranted only for the period offered by the original manufacturer of these products. Representations and
warranties made by any person, including representatives of QIAGEN, which are inconsistent or in conflict
with the conditions in this warranty shall not be binding upon the Company unless produced in writing and
approved by an officer of QIAGEN.

Appendix F
Informations de sécurité
Avant d’utiliser le QIAxcel Advanced, il est impératif de lire attentivement ce manuel et de porter une
attention particulière aux informations de sécurité. Afin de garantir un fonctionnement de l’appareil en toute
sécurité et de maintenir l’appareil en bon état de marche, il est impératif de suivre les instructions et les
informations de sécurité fournies dans le présent manuel d’utilisation.
Les types d’informations de sécurité suivants sont fournis tout au long du manuel.
WARNING La formule « WARNING » (DANGER) est utilisée pour avertir des situations pouvant
occasionner des dommages corporels à l’utilisateur ou à d’autres personnes.
Les détails sur ces circonstances sont donnés dans un encadré semblable à celui-ci.
CAUTION Le terme « CAUTION » (AVERTISSEMENT) est utilisé pour signaler les situations
susceptibles de provoquer des détériorations de l’instrument ou d’autre matériel.
Les détails sur ces circonstances figurent dans un encadré semblable à celui-ci.
Les conseils donnés dans ce manuel ont pour but de venir compléter les exigences de sécurité habituelles en
vigueur dans le pays de l’utilisateur et non de s’y substituer.
Utilisation appropriée
WARNING/
Risque de dommages corporels et matériels [W1]
CAUTION
L’utilisation non convenable du QIAxcel Advanced peut causer des blessures ou des
détériorations de l’instrument.
Le QIAxcel Advanced ne doit être utilisé que par du personnel qualifié qui a été formé
de façon appropriée.
Seul un ingénieur du service après-vente QIAGEN est autorisé à effectuer des travaux
d’entretien sur le QIAxcel Advanced.
Procéder à la maintenance comme décrit dans la section

« Maintenance Procedures » (Procédures de Maintenance). QIAGEN facture les réparations rendues
nécessaires suite à une maintenance inappropriée.

WARNING/
CAUTION
Le QIAxcel Advanced est trop lourd pour être soulevé par une personne. Pour éviter
des dommages corporels ou matériels, ne pas soulever l’instrument tout seul.
WARNING/
CAUTION
Ne pas essayer de bouger le QIAxcel Advanced pendant son fonctionnement.
CAUTION
Détérioration de l’appareil [C1]
Eviter de renverser de l’eau ou des substances chimiques sur le QIAxcel Advanced.

Tout dommage causé par de l’eau ou des produits chimiques mettra fin à la garantie.
En cas d’urgence, éteignez le QIAxcel Advanced à l’aide de l’interrupteur d’alimentation situé à l’arrière de
l’appareil et débranchez le câble d’alimentation de la prise de courant.
CAUTION
Si « Pressure 1» indique « Low » (bas) augmentez la pression du système avant

d'utiliser la commande « unlatch » (décrochage). En enlevant la cartouche et la
décrochant à pression réduite, l'appareil peut se déteriorer.
CAUTION
Déterioration de l’instrument [C3]
Ne pas utiliser d'eau de Javel, de solvants ou de réactifs contenant des acides,

alcalins ou abrasifs pour nettoyer le QIAxcel Advanced
Sécurité électrique
Avant l’entretien, débranchez le cordon d’alimentation de la prise de courant.
WARNING
Risque d’électrocution [W4]
Toute interruption du conducteur de protection à l’intérieur ou à l’extérieur de
l’instrument, ou

déconnexion du raccord du conducteur de protection (terre) peut rendre l’instrument
dangereux. Il est interdit d’interrompre volontairement ce conducteur.
Présence de tensions mortelles dans l’instrument
Lorsque l’instrument est relié au secteur, les raccords peuvent être sous tension, et des
parties sous tension peuvent être découvertes en ouvrant des capots ou en retirant des
pièces (à l’exception de celles auxquelles il est possible d’accéder manuellement).
Afin que le QIAxcel Advanced fonctionne de manière satisfaisante et en toute sécurité, conformez-vous aux
conseils suivants :
Le câble d’alimentation doit être relié à une prise d’alimentation disposant d’un conducteur de protection
(terre/masse).
Ne réglez ni ne remplacez aucune pièce interne à l’appareil.
Ne faites pas fonctionner l’appareil si des capots ou des pièces ont été retirés.
Si du liquide a été renversé à l’intérieur de l’appareil, éteignez-le et débranchez-le de la prise

d’alimentation, puis contactez le support technique de QIAGEN.
Si vous remplacez les fusibles, ne les remplacer qu’avec des fusibles du même type et équivalent en
voltage, comme indiqué sur le fusible.
Si l’appareil devient dangereux sur le plan électrique, empêchez d’autres membres du personnel de l’utiliser
et contacter le support technique de QIAGEN ; l’appareil peut être dangereux électriquement si :
celui-ci ou le câble d’alimentation semble endommagé ;
il a été stocké dans des conditions défavorables pendant une longue période ;
il a subi des chocs sévères durant le transport.
Environnement
Conditions de fonctionnement
WARNING
Atmosphère explosive [W5]
Le QIAxcel Advanced n’est pas conçu pour fonctionner dans une atmosphère
explosive.

