SkanIt For Multiskan GO User Manual PDF

Thermo Scientific
SkanIt Software 3.2

for Multiskan GO
User Manual
R ev. 1.0
Thermo Scientific
SkanIt Software 3.2
for Multiskan GO
User Manual
Rev. 1.0, Cat no. N10597
Copyright
Copyright 2010 Thermo Fisher Scientific. All rights reserved. Reproduction of the accompanying user
documentation in whole or in part is prohibited.
Trademarks
SkanIt and Multiskan are registered trademarks of Thermo Fisher Scientific.
All other trademarks and registered trademarks are the property of their respective holders.
Remarks on screenshots
Screenshots may be slightly different on your system depending on the SkanIt Software and operating system
versions.
Disclaimer
Thermo Fisher Scientific reserves the right to change its products and services at any time to incorporate technological
developments. This manual is subject to change without prior notice as part of continuous product development.
Although this manual has been prepared with every precaution to ensure accuracy, Thermo Fisher Scientific assumes
no liability for any errors or omissions, nor for any damages resulting from the application or use of this information.
This manual supersedes all previous editions.
No liability for consequential damages
Thermo Fisher Scientific shall not be liable for any damages whatsoever arising out of the use or inability to use
this product.
Contents
Chapter 1
Introduction ......................................................................................... 17
Chapter 2
Installing SkanIt Software ................................................................ 21
Chapter 3
Getting Started .................................................................................... 31
Chapter 4
User Interface ..................................................................................... 33
Chapter 5
Session ................................................................................................ 43
Chapter 6
Layout .................................................................................................. 53
Chapter 7
Protocols ............................................................................................. 69
Chapter 8
Step Parameters .................................................................................. 73
Chapter 9
Starting a Session ............................................................................... 83
Chapter 10
Results ................................................................................................. 87
Chapter 11
Calculations ........................................................................................ 95
Chapter 12
Pathlength Correction ....................................................................... 145
Chapter 13
Reports .............................................................................................. 151
Chapter 14
Settings ............................................................................................. 159
Chapter 15
Using Help ......................................................................................... 183
Chapter 16
Multiskan GO Simulator .................................................................... 185
Chapter 17
Troubleshooting Guide ...................................................................... 187
Appendix A
Database Maintenance ..................................................................... 189
Appendix B
Registering SkanIt Software ............................................................. 197

Glossary ............................................................................................. 199
Index .................................................................................................. 201
Thermo Fisher Scientific
Thermo Scientific SkanIt Software 3.2 for Multiskan GO User Manual
Contents
About the User Manual ....................................................................... 15
Intended users ..................................................................................... 15
For more information .......................................................................... 15
Language versions of the Brief User's Guide ........................................ 15
Warnings and other markings used in the documentation ................... 16
Chapter 1
Introduction ......................................................................................... 17
SkanIt Software ................................................................................... 17
Language versions of SkanIt Software .................................................. 17
Multiskan GO ..................................................................................... 17
Automation Interface ........................................................................... 18
Chapter 2
Installing SkanIt Software ................................................................ 21

Registering SkanIt Software ................................................................. 21
Checking the PC requirements ............................................................ 21
Microsoft Windows settings ................................................................ 22
Starting the installation ........................................................................ 23
Installing the software .......................................................................... 24
Connecting an instrument ................................................................... 27
Installing SkanIt Software for different instrument types ..................... 29
Uninstalling SkanIt Software ............................................................... 29
Uninstalling the database engine .......................................................... 29
Reinstalling (repairing) the software ..................................................... 30
Technical description for system administrators ................................... 30
Chapter 3
Getting Started .................................................................................... 31

General operating procedure ................................................................ 31
Starting SkanIt Software ...................................................................... 31
Changing the language ........................................................................ 32
Working with demo sessions ............................................................... 32
Chapter 4
User Interface ..................................................................................... 33

Navigating the software ....................................................................... 33
Home view .......................................................................................... 35
Layout view ......................................................................................... 37
Protocol view ....................................................................................... 38
Results view ......................................................................................... 39
Reports view ........................................................................................ 40
Effective use of the software ................................................................. 41
Context menus .................................................................................. 41
Shortcuts ........................................................................................... 41
Chapter 5
Session ................................................................................................ 43
Session structure .................................................................................. 43
Creating a new session ......................................................................... 44
Contents
Editing and saving a session ................................................................. 44

Opening an existing session ................................................................. 46
Deleting a session from the database .................................................... 47
Exporting and importing sessions ........................................................ 47
Exporting sessions ............................................................................. 47
Importing sessions ............................................................................. 50
Importing instrument sessions ........................................................... 50
Managing folders ................................................................................ 51
Chapter 6
Layout .................................................................................................. 53
Structure of a layout ............................................................................ 53
Selecting a template ............................................................................. 54
Adding samples to a layout .................................................................. 54
Adding samples with the Fill With function ...................................... 55
Adding samples with the Fill Wizard function ................................... 60
Example of adding a concentration series .......................................... 64
Editing samples ................................................................................... 65
Clearing the layout .............................................................................. 66
Copying a sample ................................................................................ 66
Adding a new plate .............................................................................. 66
Renaming a plate ................................................................................. 66
Deleting a plate ................................................................................... 66
Viewing the original layout .................................................................. 67
Printing the current layout .................................................................. 67
Chapter 7
Protocols ............................................................................................. 69
Defining a protocol ............................................................................. 69
Adding new protocol steps ................................................................ 70
Renaming a protocol step .................................................................. 71
Deleting protocol steps ..................................................................... 71
Chapter 8
Step Parameters .................................................................................. 73

Photometric measurement ................................................................... 73
Spectrum measurement ....................................................................... 74
Kinetic Loop ........................................................................................ 75
Area definition .................................................................................... 76
Pause ................................................................................................... 77
Shake ................................................................................................... 78
Incubate .............................................................................................. 80
Plate In / Plate Out ............................................................................. 81
Chapter 9
Starting a Session ............................................................................... 83

Starting a plate session ......................................................................... 83
Starting a cuvette session ...................................................................... 85
Chapter 10
Results ................................................................................................. 87
Measurement results ............................................................................ 87
Calculation results ............................................................................... 87
Viewing kinetic curves or spectra ......................................................... 88
Disabling values from measurement data ............................................. 89
Arranging a list ................................................................................... 89
Exporting measurement and calculation data ....................................... 92
Contents
Exporting manually ........................................................................... 92

Open in Excel ................................................................................. 92
Exporting data ................................................................................ 93
Exporting automatically .................................................................... 93
Presenting results as a report .............................................................. 94
Chapter 11
Calculations ........................................................................................ 95
Adding calculations ............................................................................. 95
Deleting calculations ........................................................................... 96
Note on sample names ......................................................................... 96
Blank subtraction ................................................................................ 97
Examples of blank subtraction ........................................................... 97
Blank subtraction in kinetic measurements ........................................ 98
Basic statistics ...................................................................................... 99
Pathlength correction ........................................................................ 101
Spectral analysis ................................................................................. 102
Spectral peak search ......................................................................... 102
Spectral maximum .......................................................................... 104
Spectral minimum ........................................................................... 104
Ratio within spectrum ..................................................................... 104
Ratio between spectra ...................................................................... 105
Select wavelength range ................................................................... 105
Select single wavelength ................................................................... 105
Kinetics ............................................................................................. 106
Average rate ..................................................................................... 106
Maximum rate ................................................................................ 107
Time to maximum rate ................................................................... 109
Time to maximum rate / 2 .............................................................. 111
Time to change ............................................................................... 111
Maximum of well (Peak) ................................................................. 112
Maximum - Minimum (Change) .................................................... 113
Time to maximum (Peak) ............................................................... 113
Time to maximum (Peak) / 2 .......................................................... 113
Select reading .................................................................................. 113
Ignore readings ................................................................................ 113
Integral ............................................................................................ 114
Sum ................................................................................................ 114
Average value .................................................................................. 115
Baseline subtraction ......................................................................... 115
Precalculation .................................................................................... 117
Merge data ......................................................................................... 118
Graph ................................................................................................ 118
Viewing results as a graph ................................................................ 120
Quality control (QC) ........................................................................ 122
Example of a Quality Control calculation ........................................ 123
User-defined equation ....................................................................... 124
Quantitative curve fit ......................................................................... 127
Quantitative curve fit definition ...................................................... 128
Polynomial fit types ......................................................................... 130
Contents
Point to point .................................................................................. 131

Cubic spline .................................................................................... 131
Four parameter logistic and Log-Logit ............................................. 131
Quantitative curve fit results ........................................................... 132
Multiple roots ................................................................................. 134
Effective dose ..................................................................................... 134
Data normalization ............................................................................ 138
Qualitative classification .................................................................... 139
Parallel Line Analysis ......................................................................... 140
Performing a PLA calculation .......................................................... 141
Results of the PLA ........................................................................... 142
Chapter 12
Pathlength Correction ....................................................................... 145