WARNING
Risque d’explosion [W6]
Le QIAxcel Advanced a été conçu pour l’utilisation des réactifs et substances fournis
par les kits QIAxcel. L’utilisation des réactifs et substances autres que celles indiquées
peut entrainer un risque d’incendie ou d’explosion.
CAUTION
La lumière directe du soleil peut décolorer des parties de l’instrument et endommager

des parties en plastique. Placer le QIAxcel Advanced en dehors de la lumière directe
du soleil.
CAUTION
Déterioration de la cartouche [C5]
Lors de l’utilisation de la cartouche de Gel, ne pas la laisser plus de 15 minutes hors

de la position d’arrêt (« Wash park ») du compartiment des liquides. Au-delà de cette
période, les extrémités des capillaires risquent de se dessécher et d’influencer le bon
fonctionnement de la cartouche. Des capillaires desséchés mettront fin à la garantie.
Les extrémités des capillaires sont en verre et sont très fragiles.
Faites attention à ne pas heurter une surface dure. Cela pourrait les casser et influencer
le bon fonctionnement de la cartouche. Des extrémités de capillaires cassées mettront
fin à la garantie.
CAUTION
Déterioration de la cartouche [C6]
Si vous utilisez moins de 12 échantillons, les puits vides doivent être remplis de tampon
de dilution QX ADN ou ARN. Si les puits restent vides, les capillaires non-utilisés
peuvent s’abîmer.

Produits chimiques
WARNING
Substances chimiques dangereuses [W7]
Certaines substances chimiques utilisées avec cet instrument peuvent être dangereuses
ou peuvent le devenir après que le protocole ait été effectué.
Toujours porter des lunettes de protection, deux paires de gants et une blouse de
laboratoire.
La personne responsable (par exemple le Chef du laboratoire) doit prendre les

précautions nécessaires pour assurer la sécurité de l’environnement du poste de travail
et pour être sûr que les opérateurs de l’instrument sont suffisamment formés et non
exposés à des quantités dangereuses de substances toxiques (chimiques ou
biologiques) comme défini dans « Material Safety Data Sheets (MSDS) » ou des
documents « OSHA, ACGIH ou COSHH ».
L’évacuation des vapeurs et déchets doit être conforme à tous règlements et

dispositions légales - au plan national, départemental et local - concernant la santé et
la sécurité.
WARNING
Risque de feu [W8]
Lors du nettoyage du QIAxcel Advanced avec un désinfectant à base d’alcool, laisser

la porte du QIAxcel Advanced ouverte pour permettre aux vapeurs inflammables de
s’évaporer.
Mise au rebut des déchets

Les consommables et flacons utilisés peuvent contenir des agents chimiques dangereux. Ces déchets doivent
être convenablement collectés et mis au rebut conformément aux règles de sécurité locales.
Pour savoir comment mettre au rebut le QIAxcel Advanced, voir l'annexe A (« Appendix A »).
Dangers mécaniques
La porte à cartouche et la porte à échantillons du QIAxcel Advanced doivent être fermées à tout moment
pendant l’usage de l’instrument.

WARNING
Eléments mobiles [W9]
Afin d’éviter tout contact avec les éléments mobiles du QIAxcel Advanced lorsqu’il est
en marche, toujours fermer les portes de l’instrument pour les échantillons et pour la
cartouche.
Si les détecteurs ne fonctionnent pas correctement, contacter le Support Technique

QIAGEN.
Symboles sur le QIAxcel Advanced
Symbole Emplacement Description
Plaquette à l'arrière de Marquage CE

l'appareil
Plaquette à l'arrière de Marquage CSA pour le Canada

l'appareil et les Etats-Unis
Plaquette à l'arrière de Fabricant légal

l'appareil
Plaquette à l'arrière de Symbole DEEE

l'appareil
Plaquette à l'arrière de Marquage FCC de la

l'appareil commission fédérale des
communications des Etats Unis
Plaque à l’arrière de Marque RCM pour l’Australie et

l’appareil la Nouvelle-Zélande

Appendix G
Sicherheitshinweise
Vor der Inbetriebnahme des QIAxcel Advanced sollten Sie dieses Handbuch sorgfältig durchlesen –
beachten Sie insbesondere die Sicherheitshinweise. Die Gebrauchsanweisungen und Sicherheitshinweise im
Handbuch müssen befolgt werden, um einen sicheren Betrieb des Geräts zu gewährleisten und das Gerät in
einem sicheren Zustand zu erhalten.
In diesem Handbuch werden die folgenden beiden Kategorien von Sicherheitshinweisen verwendet:
WARNING „WARNING“ (WARNUNG) weist auf Situationen und Umstände hin, die zu einer
Verletzung des Benutzers oder anderer Personen führen können.
Nähere Angaben zu der Art der Gefährdung und der Vermeidung solcher Situationen
werden in einem Textfeld wie diesem neben der Warnung gemacht.
CAUTION Der Begriff „CAUTION“ (ACHTUNG) weist Sie auf Situationen hin, in denen das Gerät
oder andere Geräte beschädigt werden könnten.
Nähere Einzelheiten über diese Situationen werden in einem Textfeld wie diesem
beschrieben.
Die in diesem Handbuch enthaltenen Hinweise stellen eine Ergänzung und keinen Ersatz der üblichen
Sicherheitsanforderungen dar, die im jeweiligen Land gelten.
Sachgemäße Handhabung
WARNING/
Verletzungsgefahr und Beschädigung des Gerätes [W1]
CAUTION
Die unsachgemäße Bedienung des QIAxcel Advanced kann zu einer Verletzung des
Benutzers oder zur Beschädigung des Gerätes führen.
Die Bedienung des QIAxcel Advanced darf nur durch qualifiziertes Personal, das
entsprechend geschult wurde, erfolgen.
Die Wartung des QIAxcel Advanced darf nur durch Mitarbeiter des QIAGEN
Kundendienstes durchgeführt werden.
Führen Sie alle Wartungsarbeiten gemäß den Anweisungen in Abschnitt „Maintenance Procedures
“ (Wartungsarbeiten) dieses Handbuchs durch. QIAGEN stellt alle Reparaturen in Rechnung, die
nachweislich auf eine inkorrekte Wartung zurückzuführen sind.

WARNING/
CAUTION
Der QIAxcel Advanced ist zu schwer um von einer Person gehoben zu werden. Um
Verletzungen des Benutzers oder eine Beschädigung des Gerätes zu vermeiden ist
davon abzusehen, das Gerät alleine zu heben.
WARNING/
CAUTION
Den QIAxcel Advanced während eines Laufes nicht bewegen.
CAUTION
Beschädigung des Gerätes [C1]
Vermeiden Sie es, Wasser oder Chemikalien auf dem QIAxcel Advanced zu
verschütten. Durch verschüttetes Wasser oder verschüttete Chemikalien verursachte
Geräteschäden sind nicht durch die Garantie abgedeckt.
Schalten Sie im Notfall den QIAxcel Advanced aus (der Netzschalter befindet sich auf der Geräterückseite),
und ziehen Sie den Netzstecker aus der Steckdose.
CAUTION
Wenn die Statusanzeige Pressure 1, Low (niedrig) anzeigt, erhöhen Sie den
Systemdruck bevor Sie unlatch (Entriegelung) auslösen. Das Herausnehmen der
Kartusche und die Entriegelung bei niedrigem Druck kann das Gerät beschädigen.
CAUTION
Verwenden Sie keine Bleichmittel, Lösungsmittel oder säure-, laugen- oder scheuermittel-
haltige Reagenzien zur Reinigung des QIAxcel Advanced.
Schutz vor Stromschlag

Ziehen Sie die Netzanschlusskabel aus den Steckdosen, bevor Sie Wartungsarbeiten am Gerät vornehmen.

WARNING
Gefährdung durch Elektrizität [W4]
Jede Unterbrechung des Schutzleiters (Erdungs- bzw. Masseleiter) im Gerät oder

außerhalb des Geräts und jede Abtrennung des Schutzleiters am Anschluss der
Netzleitung erhöht die Gefahr eines Stromschlags.
Eine absichtliche Unterbrechung der Schutzleiterverbindung ist verboten.
Gefährliche Spannung im Gerät
Auch in ausgeschaltetem Zustand kann an einigen Stellen im Gerät Netzspannung

anliegen, wenn das Gerät am Stromnetz angeschlossen ist. Das Öffnen oder Entfernen
von Gehäuseteilen kann diese stromführenden Teile freilegen.
Um einen zufriedenstellenden und sicheren Betrieb des QIAxcel Advanced zu gewährleisten, befolgen Sie
bitte die nachstehenden Hinweise:
Die Geräte-Netzkabel müssen an Wechselstrom-Steckdosen mit Schutzleiter (Erdungs-/Masseleiter)

angeschlossen werden.
Nehmen Sie im Geräteinneren keine Einstellungen an Teilen vor und wechseln Sie keine Teile aus.
Nehmen Sie das Gerät nicht in Betrieb, wenn Abdeckungen oder Teile entfernt worden sind.
Falls Flüssigkeit auf dem Gerät verschüttet wird und in das Gerät läuft, dann schalten Sie es sofort aus,
trennen Sie es von der Netzspannung (Stecker ziehen!) und setzen Sie sich mit dem Technischen Service
von QIAGEN in Verbindung.
Beim Austausch der Netzsicherung ersetzen Sie diese nur durch eine desselben Typs und der Stromstärke,
die auf dem Etikett/Typenschild angegeben ist.
Falls die elektrische Sicherheit bei der Bedienung des Geräts nicht mehr gewährleistet werden kann, muss
das Gerät gegen unbefugte oder unabsichtliche Benutzung gesichert werden. Kontaktieren Sie
anschließend den Technischen Service von QIAGEN. Die elektrische Sicherheit des Geräts ist nicht mehr
gegeben, wenn:
das Gerät oder das Netzkabel beschädigt erscheint;
das Gerät längere Zeit unter ungünstigen Bedingungen gelagert wurde;
das Gerät unsachgemäß transportiert worden ist.

Umgebungsbedingungen
Betriebsbedingungen
WARNING
Explosionsfähige Atmosphären [W5]
Der QIAxcel Advanced darf nicht in explosionsfähigen Atmosphären betrieben werden.
WARNING
Explosionsgefahr [W6]
Der QIAxcel Advanced ist ausschließlich mit Reagenzien und Substanzen aus den
QIAxcel Kits zu benutzen. Die Benutzung von anderen Reagenzien oder Substanzen
kann Feuer oder eine Explosion auslösen.
CAUTION
Direktes Sonnenlicht kann Teile des Gerätes bleichen und Plastikteile schädigen. Der
QIAxcel Advanced darf nicht ins direkte Sonnenlicht gestellt werden.
CAUTION
Beschädigung der Kartusche [C5]
Die Gel Cartridge sollte nicht länger als 15 Minuten außerhalb der Parkposition (Wash
park) des Solution Trays aufbewahrt werden. Wird dieser Zeitrahmen überschritten,
trocknen die Spitzen der Kapillaren aus. Ausgetrocknete Kapillarspitzen sind nicht
durch die Garantie abgedeckt.
Die Kapillarspitzen sind aus Glas und sehr zerbrechlich. Achten Sie darauf, die Spitzen
nicht auf harte Oberflächen aufzusetzen. Dadurch können die Kapillaren brechen und
damit die Funktion der Cartridge beeinträchtigen. Zerbrochene Kapillarspitzen sind
nicht durch die Garantie abgedeckt.