Microwell pathlength ......................................................................... 145
Creating a K-factor ............................................................................ 146
Pathlength correction with microplates .............................................. 147
Pathlength correction with cuvettes ................................................... 148
Chapter 13
Reports .............................................................................................. 151

Measurement and calculation reports ................................................. 151
Creating a report ............................................................................... 151
Editing a report ................................................................................. 152
Editing a report item ......................................................................... 153
Exporting the report .......................................................................... 154
Exporting manually ......................................................................... 154
Open in Excel ............................................................................... 154
Exporting data .............................................................................. 154
Exporting automatically .................................................................. 154
Printing a report ............................................................................... 157
Printing a report manually .............................................................. 157
Printing a report automatically ........................................................ 157
Sending a report via email ............................................................... 157
Chapter 14
Settings ............................................................................................. 159

Options ............................................................................................. 159
General ........................................................................................... 159
Database ......................................................................................... 160
Results ............................................................................................. 161
Reporting ........................................................................................ 162
Colors ............................................................................................. 163
Plate Template ................................................................................ 163
Setting a plate template as default ................................................. 164
Creating a new plate template ....................................................... 164
Editing a plate template ................................................................ 165
Deleting a plate template .............................................................. 166
Saved curves .................................................................................... 166
K-Factors ........................................................................................ 168
Instruments ....................................................................................... 169
Instrument Setup ............................................................................ 169
Setting the default instrument ....................................................... 170
Adding an instrument to the SkanIt Software database manually ... 170
Contents
Creating an instrument report ....................................................... 171

Instrument Settings ......................................................................... 172
Instrument temperature ................................................................ 172
Power Save .................................................................................... 173
User Management ............................................................................. 173
Password Options ........................................................................... 174
Users ............................................................................................... 175
Adding a new user ......................................................................... 175
Viewing and editing user information ........................................... 177
Changing the login password ........................................................ 177
Groups ............................................................................................ 179
Adding a new user group .............................................................. 179
Viewing and editing group information ........................................ 180
Laboratory information ................................................................... 181
Chapter 15
Using Help ......................................................................................... 183
Chapter 16
Multiskan GO Simulator .................................................................... 185
Chapter 17
Troubleshooting Guide ...................................................................... 187
Appendix A
Database Maintenance ..................................................................... 189

Selecting the database in SkanIt Software .......................................... 189
Starting Database Maintenance ......................................................... 189
Creating a backup file ........................................................................ 190
Restoring a backup file ...................................................................... 190
Archiving sessions .............................................................................. 191
Creating a new database ..................................................................... 192
Deleting the database ......................................................................... 193
Attaching the database ....................................................................... 194
Appendix B
Registering SkanIt Software ............................................................. 197

Glossary ............................................................................................. 199
Index .................................................................................................. 201
Contents
10
Figures
Figure 1-1
Figure 11-1
Figure 11-2
Figure 11-3
Figure 11-4
Figure 11-5
Figure 11-6
Figure 11-7
Figure 11-8
Multiskan GO with cuvette spectrophotometer .................. 18

Determining the maximum rate with window value 2 ....... 107
Determining the time to maximum rate ........................... 109
Integral calculation ....................................................... 114
Example of an absorbance curve ..................................... 115
Determining the average value of a kinetic measurement .. 115
Determining the baseline subtracted kinetic curve ........... 116
An example of a graph with photometric measurement
results ......................................................................... 120
Effective dose (ED) determination ................................... 135
11
Figures
12
Tables
Table 2-1
Table 4-1
Table 4-2
Table 11-1
Table 14-1
Minimum PC requirements ............................................... 22

Keyboard shortcuts ......................................................... 41
Function key shortcuts ..................................................... 42
The minimum number of calibrators required in different curve
fit types ....................................................................... 129
Rights of the different security groups ............................. 174
13
Tables
14
About the User Manual

Intended users
The user manual has been written for the users of the Thermo Scientific
Multiskan GO spectrophotometer and provides information on Thermo
Scientific SkanIt Software 3.2 for Thermo Scientific Multiskan GO. The
manual contains the operating instructions for Thermo Scientific SkanIt
Software 3.2 Research Edition (RE).
Read the manual in its entirety before using the software.
For more information
For instrument-related issues, refer to the Thermo Scientific Multiskan GO

User Manual (Cat. no. N10588). The instrument and software user manuals
can be found in PDF format on the Thermo Scientific SkanIt Software
installation CD. After installation, the user manuals open at the same
location as the software itself:
Start > All Programs > Thermo SkanIt Software > SkanIt for Multiskan GO
> SkanIt for Multiskan GO 3.2 User Manual.
For the latest information on products and services, visit our website on the
Internet at:
http://www.thermoscientific.com
http://www.thermoscientific.com/readingroom
In an effort to produce useful and appropriate documentation, we appreciate
your comments on this user manual to your local Thermo Fisher Scientific
representative.
Language versions of
the Brief User's Guide
The language versions of the Thermo Scientific SkanIt Software Multiskan

GO Brief User's Guide can be found on the SkanIt Software installation CD
in the Manuals folder.
15
About the User Manual

Warnings and other markings used in the documentation
Warnings and other

markings used in the
documentation
The following symbols and markings appear in this manual.
Caution Risk of damage to the instrument, other equipment or

loss of performance or function in a specific application.
Note Marks a tip, important information that is useful in the
optimum operation of the system, or an item of interest.
Tip Gives a helpful hint for getting the most out of the software
functionality.
16
Chapter 1
Introduction
SkanIt Software
SkanIt Software 3.2 for Multiskan GO is used to control all of the

instrument functions, and it provides data processing as well as reporting
functions.
The information that is needed to define and run an assay is saved in an
entity called a session. SkanIt Software enables you to build sessions for your
own applications and to run or modify ready-made sessions.
With SkanIt Software you can:
Create and edit sessions
Perform calculations and export data
Create and print measurement and calculation reports
Export and import sessions between SkanIt Software databases on

different PCs
Import sessions exported from the instrument's internal software.
The sessions are made and stored in a database on the PC by using SkanIt
Software. Once you have created a session, you can run it directly from the
software.
Language versions of
SkanIt Software
The SkanIt Software user interface language can be freely chosen from the
Settings. The following languages are available: English (default), German,
French, Spanish, Portuguese, Japanese, Chinese and Russian.
For more information on changing the language, see Chapter 14: Settings.
Note The online help is available only in English.
Multiskan GO
The Multiskan GO is a high-quality monochromator-based UV/VIS

spectrophotometer. It is used in spectral scanning, end-point and kinetic
measurements to measure absorbance in the 2001000 nm wavelength
range from appropriate 96- or 384-well microplates with and without lids
17
Introduction
Automation Interface
and various types of cuvettes (only with the cuvette version). The instrument
allows incubation up to 45C and shaking of the microplate.
The instrument can be used by itself with the internal software for quick
and simple plate and cuvette measurements or by controlling it with SkanIt
Software 3.2. The Multiskan GO is robotic compatible and can be connected
to plate handling devices such as stackers. The unique Power Save function
lowers its energy consumption. The Multiskan GO can be used in a variety
of applications, including nucleic acid and protein analysis, ELISA assays,
enzyme assays, cytotoxicity and cell proliferation assays as well as apoptosis
assays.
Figure 1-1. Multiskan GO with cuvette spectrophotometer

The Multiskan GO is available in the following configurations:
Multiskan GO 100240 V Cat. no. 51119200 and 51119250 (Japan)
96- and 384-well plate reading, shaking and incubation
Multiskan GO with cuvette 100240 V Cat. no. 51119300 and

51119350 (Japan)
96- and 384-well plate reading, shaking, incubation, and cuvette

reading with incubation
For more information, see the Multiskan GO User Manual (Cat. no.
N10588).
Note This manual covers the operation SkanIt Software with the
Multiskan GO with the cuvette port. If you have the Multiskan
GO without the cuvette port, you can ignore the references to
cuvette use.
18
SkanIt Software 3.2 can be integrated with and controlled via an automation
environment. This can be done by incorporating MIB Automation Interface
Introduction
to the SkanIt installation. The required version is MIB Automation Interface

3.0.0.6. For details, refer to the Thermo Scientific MIB Automation Interface
Version 3.0 User Manual (Cat. no. N08444).
19
Introduction
20
Chapter 2
Installing SkanIt
This chapter contains information that is necessary for a successful
installation of SkanIt Software. Read these instructions before you start to
install SkanIt Software.
Note Failure to follow these instructions may lead to an
unsuccessful installation of SkanIt Software.
Registering SkanIt
Software
You need an installation code for SkanIt Software. To receive the code, you
have to register SkanIt Software by filling out the registration form on our
website at:
www.thermoscientific.com/skanit
For more information, see Appendix B: Registering SkanIt Software.
During software registration you will need the instrument serial number
and the CD serial number that is printed on the installation CD package.
The code that you receive as a result of the registration is sent to the email
address that you enter on the registration page. When you log in for the
first time, the software asks you to enter the code (see Enter the Installation
Code in Connecting an instrument on page 27).
Note You can also install SkanIt Software without registering it
first. The Software will work for 30 days without the installation
code. During this period, the code is asked every time you log in.
Checking the PC
requirements
Check that the PC meets the requirements that are needed for using SkanIt
Software.
The table below lists the minimum PC requirements for SkanIt Software
version 3.2.
21
Installing SkanIt
Microsoft Windows settings
Table 2-1. Minimum PC requirements

Minimum PC requirements
Supported operating systems
Microsoft Windows 7
Microsoft Windows Vista with Service Pack 2 (or later)
Microsoft Windows XP Professional with Service Pack 3
(or later)
Disk space
5 GB free hard disk space
Processor
Dual-core processor
Memory
2 GB RAM
Available USB port
Pointing device
Mouse or equivalent is necessary
CD-ROM drive
Monitor and color settings
XGA monitor with 1024 x 768 resolution
Browser
Microsoft Internet Explorer 6.0 (or later)
If you do not have the correct Service Packs installed, you can download
them from the Microsoft website at:
www.microsoft.com
Microsoft Windows
settings
In the Power Options Properties, ensure that the Turn off hard disks, System
standby and System hibernates settings are set to Never. In long kinetic sessions
the computer is seemingly in an idle state, as the data flow is not monitored.
Therefore, if the power option setting is not set to Never, the computer may
turn off the power in the middle of a measurement. The power options
settings can be checked and changed in the Power Options Properties
window:
Windows XP:
Start > Settings > Control Panel > Power Options > Power Schemes > Turn
off hard disk/System standby/System hibernates > Never
Windows Vista or Windows 7:
Start > Control Panel > Power Options > Change when the computer sleeps
> Change advanced power settings > Turn off hard disk after > Never
> Put the computer to sleep > Never
22
Installing SkanIt
Starting the installation
> Change advanced power settings > Sleep > Hibernate after > Never
Starting the
installation
To start the SkanIt Software 3.2 for Multiskan GO installation, follow these
steps:
Note SkanIt Software cannot be installed on a network drive.
Note You have to be logged on to your computer with
administrator privileges to install SkanIt Software.
Note You can stop the installation procedure at any stage by
clicking Cancel. The setup returns your system to the previous
state.
1.
Check that the PC requirements in Table 2-1 are met.
2.
Insert the SkanIt Software installation CD into the CD-ROM drive

of your PC.
3.
The Welcome to ThermoFisher Software Setup dialog opens

automatically. If the dialog does not open, start the installation from
the CD by double-clicking the Setup.exe file.
The SkanIt Software Setup checks that all the software and system
requirements are met. The setup installs the required components:
4.
SkanIt Software 3.2, always installed
Microsoft SQL Server 2008 R2 Express, installed if not found on

your PC
Microsoft .NET Framework 3.5 SP1, installed if not found on

your PC
Microsoft Visual C++ 2005 SP1
Windows Installer 4.5, installed if not found on your PC.
Close all other programs on your computer and click Next.
23
Installing SkanIt
Installing the software
5.
Click Install Software Prerequisites to install the software required

before installing SkanIt Software.
If a restart is requested during the installation of software prerequisites, it

should be confirmed. After the restart, click Install Software Prerequisites
to continue the installation.
After all the prerequisites have been installed, you can proceed with the
actual software installation.
When the prerequisites have been installed, the SkanIt for Multiskan GO
Setup will proceed with the actual SkanIt Software installation.
1.
24
In the SkanIt for Multiskan GO 3.2 dialog, click Install Software to

start the Setup Wizard.
Installing SkanIt
The wizard guides you through the entire installation procedure. In

the Setup Wizard dialog, click Next.
2.
Read the Licence Agreement and click I Agree to accept it and proceed
with the installation. Click Next.
3.
Fill in your customer information and click Next.
4.
Select the installation location and click Next.

The Setup Wizard suggests a location for the program files. Change
the suggested location only if absolutely necessary. Click Browse to
select another folder or drive.
Click Disk Cost to view the available disk space on the available drives.
The recommended minimum free disk space for SkanIt Software is 5
GB.
5.
The Setup Wizard is now ready to install SkanIt Software for Multiskan
GO on your computer. Click Next to start the installation.
6.
Accept or modify the information in the SkanIt Database Configuration.
25
Installing SkanIt
Create a new database. SkanIt Software is connected to an existing

database engine (the one that was installed in the prerequisites)
and a new SkanIt Software database will be created.
Use an existing database. If you have previously created a database,

SkanIt Software is connected to an existing database engine and
an existing SkanIt Software database will be used.
Server Name. This is the name of the database engine (SQL Server)
in which the SkanIt Software database will be created. The database
engine has the instance name THERMO, separated by a backslash
(\).
DB Name. The name of the SkanIt Software database which you

want to create. The default name is Skanit_GO_RE. If the database
with the defined name already exists, an error message is displayed.
The existing database will not be overwritten.
Click Configure.
The installation proceeds with the database configuration. Wait until
it has finished even if the installation seems not to respond. This may
take several minutes.
7.
You will receive a confirmation message when the installation is

complete. Click Close.
Click OK in the Thermo Fisher Scientific Software Setup dialog
indicating that the installation is complete.
8.
26
In the SkanIt for Multiskan GO 3.2 dialog, click Exit to finish the
installation.
Installing SkanIt
Connecting an instrument
Note The installation of a new database engine does not affect

any other installed database engines.
Note If the installation fails, SkanIt will be removed but third
party components (SQL server and Microsoft .NET) may remain
installed. When reinstalling SkanIt Software, the installation detects
this and takes it into account.
After the installation, the setup directly proceeds with connecting an
instrument to the software. If you want to make a connection to an
instrument, proceed with Connecting an instrument on page 27. If you
do not want to make a connection to an instrument, proceed with Step 4
in section Connecting an instrument.
If you do not set up a connection to any instrument at this point, the
simulator will be set as a default instrument.
Connecting an
instrument
After installing the software (see Installing the software on page 24), you
can connect the instrument to the software.
1.
Ensure that the instrument is switched off.
2.
Connect the instrument to the computer by using a USB cable.
3.
Switch on the instrument. Wait for the instrument to finish initializing.

In the ThermoFisher Scientific Software Setup dialog, click OK.
4.
Log in to SkanIt Software. Use admin as your Username and leave the
Password field empty. Click Login.
5.
Enter the CD Serial number and Installation Code.
27
Installing SkanIt
Connecting an instrument
The CD serial number is printed on the cover of the SkanIt Software

CD. You receive the installation code from:
http://www.thermoscientific.com/skanit
Note You must enter the CD serial number, but SkanIt Software
can be used for 30 days without entering the installation code. If
you do not enter the code, the software will ask for the code every
time when you log in. If the code is not entered in 30 days, you
can open the software but sessions cannot be run.
Click OK.
After you have logged in, the software searches for new instruments
and makes the connection automatically.
28
Installing SkanIt
Uninstalling the database engine
6.
Select an instrument from the list. The selected instrument is set as

the default instrument. Click OK.
If no instruments are found, the software reminds you to check that
the cables are connected and the instrument is switched on.
If no instrument is available, click Cancel. The simulator will be set

as the default instrument if you have not connected any instruments
earlier. You can also connect an instrument to the software later (for
more information, see Starting SkanIt Software on page 31 and
Adding an instrument to the SkanIt Software database manually on
page 170).
Installing SkanIt
Software for different
instrument types
SkanIt Software is published separately for different instrument types. If

you want to use the same PC to operate several instruments, such as
Varioskan Flash, Multiskan FC and Appliskan, you need to install separate
versions of SkanIt Software onto your PC.
Uninstalling SkanIt
Software
You can uninstall SkanIt Software by clicking Add or Remove Programs

in the Windows Control Panel.
Click Remove. You are asked to confirm the removal of the program. Click
Yes. The SkanIt Software is uninstalled.
Removing SkanIt Software will not remove the database engine or the
Microsoft .NET Framework, because they may be used by other software
applications.
Uninstalling the
database engine
Backup the database with a database maintenance tool, if you choose to

delete the SkanIt database engine. The following files will remain in the
installation folder after the uninstallation: SkanIt_GO_RE.mdf and
SkanIt_GO_RE.ldf.
29
Installing SkanIt
Technical description for system administrators
You can delete these files, make a backup copy of them, or attach them to
a database engine (Microsoft SQL Server 2008 R2 Express) using Database
Maintenance (see Appendix A: Database Maintenance).
The database engine can be uninstalled by clicking Add or Remove
Programs in the Windows Control Panel.
Caution Do not delete the database engine if any of your other
software applications uses it.
Reinstalling (repairing)
the software
The repairing mode is not supported. You have to uninstall SkanIt Software
and then install a fresh copy.
Technical description
for system
administrators
The system does not open any communication ports on the target computer.
Communication with Multiskan GO is handled via a USB port. Installation
configures the SQL Server to accept only local connections.
30
The installation grants the Windows Users group full privileges to the SkanIt
configuration files in the installation folder (default c:\Program
Files\Thermo\SkanIt for GO 3.2\). The installation also grants the Windows
Network Service user full privileges to the data folder located in the
installation folder.
Chapter 3
Getting Started
This chapter contains information that helps you get started with the
software after the installation.
General operating
procedure
Starting SkanIt
Software
The general operating procedure with SkanIt Software is as follows:
Start SkanIt Software.
Open an existing session or create a new one.
Edit the session (protocol, layout and calculations) if necessary and save
it.
Start the session.
Perform calculations.
Create a report.
Export the results.
1.
Start the software from the Start menu:

Start > Programs > Thermo SkanIt Software > SkanIt for Multiskan
GO > SkanIt for Multiskan GO 3.2.
or double-click the Skanit for Multiskan GO 3.2 shortcut icon on
your desktop.
2.
The SkanIt Login dialog opens.
31
Getting Started
Working with demo sessions
Note When you log in for the first time, enter admin in the
User name field and leave the Password field empty. Use SkanIt
User Management to create new users (see Adding a new user
on page 175) and to change the administrator password to protect
data security (see Changing the login password on page 177).
3.
Type your user name and password and click Login. The software
starts to load. The software will try to connect to the default instrument
if the Connect to default instrument at startup setting is selected in
the Settings > Options > General menu.
When the software is ready for use, the main window opens. You can now
create a new session (see Creating a new session on page 44), open an
existing session (see Opening an existing session on page 46) or open a
demo session (see next section Working with Demo Sessions).
Changing the language
Working with demo

sessions
To change the user interface language of SkanIt Software:

1.
Click Settings in the Home view.
2.
In the General dialog, select the desired language from the list.
3.
Click Close and restart SkanIt Software for the change to take effect.
SkanIt Software provides demo sessions in the Recent Sessions list of the
Home view. More demo sessions are available in the Thermo Fisher
Scientific > Demo Sessions folder.
To open a demo session, click the session in question and follow the
instructions in the Protocol view of each session. You can freely edit a demo
session, save it with a new name, perform calculations and create reports.
The original demo sessions cannot be deleted.
32
Chapter 4
User Interface
This chapter describes the functionality of the user interface. It provides
information on its features, the toolbars and functions and tells you how
you can use them effectively.
Navigating the
software
When you log into SkanIt Software for Multiskan GO, the main (Home)
view opens.
The SkanIt Software user interface is divided into five views: Home, Layout,
Protocol, Results and Reports. You can easily navigate from view to view
by clicking the desired tab on the navigation bar. The tabs are visible in
every view of the software, and they become active after you open a new or
an existing session.
Toolbar (1)
The toolbar contains the most frequently used functions. The toolbar also
shows the currently open session, and the name and the version of the
software. The toolbar is displayed in every view.
New creates a new session.
33
User Interface
Navigating the software
Open launches the Open Session dialog for opening an existing session.
Save saves the session that is currently open.
Show Help opens the SkanIt Software Help.
Application menu (2)
Open the Application menu by clicking the SkanIt Software icon.
The New, Open and Save buttons function as on the toolbar.
Save As saves a session with a new name.
Lock locks the software to prevent unauthorized use. Only a user who
has locked the software or an administrator can unlock the software.
Help opens the SkanIt Software Help.
About provides information on the SkanIt Software application.
Exit closes SkanIt Software.
Navigation bar (3)
The navigation bar displays the tabs for the Home, Layout, Protocol,
Results and Reports views.
Action panels (4)
Action panels include the available functions that differ in each view.
If the window is too small, all action panels and function buttons are not
displayed. In this case, black arrows indicate the missing buttons. Other
possible unavailable action panels and buttons become available by enlarging
the window size.
Status bar (5)
The status bar at the bottom of the view displays the following information:
The connected instrument. When the software is connected to an

instrument, the icon is displayed with instrument information, and
the Disconnect and the
34
Plate In and
Plate Out buttons are
User Interface
Home view
active. When an instrument is not connected, the

icon, instrument
information and the Connect button are displayed.
If the Disconnect/Connect and the Plate In/Plate Out buttons are
not visible, you have to enlarge the window size.
Home view
The temperature of the instrument's plate measurement chamber and

cuvette port (if an instrument is connected) as well as the target
temperature if set.
The logged-in user (for example, admin)
The Home view opens every time you log into SkanIt Software. In the
Home view, you can perform basic functions that concern sessions and
instrument operation, and access the software settings.
The Home view includes the following parts and functions:

Recent Sessions (1)
Recent Sessions lists the recently used and pinned sessions.
You can set the number of sessions that are displayed in the list (for more
information, see General on page 159). You can also click the pin beside
the session name to pin or unpin the session. If a session is pinned, it is
35
User Interface
Home view
always shown in the list regardless of use. If a session is not pinned, it will
drop off the list if you do not use it frequently.
Session action panel (2)
New creates a new session (see Creating a new session on page 44).
New K-factor creates a new K-factor (see Chapter 12: Pathlength

Correction).
Open launches the Open Session dialog for opening an existing session
(see Opening an existing session on page 46).
Save saves the current session in the database (see Editing and saving
a session on page 44).
Save As opens the Save As dialog for saving the current session with a
new name (see Editing and saving a session on page 44).
Import imports sessions that are exported from another SkanIt Software
for Multiskan GO database or from the instrument's internal software (see
Exporting and importing sessions on page 47).
Export exports selected sessions as a separate file (*.msz) that can be
imported to another SkanIt Software for Multiskan GO database (see
Exporting and importing sessions on page 47).
System action panel (3)
Settings opens a dialog for defining the instrument and

software-related settings.
Help opens the SkanIt Software Help.
Instrument action panel (4)
Connect opens the connection to the instrument that is selected from
the list. This icon is visible when the software is not connected to an
instrument.
36
User Interface
Layout view
Disconnect closes the connection to the instrument. This icon is

visible when the software is connected to an instrument.
Set Temperature opens a dialog for setting the instrument temperature.
This button is displayed only when an instrument is connected.
Plate In runs the plate into the instrument. This function is active if
an instrument is connected.
Plate Out runs the plate out of the instrument. This function is active
if an instrument is connected.
Start begins the measurement (see Chapter 9: Starting a Session).
Layout view
In the Layout view, you can define the sample layout for the session.
The Layout view includes the following parts and functions:

The Action panels (1) include the functions that are available in the Layout
view.
For more information on the button functions, see Chapter 6: Layout.
37
User Interface
Protocol view
The Current template (2) shows either the selected plate type or cuvette.
The Plate tabs (3) show the plates that are added to the plate layout. Click
a tab to select the plate.
The Layout pane (4) shows the plate or cuvette set and its contents.
The Zoom slider (5) enables you to increase or decrease the magnification
of the layout.
The Description field (6) shows the optional description that the user can
define for the layout.
Protocol view
In the Protocol view, you can add and define the protocol steps for the
session.
The Protocol steps (1) tree view shows the added steps in hierarchical order.
The Main pane (2) shows the protocol properties of a session or if you click
a protocol step, the pane shows the parameters of the protocol step in
question.
The Action panels (3) include the functions that are available in the
Protocol view.
For more information on the function of the buttons, see Chapter 8: Step
Parameters.
38
User Interface
Results view
Results view
In the Results view, you can view the results after the measurement. You
can also add calculations to measurement data and view these results here.
The Results tree (1) shows the measurement and calculation steps in
hierarchical order.
The Main pane (2) shows the measurement or calculation results as a table
or list. You can choose the display format with the tabs (3).
The Toolbar (4) includes functions for editing steps.
The Action panels (5) include the calculations and other functions that are
available in the Results view.
For more information on the functions of the buttons, see Exporting
measurement and calculation data on page 92 and Chapter 11:
Calculations.
39
User Interface
Reports view
Reports view
In the Reports view, you can create a report to which you can add the
measurement and calculation results of your choice.
The Reports tree (1) shows the individual measurement and calculation
results that have been added to the report in hierarchical order.
The Toolbar (2) includes functions for editing the report.
For more information, see Editing a report on page 152.
The Main pane (3) shows the selected measurement or calculation results
in the report.
The Action panels (4) include functions that are available in the Reports
view. For more information on the action panel buttons, see Creating a
report on page 151, Exporting the report on page 154 and Printing a
report on page 157.
40
User Interface
Effective use of the software
Effective use of the