CAUTION
Beschädigung der Kartusche [C6]
Wenn weniger als 12 Proben verarbeitet werden, füllen Sie die leeren Probenbehältern
mit QX DNA Verdünnungspuffer oder QX RNA Verdünnungspuffer. Andernfalls können
Schäden an den kapillaren Kanälen entstehen.
Chemikalien
WARNING
Gefährliche Chemikalien [W7]
Einige der in Verbindung mit diesem Gerät verwendeten Chemikalien sind

gesundheitsgefährdend oder können nach Beendigung eines Protokoll-Laufs
gesundheitsgefährdend werden. Es sollten immer Sicherheitsbrille, zwei Paar
Handschuhe und ein Laborkittel getragen werden. Der Betreiber der Anlage ist für die
Gewährleistung der Sicherheit am Arbeitsplatz verantwortlich. Er hat sicherzustellen,
dass die Bediener des Gerätes ausreichend geschult sind und nicht
gesundheitsgefährdenden Konzentrationen toxischer Substanzen (chemischer oder
biologischer) ausgesetzt sind, so wie dies in den Sicherheitsdatenblättern oder in
anderen zu beachtenden Dokumenten festgelegt ist.
Bei der Behandlung von Abluft und bei der Abfallbeseitigung sind alle gesetzlichen
Regelungen zur Gesundheit und Sicherheit auf nationaler, regionaler und lokaler Ebene
zu berücksichtigen.
WARNING
Feuergefahr [W8]
Beim Reinigen des QIAxcel Advanced mit einem auf Alkohol basierenden
Desinfektionsmittel muss die Tür des QIAxcel Advanced offen gelassen werden, damit
die brennbaren Dämpfe entweichen können.
Entsorgen von Abfällen

Benutzte Verbrauchsartikel und Behälter könnten gefährliche Chemikalien enthalten. Derartige Abfälle
müssen gesammelt und gemäß den geltenden kommunalen Sicherheitsbestimmungen entsorgt werden.
Weitere Informationen zur Entsorgung vom QIAxcel Advanced finden Sie im Anhang A
(„Appendix A”).

Gefahren durch mechanische Teile
Die Klappen für den Proben- und Cartridge-Einsatz des QIAxcel Advanced müssen während des Betriebs
geschlossen sein.
WARNING
Bewegliche Geräteteile [W9]
Um jeglichen Kontakt mit beweglichen Geräteteilen während des Laufes zu vermeiden,

darf der QIAxcel Advanced nur benutzt werden, wenn die Klappen für den Proben- und
Cartridge-Einsatz geschlossen sind. Sollten die Sensoren nicht ordnungsgemäß
funktionieren, kontaktieren Sie bitten den Technischen Service von QIAGEN.
Symbole auf dem QIAxcel Advanced
Symbol Fundstelle Beschreibung
Plakette auf der Rückseite des CE-Zeichen

Gerätes
Plakette auf der Rückseite des CSA-Zeichen für Kanada und die
Gerätes USA
Plakette auf der Rückseite des Hersteller i.S.d. Gesetzes

Gerätes
Plakette auf der Rückseite des WEEE-Zeichen

Gerätes
Plakette auf der Rückseite des FCC Markierung der Federal

Gerätes Communications Kommission der
USA
Plakette auf der Rückseite des RCM-Zeichen für Australien und

Gerätes Neuseeland

Appendix H
License terms
DotNetZip License
QIAxcel ScreenGel uses the DotNetZip library version 1.9.1.8, which is licensed under the Microsoft Public
License (Ms-PL).
Microsoft Public License (Ms-PL)
This license governs use of the accompanying software, the DotNetZip library
("the software"). If you use the software, you accept this license. If you do
not accept the license, do not use the software.
1. Definitions
The terms "reproduce," "reproduction," "derivative works," and "distribution"

have the same meaning here as under U.S. copyright law.
A "contribution" is the original software, or any additions or changes to the

software.
A "contributor" is any person that distributes its contribution under this

license.
"Licensed patents" are a contributor's patent claims that read directly on its
contribution.
2. Grant of Rights
(A) Copyright Grant- Subject to the terms of this license, including the license
conditions and limitations in section 3, each contributor grants you a non-
exclusive, worldwide, royalty-free copyright license to reproduce its
contribution, prepare derivative works of its contribution, and distribute its
contribution or any derivative works that you create.
(B) Patent Grant- Subject to the terms of this license, including the license
exclusive, worldwide, royalty-free license under its licensed patents to make,
have made, use, sell, offer for sale, import, and/or otherwise dispose of its
contribution in the software or derivative works of the contribution in the
software.
3. Conditions and Limitations
(A) No Trademark License- This license does not grant you rights to use any
contributors' name, logo, or trademarks.

(B) If you bring a patent claim against any contributor over patents that you
claim are infringed by the software, your patent license from such contributor
to the software ends automatically.
(C) If you distribute any portion of the software, you must retain all
copyright, patent, trademark, and attribution notices that are present in the
software.
(D) If you distribute any portion of the software in source code form, you may
do so only under this license by including a complete copy of this license with
your distribution. If you distribute any portion of the software in compiled or
object code form, you may only do so under a license that complies with this
license.
(E) The software is licensed "as-is." You bear the risk of using it. The
contributors give no express warranties, guarantees or conditions. You may have
additional consumer rights under your local laws which this license cannot
change. To the extent permitted under your local laws, the contributors exclude
the implied warranties of merchantability, fitness for a particular purpose and
non-infringement.
The following licenses govern use of the accompanying software, the

DotNetZip library ("the software"). If you use the software, you accept these
licenses. If you do not accept the license, do not use the software.
The managed ZLIB code included in Ionic.Zlib.dll and Ionic.Zip.dll is modified

code, based on jzlib.
The following notice applies to jzlib:

----------------------------------------------------------------------
Copyright (c) 2000,2001,2002,2003 ymnk, JCraft,Inc. All rights reserved.
Redistribution and use in source and binary forms, with or without

modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,

this list of conditions and the following disclaimer in the documentation and/or
other materials provided with the distribution.
3. The names of the authors may not be used to endorse or promote products
derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL JCRAFT, INC.
OR ANY CONTRIBUTORS TO THIS SOFTWARE BE LIABLE FOR ANY DIRECT, INDIRECT,
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
----------------------------------------------------------------------
jzlib is based on zlib-1.1.3.
The following notice applies to zlib:
----------------------------------------------------------------------
Copyright (C) 1995-2004 Jean-loup Gailly and Mark Adler
The ZLIB software is provided 'as-is', without any express or implied

warranty. In no event will the authors be held liable for any damages arising
from the use of this software.
Permission is granted to anyone to use this software for any purpose,

including commercial applications, and to alter it and redistribute it freely,
subject to the following restrictions:
1. The origin of this software must not be misrepresented; you must not claim
that you wrote the original software. If you use this software in a product, an
acknowledgment in the product documentation would be appreciated but is not
required.
2. Altered source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
3. This notice may not be removed or altered from any source distribution.
Jean-loup Gailly [email protected]

Mark Adler [email protected]
----------------------------------------------------------------------
The managed BZIP2 code included in Ionic.BZip2.dll and Ionic.Zip.dll is modified

code, based on the bzip2 code in the Apache commons compress library.
The original BZip2 was created by Julian Seward, and is licensed under
the BSD license.

The following license applies to the Apache code:
----------------------------------------------------------------------
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the
* specific language governing permissions and limitations
* under the License.
*/
LibSVM License
QIAxcel ScreenGel uses the LibSVM which is licensed under the following copyright:
Copyright (c) 2000-2012 Chih-Chung Chang and Chih-Jen Lin

All rights reserved.
Redistribution and use in source and binary forms, with or without

modification, are permitted provided that the following conditions are
met:
1. Redistributions of source code must retain the above copyright

notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright

notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
3. Neither name of copyright holders nor the names of its contributors

may be used to endorse or promote products derived from this software
without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS

``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR

CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
LinqToExcel License
QIAxcel ScreenGel uses the LinqToExcel library, version 1.7.1, which is licensed under the MIT License
(MIT) copyright:
Copyright (c) 2008-2013 Paul Yoder
Permission is hereby granted, free of charge, to any person obtaining a copy of

this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
the Software, and to permit persons to whom the Software is furnished to do so,
subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
iTextSharp License and Remotion License

QIAxcel ScreenGel uses the "iTextSharp" library, version 4.1.7.0, and the Remotion library, version
1.13.52.2, which are licensed under the GNU LESSER GENERAL PUBLIC LICENSE, version 3.
GNU LESSER GENERAL PUBLIC LICENSE

Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>

Everyone is permitted to copy and distribute verbatim copies of this license
document, but changing it is not allowed.
This version of the GNU Lesser General Public License incorporates the terms and
conditions of version 3 of the GNU General Public License, supplemented by the
additional permissions listed below.

0. Additional Definitions.
As used herein, "this License" refers to version 3 of the GNU Lesser General
Public License, and the "GNU GPL" refers to version 3 of the GNU General Public
License.
"The Library" refers to a covered work governed by this License, other than an
Application or a Combined Work as defined below.
An "Application" is any work that makes use of an interface provided by the

Library, but which is not otherwise based on the Library. Defining a subclass of
a class defined by the Library is deemed a mode of using an interface provided
by the Library.
A "Combined Work" is a work produced by combining or linking an Application with

the Library. The particular version of the Library with which the Combined Work
was made is also called the "Linked Version".
The "Minimal Corresponding Source" for a Combined Work means the Corresponding
Source for the Combined Work, excluding any source code for portions of the
Combined Work that, considered in isolation, are based on the Application, and
not on the Linked Version.
The "Corresponding Application Code" for a Combined Work means the object code
and/or source code for the Application, including any data and utility programs
needed for reproducing the Combined Work from the Application, but excluding the
System Libraries of the Combined Work.
1. Exception to Section 3 of the GNU GPL.
You may convey a covered work under sections 3 and 4 of this License without
being bound by section 3 of the GNU GPL.
2. Conveying Modified Versions.
If you modify a copy of the Library, and, in your modifications, a facility

refers to a function or data to be supplied by a Application that uses the
facility (other than as an argument passed when the facility is invoked), then
you may convey a copy of the modified version:
a) under this License, provided that you make a good faith effort to ensure
that, in the event an Application does not supply the function or data, the
facility still operates, and performs whatever part of its purpose remains
meaningful, or
b) under the GNU GPL, with none of the additional permissions of this License
applicable to that copy.