software
Context menus
You can speed up the use of SkanIt Software by using context menus and
shortcut keys as described below.
When using the software, you can often open a context sensitive menu by
right-clicking the mouse. For example, in the Protocol and Results views,
you can also edit and add steps by right-clicking in the tree view and selecting
the function from the context menu. Context menus allow quick access to
functions that are relevant to the situation. Some functions, such as advanced
graph properties and enabling or disabling values from measurement data
in the Results list view, are available only from the context menu.
Context menus are available in all measurement result lists, in the plate
layout view, and in the protocol and result trees.
Shortcuts
You can select menus by pressing Alt and the underlined letter; for example,
Settings is selected by pressing Alt+S.
Some of the operations have keyboard shortcuts. These are presented in
Table 4-1.
Table 4-1. Keyboard shortcuts
Operation
Keyboard shortcut
Create a new session
Ctrl+N
Open an existing session
Ctrl+O
Save a session
Ctrl+S
Save a session with a new name
Ctrl+Shift+S
Delete a step or result
Del
Open the Home view
Alt+H
Open the Layout view
Alt+L
Open the Protocol view
Alt+P
Open the Results view
Alt+R
Open the Reports view
Alt+E
Open the Settings menu
Alt+S
Open the Import dialog
Alt+I
Open the Export dialog
Alt+X
Some of the operations have function key shortcuts. These are presented in
Table 4-2.
41
User Interface
Effective use of the software
Table 4-2. Function key shortcuts
42
Operation
Function key shortcut
Open the help application
F1
Rename a protocol step or result
F2
Run a session
F5
Run the plate in
F9
Run the plate out
F10
Connect to the default instrument
F11
Disconnect from the default instrument
F12
Chapter 5
Session
This chapter describes the structure of a session and how you can create and
edit the sessions.
Session structure
A session includes all the definitions that are required for successful
measurement and result data processing. You can create a new session, save
the current session and open an existing one. Only one session can be open
at a time.
The structure of a session:
Layout defines the plate type or cuvette set and the samples in each well
or cuvette. Sample properties, such as concentrations or dilutions, can
also be defined.
Protocol defines the protocol steps and parameters which are required
for the instrument to perform actions.
Results shows the raw measurement data and the defined calculations
with the results.
Reports presents the selected measurement and calculation results as a

report.
Running a session produces measurement data. The measurement data
is processed with the calculations that you define in the results. You can
run a session several times and each execution produces new
measurement data. The executed sessions are saved automatically and
they can be opened or exported separately.
The functions of the Session action panel in the Home view are described
in the following sections.
43
Session
Editing and saving a session
Creating a new
session
In the Home view, click the New icon on the toolbar. A new session is now
created and the Layout view opens.
You can start creating a session by defining the layout and adding protocol
steps (see Chapter 6: Layout and Chapter 7: Protocols).
Editing and saving a

session
1.
In the Home view, click Save or Save As on the toolbar or on the

Session action panel.
Note If you use the Save As command for an executed session,
the new session, which is created, does not contain any measured
data of the original session.
44
Session
Editing and saving a session
2.
Enter a name for the session in the Session name field. You can save
the session in an existing folder or create a new folder for the session
in the tree view. Click New Folder or right-click the parent tree to
create a new folder under it. Click OK to save the changes.
If a new session is saved before starting the measurement, a separate session

without measurement data is created. This session is marked with in the
session list. You can always edit this session for new measurements, and it
never contains any measurement data.
When you start a session, an executed session is created. This session, which
has been run and includes measurement data, is marked with . You can
edit the layout, calculations and reports of an executed session. Any changes
made after the measurement must be saved separately.
When you edit a protocol of a session that includes measurement data, the
software informs you that a new session has to be created. If you accept this,
the software will automatically create an identical new session but without
results.
If a new session is not saved before starting the measurement, only an
executed session is created and automatically saved in the SkanIt Software
folder.
45
Session
Opening an existing session
Opening an existing
session
In the Home view, click Open on the Session action panel.
The Open Session dialog shows all the sessions that are currently in the
database in a hierarchical tree view. In this dialog you can create new folders,
rename folders, move sessions between folders, and delete folders and
sessions. The sessions without measurement data are marked with , the
executed sessions with measurement data are marked with .
You can open a session with no measurement data or a particular executed
session that includes the measurement data of the session that has been run.
To open an existing session:
46
1.
Click a session in an appropriate folder in the tree view.
2.
Click Open or double-click the session.
Session
Exporting and importing sessions
Deleting a session
from the database
To delete a session from the database on the PC:
Exporting and
importing sessions
1.
In the Home view, click Open.
2.
In the Open Session dialog, select the desired session from the tree view.
3.
Click Delete, or right-click the session and click Delete. You can select
multiple sessions by pressing the Ctrl key while selecting the sessions.
If the session is currently open, you cannot delete it unless you first
close it.
SkanIt Software does not save sessions to separate files, but uses a database
instead. Sessions can be exported as a separate file (*.msz) that can be
imported to another SkanIt Software for Multiskan GO database.
It is also possible to import plate measurement sessions directly from the
Multiskan GO instrument using a USB memory device.
Exporting sessions
1.
In the Home view, click Export. The Export Data dialog opens.
47
Session
2.
In the hierarchical tree, select the checkbox beside the sessions that
you want to export.
3.
Click Browse to select the file path.
4.
Select a location for the SkanIt data file (*.msz).
5.
Enter a name for the file.
6.
Click Save. The _GO suffix is added to the filename to distinguish

it from data that is exported from other instruments.
7.
Click OK.
You will receive a message which informs you whether the export
procedure was successful.
Importing sessions
1.
48
In the Home view, click Import. The Import Data/Import Options

dialog opens.
Session
2.
3.
Select the SkanIt data file (*.msz) by browsing in the Open dialog.
4.
Click Open. The file path appears in the File location field in the Import
Options dialog.
5.
Click Next.
In the Import Data/Definitions done dialog, you can view the sessions
that are imported. If there are already sessions with the same name in
the database, the sessions in the database will not be overwritten. The
software automatically adds a new number to the file name of the new,
imported sessions to distinguish them from previously imported
sessions.
49
Session
6.
Select a folder to which you want to import the selected sessions. You
can also create a new folder.
7.
Click Finish.
You will receive a message which informs you whether the import
The imported session is shown in the folder tree with the text [import] in
front of it.
Importing instrument
sessions
To import an instrument session, you must first export the session from the
Multiskan GO internal software. You can import only microplate sessions
this way. Cuvette sessions exported from the instrument cannot be imported
to SkanIt Software.
1.
In the Home view, click Import. The Import Data/Import Options

dialog opens.
2.
3.
Select the session file (*.txt) by browsing in the Open dialog. Set the
file type to Multiskan GO Data File.
4.
Click Open. The file path appears in the File location field in the Import
Options dialog.
5.
Click Next.
6.
Select a folder to which you want to import the selected sessions. You
can also create a new folder.
7.
Click Finish.
You will receive a message which informs you whether the import
The imported session is shown in the folder tree with the text [Imported
from instrument] in front of it.
SkanIt Software automatically adds unknown samples to the layout based
on the wells measured with the instrument session. You can edit the sample
50
Session
Managing folders
types in the layout, for example, by changing the unknown samples to

blanks, calibrators or controls to be able to perform calculations.
Managing folders
Sessions are managed by using a tree view.

The root folder in the tree view is SkanIt Software under which you can
create new folders. A new session is stored in the root folder by default. The
Thermo Fisher Scientific folder has demonstration sessions created by Thermo
Fisher Scientific. It is not possible to remove the root folder or the Thermo
Fisher Scientific folder and its sessions, but you can move the sessions to
another folder.
Sessions can be organized and stored in folders that you can easily create,
move, rename or delete in the Open Session dialog.
To create, rename or delete a folder, click the appropriate button on the

toolbar, or right-click the folder in question and select the action from the
menu.
To move a folder or a session, drag it to the correct folder in the tree view.
51
Session
Managing folders
52
Chapter 6
Layout
This chapter describes how to define samples on the layout.
Structure of a layout
The layout defines the plate template or cuvette set and the samples in the
session. Internal calculations on the measured data are made based on the
layout.
The following sample types can be used in a layout:
Unknown samples are the samples under investigation.
Blank samples are used for blank subtraction.
Calibrators are samples with known concentrations used for quantitative

analysis (see Quantitative curve fit on page 127).
Control samples are used for quality control (see Quality control (QC)
on page 122) and for qualitative analysis (see Qualitative classification
on page 139).
Empty wells remain empty and are not measured.
If there are no samples in the layout when you start the measurement, the
software asks you if you want to fill the layout with unknown samples.
53
Layout
Adding samples to a layout
Selecting a template
After you click New in the Home view to create a new session, the Layout
view opens.
You can now define the layout.
Select the appropriate 96-well or 384-well plate or cuvette template for the
layout from the list.
You can define several plate layouts, but only a single cuvette set with up
to 32 cuvettes.
Adding samples to a
layout
54
You can add samples to a layout in two ways:
Use the Fill With function. It allows you to perform most layout
defining actions, except adding specific blanks and dilutions for
unknowns or loading sample IDs from a text file.
Use the more advanced Fill Wizard for microplates. This feature is not
available for cuvette sets.
Layout
Adding samples with the