3. Object Code Incorporating Material from Library Header Files.
The object code form of an Application may incorporate material from a header
file that is part of the Library. You may convey such object code under terms
of your choice, provided that, if the incorporated material is not limited to
numerical parameters, data structure layouts and accessors, or small macros,
inline functions and templates(ten or fewer lines in length), you do both of the
following:
a) Give prominent notice with each copy of the object code that the Library is
used in it and that the Library and its use are covered by this License.
b) Accompany the object code with a copy of the GNU GPL and this license
document.
4. Combined Works.
You may convey a Combined Work under terms of your choice that, taken together,
effectively do not restrict modification of the portions of the Library
contained in the Combined Work and reverse engineering for debugging such
modifications, if you also do each of the following:
a) Give prominent notice with each copy of the Combined Work that the Library is
used in it and that the Library and its use are covered by this License.
b) Accompany the Combined Work with a copy of the GNU GPL and this license
document.
c) For a Combined Work that displays copyright notices during execution, include
the copyright notice for the Library among these notices, as well as a reference
directing the user to the copies of the GNU GPL and this license document.
d) Do one of the following:
0) Convey the Minimal Corresponding Source under the terms of this License, and
the Corresponding Application Code in a form suitable for, and under terms that
permit, the user to recombine or relink the Application with a modified version
of the Linked Version to produce a modified Combined Work, in the manner
specified by section 6 of the GNU GPL for conveying Corresponding Source.
1) Use a suitable shared library mechanism for linking with the Library. A
suitable mechanism is one that (a) uses at run time a copy of the Library
already present on the user's computer system, and (b) will operate properly
with a modified version of the Library that is interface-compatible with the
Linked Version.

e) Provide Installation Information, but only if you would otherwise be required
to provide such information under section 6 of the GNU GPL, and only to the
extent that such information is necessary to install and execute a modified
version of the Combined Work produced by recombining or relinking the
Application with a modified version of the Linked Version. (If you use option
4d0, the Installation Information must accompany the Minimal Corresponding
Source and Corresponding Application Code. If you use option 4d1, you must
provide the Installation Information in the manner specified by section 6 of the
GNU GPL for conveying Corresponding Source.)
5. Combined Libraries.
You may place library facilities that are a work based on the Library side by
side in a single library together with other library facilities that are not
Applications and are not covered by this License, and convey such a combined
library under terms of your choice, if you do both of the following:
a) Accompany the combined library with a copy of the same work based on the
Library, uncombined with any other library facilities, conveyed under the terms
of this License.
b) Give prominent notice with the combined library that part of it is a work
based on the Library, and explaining where to find the accompanying uncombined
form of the same work.
6. Revised Versions of the GNU Lesser General Public License.
The Free Software Foundation may publish revised and/or new versions of the GNU
Lesser General Public License from time to time. Such new versions will be
similar in spirit to the present version, but may differ in detail to address
new problems or concerns.
Each version is given a distinguishing version number. If the Library as you

received it specifies that a certain numbered version of the GNU Lesser General
Public License "or any later version" applies to it, you have the option of
following the terms and conditions either of that published version or of any
later version published by the Free Software Foundation. If the Library as you
received it does not specify a version number of the GNU Lesser General Public
License, you may choose any version of the GNU Lesser General Public License
ever published by the Free Software Foundation.
If the Library as you received it specifies that a proxy can decide

whether future versions of the GNU Lesser General Public License shall apply,
that proxy's public statement of acceptance of any version is permanent
authorization for you to choose that version for the Library.

Log4Net License and Stateless License
QIAxcel ScreenGel uses the Log4Net library, version 1.2.11.0, and the Stateless library, version 2.2.1.1,
which are licensed under the Apache License.
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
1. Definitions.
"License" shall mean the terms and conditions for use, reproduction, and
distribution as defined by Sections 1 through 9 of this document.
"Licensor" shall mean the copyright owner or entity authorized by the copyright
owner that is granting the License.
"Legal Entity" shall mean the union of the acting entity and all other entities
that control, are controlled by, or are under common control with that entity.
For the purposes of this definition, "control" means (i) the power, direct or
indirect, to cause the direction or management of such entity, whether by
contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the
outstanding shares, or (iii) beneficial ownership of such entity.
"You" (or "Your") shall mean an individual or Legal Entity exercising

permissions granted by this License.
"Source" form shall mean the preferred form for making modifications, including
but not limited to software source code, documentation source, and configuration
files.
"Object" form shall mean any form resulting from mechanical transformation or
translation of a Source form, including but not limited to compiled object code,
generated documentation, and conversions to other media types.
"Work" shall mean the work of authorship, whether in Source or Object form, made
available under the License, as indicated by a copyright notice that is included
in or attached to the work(an example is provided in the Appendix below).
"Derivative Works" shall mean any work, whether in Source or Object form, that
is based on (or derived from) the Work and for which the editorial revisions,
annotations, elaborations, or other modifications represent, as a whole, an
original work of authorship. For the purposes of this License, Derivative Works
shall not include works that remain separable from, or merely link (or bind by
name) to the interfaces of, the Work and Derivative Works thereof.

"Contribution" shall mean any work of authorship, including the original version
of the Work and any modifications or additions to that Work or Derivative Works
thereof, that is intentionally submitted to Licensor for inclusion in the Work
by the copyright owner or by an individual or Legal Entity authorized to submit
on behalf of the copyright owner. For the purposes of this definition,
"submitted" means any form of electronic, verbal, or written communication sent
to the Licensor or its representatives, including but not limited to
communication on electronic mailing lists, source code control systems,and issue
tracking systems that are managed by, or on behalf of, the Licensor for the
purpose of discussing and improving the Work, but excluding communication that
is conspicuously marked or otherwise designated in writing by the copyright
owner as "Not a Contribution."
"Contributor" shall mean Licensor and any individual or Legal Entity on behalf
of whom a Contribution has been received by Licensor and subsequently
incorporated within the Work.
2. Grant of Copyright License. Subject to the terms and conditions of this

License, each Contributor hereby grants to You a perpetual, worldwide, non-
exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce,
prepare Derivative Works of, publicly display, publicly perform, sublicense, and
distribute the Work and such Derivative Works in Source or Object form.
3. Grant of Patent License. Subject to the terms and conditions of this License,
each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-
charge, royalty-free, irrevocable(except as stated in this section) patent
license to make, have made, use, offer to sell,sell, import, and otherwise
transfer the Work,where such license applies only to those patent claims
licensable by such Contributor that are necessarily infringed by their
Contribution(s) alone or by combination of their Contribution(s) with the Work
to which such Contribution(s) was submitted. If You institute patent litigation
against any entity (including a cross-claim or counterclaim in a lawsuit)
alleging that the Work or a Contribution incorporated within the Work
constitutes direct or contributory patent infringement, then any patent licenses
granted to You under this License for that Work shall terminate as of the date
such litigation is filed.
4. Redistribution. You may reproduce and distribute copies of the Work or

Derivative Works thereof in any medium, with or without modifications, and in
Source or Object form, provided that You meet the following conditions:
(a) You must give any other recipients of the Work or Derivative Works a copy of
this License; and
(b) You must cause any modified files to carry prominent notices stating that
You changed the files; and
(c) You must retain, in the Source form of any Derivative Works that You
distribute, all copyright, patent, trademark, and attribution notices from the
Source form of the Work, excluding those notices that do not pertain to any part
of the Derivative Works; and

(d) If the Work includes a "NOTICE" text file as part of its distribution, then
any Derivative Works that You distribute must include a readable copy of the
attribution notices contained within such NOTICE file, excluding those notices
that do not pertain to any part of the Derivative Works, in at least one of the
following places: within a NOTICE text file distributed as part of the
Derivative Works; within the Source form or documentation, if provided along
with the Derivative Works; or, within a display generated by the Derivative
Works, if and wherever such third-party notices normally appear. The contents of
the NOTICE file are for informational purposes only and do not modify the
License. You may add Your own attribution notices within Derivative Works that
You distribute, alongside or as an addendum to the NOTICE text from the Work,
provided that such additional attribution notices cannot be construed as
modifying the License.
You may add Your own copyright statement to Your modifications and may provide
additional or different license terms and conditions for use, reproduction, or
distribution of Your modifications, or for any such Derivative Works as a whole,
provided Your use, reproduction, and distribution of the Work otherwise complies
with the conditions stated in this License.
5. Submission of Contributions. Unless You explicitly state otherwise, any

Contribution intentionally submitted for inclusion in the Work by You to the
Licensor shall be under the terms and conditions of this License, without any
additional terms or conditions. Notwithstanding the above, nothing herein shall
supersede or modify the terms of any separate license agreement you may have
executed with Licensor regarding such Contributions.
6. Trademarks. This License does not grant permission to use the trade names,
trademarks, service marks, or product names of the Licensor, except as required
for reasonable and customary use in describing the origin of the Work and
reproducing the content of the NOTICE file.
7. Disclaimer of Warranty. Unless required by applicable law or agreed to in

writing, Licensor provides the Work (and each Contributor provides its
Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
KIND, either express or implied, including, without limitation, any warranties
or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
PARTICULAR PURPOSE. You are solely responsible for determining the
appropriateness of using or redistributing the Work and assume any risks
associated with Your exercise of permissions under this License.
8. Limitation of Liability. In no event and under no legal theory, whether in

tort (including negligence), contract, or otherwise, unless required by
applicable law (such as deliberate and grossly negligent acts) or agreed to in
writing, shall any Contributor be liable to You for damages, including any
direct, indirect, special, incidental, or consequential damages of any character
arising as a result of this License or out of the use or inability to use the
Work (including but not limited to damages for loss of goodwill, work stoppage,
computer failure or malfunction, or any and all other commercial damages or
losses), even if such Contributor has been advised of the possibility of such
damages.

9. Accepting Warranty or Additional Liability. While redistributing the Work or
Derivative Works thereof, You may choose to offer, and charge a fee for,
acceptance of support, warranty, indemnity, or other liability obligations and/
or rights consistent with this License. However, in accepting such obligations,
You may act only on Your own behalf and on Your sole responsibility, not on
behalf of any other Contributor, and only if You agree to indemnify, defend, and
hold each Contributor harmless for any liability incurred by, or claims asserted
against, such Contributor by reason of your accepting any such warranty or
additional liability.
END OF TERMS AND CONDITIONS
APPENDIX: How to apply the Apache License to your work.
To apply the Apache License to your work, attach the following boilerplate
notice, with the fields enclosed by brackets "[]" replaced with your own
identifying information. (Don't include the brackets!) The text should be
enclosed in the appropriate comment syntax for the file format. We also
recommend that a file or class name and description of purpose be included on
the same "printed page" as the copyright notice for easier identification within
third-party archives.
Copyright [yyyy] [name of copyright owner]
Licensed under the Apache License, Version 2.0 (the "License"); you may not use
this file except in compliance with the License. You may obtain a copy of the
License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed

under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations
under the License.
Windows Installer XML (WiX) License

The installer of the QIAxcel ScreenGel Software uses the Windows Installer XML, version 3.7 which is
licensed under the Microsoft Reciprocal License (MS-RL).
Microsoft Reciprocal License (Ms-RL)
This license governs use of the accompanying software. If you use the software,
you accept this license. If you do not accept the license, do not use the
software.