Fill With function
The Fill With function is an easy way to create a layout. You can use it to
add blanks, unknowns, controls and calibrators with possible concentrations
and replicates to the layout.
To add samples to the layout:
1.
Paint the wells or cuvettes with the left mouse button.
2.
Right-click or click the Fill With icon.
3.
Select the desired sample type from the menu and define its parameters
4.
Click OK to add the samples to the layout.
55
Layout
Filling in sample type information
UNKNOWNS:
Samples:
Name. The sample name is suggested automatically. The name consists

of an abbreviation of the sample and of running numbers, for example,
Un_0001, Un_0002, and so on. You can change the name, but the
running numbers after the abbreviation cannot be deleted.
If you select several plate wells for a sample type, you have to define the
order in which the wells are filled with individual samples and their possible
replicates:
Fill as...
56
Individual samples. All selected wells or cuvettes have individual

samples without replicates.
All replicates. All selected wells or cuvettes have replicates of one sample.
Horizontal samples with replicates. Individual samples are placed

horizontally and replicates are added below each individual sample.
(Not for cuvettes.)
Vertical samples with replicates. Individual samples are added vertically

and replicates are added next to each individual sample. (Not for
cuvettes.)
Layout
CALIBRATORS:
You have to define concentrations for calibrators:
Concentrations:
Single. When Single is selected, all the selected wells or cuvettes have
the same concentration.
Value. The concentration value.
Unit. The unit for the concentration.
57
Layout
58
Series. When Series is selected, a mathematically regularly-changing

concentration series is created.
Initial value. The initial concentration value.
Op. Defines the mathematical operator in the formula for the series.
The choices are multiplication (*), division (/), subtraction (-) and
addition (+). The concentrations increase or decrease from the initial
value by the steps defined in the Step by field.
Step by. The factor for the concentration series.
Unit. The unit for a concentration.
Layout
Values. When Values is selected, the concentration series is created by

entering the values one by one.
Add. Adds the selected value to the list.
Remove. Removes the value that you select from the list.
Clear. Clears all values from the list.
Unit. The unit for a concentration.
Use the arrow keys to move the order of the values.
59
Layout
Adding samples with the

Fill Wizard function
The Fill Wizard allows you to create a plate layout with more advanced
features. The Fill wizard is available only for defining plate layouts.
Click the Fill Wizard icon in the Layout view to open the Fill Wizard
dialog.
Select the desired Samples, Replicates, and Concentrations or Dilutions, and
click Add or Add and Close to confirm the selection.
The Fill Wizard dialog includes the following functions:

Samples:
60
Layout
Type. Select the type of sample from the list. The available types are:
Blank, Calibrator, Control, Empty and Unknown.
Name. The sample name is suggested automatically. The name consists

of an abbreviation of the sample and of running numbers, for example,
Un_0001, Un_0002, and so on. You can change the name, but the
running numbers after the abbreviation cannot be deleted.
Group. The name of the sample group. The default group is Assay.
Different group names can be used when several sets of samples must
be separated from each other. When samples are defined to different
groups, certain result calculations can be performed separately for each
group. For example, two different calibrator series with their own
unknown samples can be added to the same plate by defining the samples
to different groups (for example, Assay1 and Assay2). Therefore, the
correct calibrator group for each set of unknown samples can be selected
by the group name when calculating the concentrations with the
Quantitative curve fit step.
No. of samples/No. of unknowns. The number of samples of the

selected type.
Ask number of unknowns at start. Lets you define the layout without
having to know the number of unknown samples. When this option is
selected, you can define the starting point, filling directions for samples
and replicates, but not dilutions or specific blanks. The layout shows
the first unknown sample and its replicates, as well as an arrow depicting
the filling direction of the following unknowns. The number of samples
is asked when you start the session.
Primary filling direction. Selects the filling direction of the samples

in the plate layout.
Replicates:
No. of replicates. Enter the number of replicates for each sample of the
selected type.
Specific blanks. Select the number of specific blanks (individual sample

blanks) in use: none, one or two. Specific blanks can be used if different
samples have somewhat different blank characteristics and all samples
require individual blanks. Specific blanks do not have to be used if one
61
Layout
general blank can be used for all samples. For more information, see
Blank subtraction on page 97.
Primary filling direction. Selects the filling direction of the

replicates in the plate layout.
Concentrations or Dilutions:
Dilutions are available for Unknowns, and Concentrations for Controls and
Calibrators.
Series. When series is selected, a mathematically regularly-changing dilution
or concentration series is created for the selected wells.
Initial value. The initial concentration or dilution value.

Note A dilution value of 1:1 means that the sample is not diluted
(=1/1), a dilution of 1:2 means that the sample is diluted in half
(=1/2), a dilution of 1:3 is 1/3, and so on.
Op. Operator includes the mathematical symbols for multiplication (*),

division (/), subtraction (-) and addition (+). By selecting the operator,
the concentrations in the series increase or decrease from the initial value
by the steps defined in the Step by field.
Step by. The factor for the concentration or dilution series.
No. of dilutions. The number of dilutions of the unknown sample.
Unit. The unit for the dilution or concentration.
Values. When values is selected, the concentration or dilution series is added

by entering the values one by one:
62
Layout
Add. Adds the selected value to the list.
Remove. Removes the value that you select from the list.
Clear. Clears all the values.
Unit. The unit for the dilution or concentration.
Current plate. Indicates the number of the plate and the total number
of the plates. You can change the plate by using the arrow keys.
The well from which the filling starts is marked with a red dot. You can
change the starting point by clicking another well.
Clear Selection. Clears the samples that you have selected.
Clear All. Clears all the samples from the layout.
Sample IDs:
63
Layout
Load. You can load a text file (.txt) containing the IDs of the unknown
samples. The unknowns will be named according to the IDs in the file.
The Load ID function is only available for Unknowns. Each line in the
text file represents one sample. No spaces are allowed and the sample
names must be separated by line breaks.
Clear. Clears all sample IDs from the list.
Remove. Removes individual sample IDs from the list.
Toolbar buttons:
Add. Adds the set sample information to the wells.
Add and Close. Adds the sample information to the wells and closes
the Fill Wizard.
Close. Closes the Fill Wizard.
When you have entered all sample information to the plate, click Close. If
all the samples did not fit onto one plate, the software adds new plates
automatically.
Example of adding a
concentration series
64
To create a vertically increasing concentration series 1, 10, 100, 1000,

10000 with two replicates for each concentration, make the following
selections in the Fill Wizard dialog:
Layout
Editing samples
Click Add. Five calibrators, with two replicates each, are added to the layout.
Editing samples
You can edit the properties of the samples in the layout. The calculations
will be updated according to the changes.
1.
In the Layout view, select the samples by painting them with the left
mouse button.
2.
Click the Edit... icon.
3.
In the Edit Samples dialog, you can change the Name, Type,
Concentration/Dilution, Unit or Group of a sample. You can edit only
the samples that you selected from the layout.
To edit samples one by one, click the property of a sample that

you want to edit, and then enter the new value.
Set Multiple. This function edits all the selected samples at once.
Select a property (Name, Type, Unit or Group), and enter the new
value in the field. Click Set to set the new value.
4.
Click OK to save the changes and Cancel to cancel them.
65
Layout
Deleting a plate
Clearing the layout

To clear samples from the layout, first paint the samples with the left mouse
button, and then click the Delete icon.
Copying a sample
To copy a sample:
1.
Click a sample that you want to copy and click the Copy icon.
2.
Click the well or cuvette to which you want to copy the sample, and
click Paste. The copied sample becomes a new replicate of the sample.
To copy more than one sample, select the same number of wells or
cuvettes to which to paste the samples as you have samples to copy.
Adding a new plate

You can add several plates to the layout. However, you cannot add plates
to an executed session.
Click New Plate to add a new plate to the layout.
Renaming a plate
To rename a plate:
1.
Click the tab of the plate that you want to rename, and select Rename
Plate.
2.
Enter a new name for the plate.
Deleting a plate
You can only delete one plate at a time from the plate layout. The last plate
cannot be deleted.
66
Layout
Printing the current layout
To delete a plate:
1.
Click the tab of the plate that you want to delete, and select Delete
Plate from the action panel.
2.
The software asks you to confirm the deletion. Click Yes to delete the
plate.
Viewing the original

layout
As the layout can be edited after the measurement, the Show Original
function enables you to view the original layout that was created before the
measurement.
1.
After you click Show Original, the original layout of the executed
session opens.
2.
You can print or export the original layout:
Printing the current

layout
Print. Prints the original layout with the printer that you
have set as default on your computer.
Export. Exports the original layout from the SkanIt Software
database as a Microsoft Excel file (*.xls), an Adobe Acrobat Portable
Document Format file (*.pdf) or a text file (*.txt) file that you can
save on your computer.
After selecting Preview, a dialog showing the layout opens and includes the
Print and Export buttons. For more information about them, see Viewing
the original layout on page 67.
67
Layout
Printing the current layout
68
Chapter 7
Protocols
This chapter describes how you can create and edit a protocol.
For more information on the content and use of protocol steps, see
Chapter 8: Step Parameters.
A protocol contains all the information that is required by the instrument
to perform the desired functions. The information includes the protocol
steps and their parameters, so that the instrument can determine the actual
plate movements and the measurement procedure. The protocol steps tell
the instrument which functions are required, and in which order the steps
are to be performed.
Defining a protocol
After you have created a new session, you can open the Protocol view to
create a protocol. Click the Protocol tab. A blank protocol appears showing
the Protocol Properties.
The Protocol Properties includes the Protocol description box into which you
can add a description, if you wish. You can then continue to add protocol
steps.
69
Protocols
Defining a protocol
After the session has been run, you cannot edit the protocol, unless you first
create a new session. To avoid this, you can save the session before it is run.
A session that is saved before execution can be edited freely.
Adding new protocol steps
To add steps to a protocol, click the desired step button on the action panel
or right-click on the Protocol steps tree and select the step from the menu.
Add steps to the Protocol Steps tree in the order in which you want them to
be executed. A new step appears automatically after the last step in the steps
tree. You can also rearrange the order of the steps by using the arrow keys
in the Protocol Steps toolbar.
The step parameters are described in Chapter 8: Step Parameters.
70
Protocols
Defining a protocol
Renaming a protocol step

To rename a protocol step:
1.
Select the step that you want to rename in the Protocol Steps tree and
click the Rename icon on the toolbar, or right-click and select Rename
from the context menu.
2.
Enter a new name for the protocol step and press Enter. The name
must not include any space characters.
Deleting protocol steps

If you delete a step that has substeps, the substeps are deleted too.
1.
Select the protocol step that you want to delete.
2.
Click the Delete icon, or right-click and select Delete from the context
menu.
3.
Click OK to confirm the deletion.
71
Protocols
Defining a protocol
72
Chapter 8
Step Parameters
This chapter describes the parameters of the protocol steps available in
SkanIt Software for Multiskan GO.
Note The Area Definition, Shake, and Plate In and Plate Out
steps are not available for cuvette measurements.
Photometric
measurement
The Photometric Measurement step is used to measure absorbance (Abs).
The Photometric Measurement step includes the following parameters:
Measurement type:
Single wavelength: Absorbance measurement at one wavelength.
Multiple wavelength: Absorbance measurement at up to five

wavelengths. The wavelengths are measured one after another from
one well before moving to the next well.
Measurement Mode:
Fast: Speed-optimized mode in which the measurement head moves

over the wells without stopping.
Precision: Precision-optimized mode in which the measurement

head stops over each measured well for maximum precision.
73
Step Parameters
Spectrum measurement
Spectrum
measurement
Wavelength(s). Set the measurement wavelength for a single wavelength

measurement and enter up to five wavelengths for a multiple wavelength
measurement. For multiple wavelength measurements, use the arrow
button to add wavelengths to the set and the cross button to remove
the selected wavelength from the set.
Step duration. If necessary, set the total time for the measurement step.
After the measurement is performed, SkanIt Software waits until the
entered duration is up before proceeding to the next step. Step duration
can be used to accurately time two protocol steps.
Use pathlength correction. Tick to use pathlength correction to

normalize microplate measurement results to correspond to a 10 mm
pathlength. You must also add a pathlength correction result step and
have or create a suitable K-factor. See Chapter 12: Pathlength
Correction.
The photometric spectrum measurement performs an absorbance

measurement over a user-defined wavelength range.
The Photometric Spectrum Scanning step has the following parameters:
74
Step Parameters
Kinetic Loop
Scanning wavelengths. Set the Start and End wavelengths (2001000

nm), and the Step size which defines the measurement resolution.
Step duration. If necessary, set the total time for the measurement step.
After the measurement is performed, SkanIt Software waits until the
entered duration is up before proceeding to the next step. Step duration
can be used to accurately time two protocol steps.
Measurement Mode:
Fast: Speed-optimized mode in which the scanning optics move

over the wavelength range without stopping.
Precision: Precision-optimized mode in which the scanning optics

stop at each wavelength for maximum precision.
Kinetic Loop
The Kinetic Loop step is used for kinetic measurements. The kinetic loop
can only be used in conjunction with the photometric measurement step.
The Kinetic Loop step includes the following parameters:
Readings. The number of times the kinetic loop is executed, that is,
the number of measurements per well per each wavelength. The range
is from 2 to 1000.
Interval [hh:mm:ss]. The time between the starting times of two

consecutive loops. If you choose the default interval (00:00:00) or a
shorter interval than the minimum reading time of the instrument, the
instrument measures as fast as possible.
75
Step Parameters
Area definition
Area definition
The Area Definition step is used when only a part of the defined wells in
the layout are used for a specific measurement step. The area definition
applies only to the steps that are placed as substeps to the area definition
step.
Area Definition is not available for cuvette measurements.
Note Area definition is unnecessary, if all the defined wells of the
plate layout are to be measured.
To define an area on the plate, in the Area Definition dialog, paint the desired
wells with the mouse. The selected wells are marked in orange.
76
Step Parameters
Pause
Pause
The Pause step is used for stopping the execution of a session for a certain
period. A message is displayed during the pause if a message has been entered
in the step parameters. The instrument continues to execute the session
after the defined pause time expires or due to user action.
The Pause step includes the following parameters:
Waiting time [hh:mm:ss]. Enter the waiting time.
Continuation options. Select the condition for continuing the session

execution. When Time expired is selected, the execution of the protocol
continues after the waiting time has expired. When Time expired or user
action is selected, the protocol continues after the waiting time has
expired or due to some user action. When User action is selected, the
77
Step Parameters
Shake
Continue button appears on the screen during the pause. When you
select this option, no Waiting time can be set.
Message. You can type a pause message that appears on the screen during
the Pause step.
Shake
The Shake step is used for shaking the microplate in order to mix the
samples.
Shake is not available for cuvette measurements.
The Shake step includes the following parameters:
78
Duration [hh:mm:ss]. The total shaking time. The maximum shaking

time is five hours.
Shaking type.
Continuous. Shaking is constant during the shaking time.
Interval. Shaking is intermittent which means that shaking and

waiting times alternate.
Step Parameters
Shake
Background. The instrument shakes the samples slowly during the

protocol's idle periods. For example, during the interval times of a
kinetic measurement. Place the Shake step before the kinetic loop
step in the protocol.
The Interval and Background shaking types also include the following
settings:
Shaking On [hh:mm:ss]. If you want the shaking to be intermittent,

enter here how long each shaking period lasts. If you want to have
a constant shake, then set the Shaking On time to equal the duration
of the shake.
Shaking Off [hh:mm:ss]. Enter how long the pause is between

shaking periods in intermittent shaking.
End with shaking On. Ends the step with shaking on.
End with shaking Off. Ends the step with shaking off.
Speed. You can choose from three different shaking speeds: low, medium
and high. This option is not available, if you choose Background as the
shaking type. Background shake is fixed to slow speed.
Note When high shaking speed is selected, ensure that the used
well volume and liquid properties do not cause spilling.
79
Step Parameters
Incubate
Incubate
The Incubate step is used to control the temperature of the incubator.
The Incubate step includes the following parameters:
Incubation time [hh:mm:ss]. The duration of the incubation.
Temperature [C]. The target temperature. The available temperature

range is from ambient + 4 to 45C. Temperatures below ambient + 4C
cannot be reached.
Leave instrument at this temperature. When this option is selected,

the incubation temperature is kept during the whole session after the
incubation has ended, or until the next incubation step is set to change
the temperature.
Wait until instrument has reached the target temperature. When

this option is selected, the incubation time is only counted from the
time that the instrument has reached the target temperature. If this
option is not selected, also the time that it takes for the instrument to
reach the target temperature is included.
Note It is possible to set the instrument temperature to be kept

at a defined temperature at all times when the instrument is
connected to SkanIt software. To use this setting, go to Home >
Settings > Instruments > Startup Temperature. See Instrument
80
Step Parameters
Plate In / Plate Out
Settings on page 172). You can also click the Set Temperature
icon directly in the Home view, see Home view on page 35.
Note The samples in the microplate usually reach the target
temperature much later than the instrument. For example, for a
96-well plate with 200 l water/well, the liquid warm-up time from
25C to 37C takes about 40 minutes.