1. Definitions
The terms "reproduce," "reproduction," "derivative works," and "distribution"

have the same meaning here as under U.S. copyright law.
A "contribution" is the original software, or any additions or changes to the

software.
A "contributor" is any person that distributes its contribution under this

license.
"Licensed patents" are a contributor's patent claims that read directly on its
contribution.
2. Grant of Rights
(A) Copyright Grant- Subject to the terms of this license, including the license
exclusive, worldwide, royalty-free copyright license to reproduce its
contribution, prepare derivative works of its contribution, and distribute its
contribution or any derivative works that you create.
(B) Patent Grant- Subject to the terms of this license, including the license
exclusive, worldwide, royalty-free license under its licensed patents to make,
have made, use, sell, offer for sale, import, and/or otherwise dispose of its
contribution in the software or derivative works of the contribution in the
software.
3. Conditions and Limitations
(A) Reciprocal Grants- For any file you distribute that contains code from the
software (in source code or binary format), you must provide recipients the
source code to that file along with a copy of this license, which license will
govern that file. You may license other files that are entirely your own work
and do not contain code from the software under any terms you choose.
(B) No Trademark License- This license does not grant you rights to use any
contributors' name, logo, or trademarks.
(C) If you bring a patent claim against any contributor over patents that you
claim are infringed by the software, your patent license from such contributor
to the software ends automatically.
(D) If you distribute any portion of the software, you must retain all
copyright, patent, trademark, and attribution notices that are present in the
software.

(E) If you distribute any portion of the software in source code form, you may
do so only under this license by including a complete copy of this license with
your distribution. If you distribute any portion of the software in compiled or
object code form, you may only do so under a license that complies with this
license.
(F) The software is licensed "as-is." You bear the risk of using it. The
contributors give no express warranties, guarantees or conditions. You may have
additional consumer rights under your local laws which this license cannot
change. To the extent permitted under your local laws, the contributors exclude
the implied warranties of merchantability, fitness for a particular purpose and
non-infringement.

Copyright information
Trademarks
QIAGEN®, Sample to Insight®, QIAgility®, QIAsymphony®, ScreenGel® (QIAGEN Group); Adobe®,

Reader® (Adobe Systems Inc.); Celeron®, Intel® (Intel Corporation); Excel®, Microsoft®, Windows®
(Microsoft Corporation). Registered names, trademarks, etc. used in this document, even when not
specifically marked as such, are not to be considered unprotected by law.
© 2010-2017 QIAGEN, all rights reserved.
1108754 11/2017 HB-0804-010

www.qiagen.com
Technical Support
www.support.qiagen.com
1108754 11/2017 HB-0804-010

HB-0804-010_1108754_UM_IAS_QX_Advanced_1117_WW

Uploaded by

Copyright:

Available Formats

HB-0804-010_1108754_UM_IAS_QX_Advanced_1117_WW

Uploaded by

Document Information

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

HB-0804-010_1108754_UM_IAS_QX_Advanced_1117_WW

Uploaded by

Copyright:

Available Formats

November 2017

For use with QIAxcel ScreenGel Software v1.6

QIAxcel Advanced User Manual 11/2017 2

Installation of AC power cord

QIAxcel ScreenGel Software

QIAxcel Advanced User Manual 11/2017 3

Modifying a process profile

QIAxcel Advanced User Manual 11/2017 4

Importing BioCalculator Data

Exporting view to clipboard

QIAxcel Advanced User Manual 11/2017 5

Standard DNA analysis

Standard RNA analysis

QIAxcel Advanced User Manual 11/2017 6

QIAxcel Advanced User Manual 11/2017 7

QIAxcel Advanced User Manual 11/2017 8

The following types of safety information appear throughout this manual:

WARNING/ Risk of personal injury and material damage [W1]

Servicing of the QIAxcel Advanced must only be performed by QIAGEN Field

QIAxcel Advanced User Manual 11/2017 1

CAUTION Damage to the instrument [C1]

CAUTION Damage to the instrument [C2]

Do not use bleach, solvents, or reagents containing acids, alkalis, or abrasives to

WARNING Electrical hazard [W3]

Any interruption of the protective conductor (earth/ground lead) inside or outside

Intentional interruption is prohibited.

Lethal voltages inside the instrument

QIAxcel Advanced User Manual 11/2017 2

Do not operate the instrument with any covers or parts removed.

The line power cord appears to be damaged.

It has been stored under unfavorable conditions for a prolonged period.

It has been subjected to severe transport stresses.

WARNING Explosive atmosphere [W4]

The QIAxcel Advanced is not designed for use in an explosive atmosphere.

WARNING Risk of explosion [W5]

CAUTION Damage to the instrument [C3]

The QIAxcel Advanced must be located out of direct sunlight.

QIAxcel Advanced User Manual 11/2017 3

CAUTION Damage to the cartridge [C5]

WARNING Hazardous chemicals [W6]

Always wear safety glasses, gloves, and a lab coat.

* OSHA: Occupational Safety and Health Administration (United States of America).

WARNING Risk of fire [W7]

QIAxcel Advanced User Manual 11/2017 4

For information on how to dispose of the QIAxcel Advanced, see Appendix A.

WARNING Moving parts [W8]

QIAxcel Advanced User Manual 11/2017 5

Symbol Location Description

Type plate on the back of the Legal manufacturer

QIAxcel Advanced User Manual 11/2017 6

About this user manual

QIAxcel ScreenGel Software

The appendices include the following:

QIAxcel Advanced methods and accessories

Data analysis algorithm descriptions

Warranty liability clause

QIAxcel Advanced User Manual 11/2017 7

Intended use of the QIAxcel Advanced

QIAxcel Advanced User Manual 11/2017 8

Task Personnel Training and experience