The Plate In and Plate Out steps are used to run the plate carrier into and
out of the instrument's measurement chamber.
Plate In or Plate Out are not available for cuvette measurements.
81
Step Parameters
82
Chapter 9
Starting a Session
The measurement can be started after the protocol is defined. If the layout
is left empty, the software asks whether to fill the layout with unknowns.
Calculations and reports can be added before or after the measurement.
Starting a plate
session
To start a plate session:

1.
Click the Start icon on the action panel.
2.
Accept the default name for the session or enter a new name in the
Name for the session field and click OK. This name is given to the
session that has been run. You can also change the name of the plate
at this stage by selecting the Change plate name check box and, for
example, by scanning the barcode of the plate into the plate name field.
The Execution view opens and the measurement starts. The Execution
dialog shows the plate layout that is measured.
83
Starting a Session
Starting a plate session
The dialog displays measurement information as the measurement

proceeds. The well that is being measured is framed in red. The
measurement values are displayed in each well. In kinetic and spectral
measurements, the measurement curves are shown in each well instead
of values. Untick Show curves to disable real-time curve display on
slower computers, in which the curve display can slow down the entire
measurement.
3.
Abort. If you want to abort the execution in the middle of the

measurement, click the Abort icon on the action panel.
If you have more than one plate in the plate layout, the software asks
you to insert the next plate into the instrument after measuring the
previous plate.
After you have inserted the plate, click OK. The measurement resumes.
84
Starting a Session
Starting a cuvette session
The measurement data is automatically saved in the database as the

measurement proceeds.
4.
Starting a cuvette
session
After the measurement session is complete, the Results view opens to

show the results.
Cuvette measurement sessions differ slightly from plate sessions by requiring

manual zeroing before the measurement. Zeroing is necessary to determine
the instrument's zero absorbance level (0.000 Abs). Zeroing is automatic
for plate measurements.
SkanIt Software checks the connected instrument for a valid zero before
session execution. If the zero is not valid, you are prompted to zero the
instrument.
Zeroing can be performed in the following ways:
Recommended method:
1.
Zero instrument without a cuvette in the cuvette port to set the

instrument's baseline to zero.
2.
Measure all samples, including the blank sample. This records the
blank sample absorbance together with the sample results, and
reveals possible contamination or interference in the assay blank
sample.
85
Starting a Session
Starting a cuvette session
3.
Subtract the blank sample absorbance from the other sample results
by adding the Blank subtraction step to the results.
Second alternative:
1.
Zero instrument with the assay blank cuvette to set the level of the
blank sample to zero.
2.
Measure all the samples. With this method, possible contamination

of the blank sample is not apparent, which can lead to incorrect
blank level subtraction.
Note Never zero the instrument with an empty cuvette as this

will lead to incorrect zero levels.
To start a cuvette session:
1.
Click the Start icon on the action panel.
2.
Accept the default session name or enter a new name.
Tick the Instrument zero box to zero the instrument, if necessary. The
box is already checked, if zeroing is required, that is, if the zero is not
valid for the measurement.
Click OK to start the measurement.
The Execution view opens to display measurement progress.
Click Abort on the action panel to cancel the measurement, if
necessary.
86
3.
The software prompts you to swap cuvettes for sessions with several
cuvettes. Press OK to resume measurement after swapping a cuvette.
4.
After the measurement session is complete, the Results view opens to

show the results.
Chapter 10
Results
This chapter describes how you can view the results after the measurement.
Measurement results
After the measurement has finished, the Results view shows the measurement
results. The measurement result steps are named after the protocol
measurement steps.
You can view the measurement data as a list or as a table. To view the results,
click the measurement step in the Results tree view and select the table or
list view from the tabs.
Note An absorbance value of exactly 6 means that the
measurement has reached the saturation level. In the table view,
the result is crossed over, and in the list view, it has a red
background.
Calculation results
In the Results view, you can define calculations and view their results as a
list or as a table and certain calculations also as a graph. To view the results,
click the step in the Results tree view and select the view type from the tabs.
For more information on defining individual calculation steps, see

Chapter 11: Calculations.
87
Results
Viewing kinetic curves or spectra
Viewing kinetic curves

or spectra
Results of kinetic or spectral measurements are shown as curves in the table

view. You can enlarge a single curve or several curves and view them in a
separate window.
1.
In the Results view, select a kinetic or spectral measurement step.

Kinetic or spectral calculations that produce data as curves, can be
viewed as curves.
2.
Click the Table tab to see the results in table format.
3.
Click a well to select a single well or, to select several wells, hold down
the Ctrl key as you click the wells or drag the mouse over the wells
you want to select.
4.
Right-click and select Show Graph. The Curve dialog opens showing,
for example, curves for several wells.
Tip Right-click the image to copy it to the clipboard as a bitmap

image for use outside SkanIt Software.
88
Results
Arranging a list
Disabling values from

measurement data
You can disable samples in the measurement data list view. The disabled
item is not used in calculations.
To disable an item, right-click the row, and then select Disable <item>
from the menu. The disabled rows are marked with a strikethrough line.
In the context menu:
Row disables the selected row.
Replicate disables the selected replicate.
Sample disables the selected sample and its replicates.
Reading disables the selected reading of all the samples in kinetic

measurements.
Wavelength disables the selected wavelength of all the samples.
To enable a disabled item, right-click the row and click Enable <item>.
Arranging a list
The list in the Results view can be arranged in several ways.

Changing the order of list items
Click a title in the title bar to sort the items in alphabetical or numerical
order. The black arrowhead indicates the sorting order which can be
ascending or descending .
89
Results
Arranging a list
Limiting the number of list items
Click the arrowhead beside a title in the title bar to open the sorting
menu. Only the items that match the criteria are displayed.
When you select Custom, the Custom AutoFilter dialog opens.
Enter the filtering criteria in the text fields on the right and select how
they are interpreted from the left.
Changing the column order
You can change the order of the columns in the list by dragging a column
header to the new location.
Grouping the list by a column
90
Drag the column header of your choice to the gray area above the list.
Results
Arranging a list
The rows in the list are grouped according to the items in the selected
column. For example, if you select the column Type as in the figure,
the rows are grouped according to sample types that appear in the plate
layout. In the example above, all sample types are present in the plate
layout. You can view and hide the items and rows that belong to each
sample type by clicking the plus and minus buttons beside the item.
You can also select multiple columns to group the items. The new
column appears in hierarchical order below the previously selected
column.
Removing a column from the list
Drag the column header to any location over the result list.
Drop the header when a cross mark appears.
The column is removed from the list.
91
Results
Exporting measurement and calculation data
Click Reset to return the list to the original form.
Modifications of the list are saved with the session and appear in the list
when you open the session again.
Exporting
measurement and
calculation data
Exporting manually
You can export measurement and calculation data for use outside SkanIt
Software either automatically each time after a session is executed or
manually afterwards.
You can export the measurement and calculation data manually either by
opening it in Microsoft Excel format or by exporting it to another file format.
Open in Excel
You can open the measurement or calculation data of a particular result step
in Microsoft Excel (*.xls) or in another spreadsheet application that is
associated with the *.xls extension. SkanIt Software supports Microsoft Excel
2003 and 2007.
92
1.
In the Results tree view, select the step that contains the data you want
to open.
2.
Click the Table or List tab to select the format in which the data is to
be displayed. When you select List, the exported list retains the
selections you made in the list view, including the sorting order and
filtering. If you select the table format, only the measurement or
calculated data and the sample names are exported.
3.
Click Open in Excel. The file is opened in Microsoft Excel or another

associated application. The data can then be edited and the file can be
saved manually.
Results
Exporting data
Alternatively, you can use the Export function to export the data of a
particular measurement or calculation step to different file formats (*.txt,*.xls
or *.html).
1.
In the Results tree view, select the step that contains the data you want
to save.
2.
Click the Table or List tab to select the format in which the data is to
be exported. The exported list retains the selections you made in the
list view, including the sorting order and filtering. If you select the
table format, only the measurement data is exported.
3.
Click Export.
4.
In the Save As dialog, select the folder in which the file will be saved.
The software suggests a name automatically, for example,
Abs_550nm-list. You can accept the name or enter a new name. The
files in Table format can only be saved as text files (*.txt). The files in
List format can be saved as text files (*.txt), Microsoft Excel files (*.xls)
or HTML files (*.html).
5.
Click Save.
Exporting automatically
To export data from a particular measurement or calculation step each time
a session is executed, add the Automatic Save step to the Results tree before
starting the measurement. To create a more detailed report including data
from several result steps, you can use the Report view as described in
Measurement and calculation reports on page 151.
To export data automatically:
1.
In the Results tree view, select the step that includes the required data.
2.
On the Export action panel, click Automatic Save. The Automatic Save
step is added to the Results tree as a substep of the selected step, and
the parameters tab is displayed.
93
Results
Format. The format in which the data will be laid out in the file: a list
or a table.
Save mode. Defines how the data is handled when the results are saved
after the measurement:
Append. The data is added to the end of the existing file.
Overwrite. The data in the existing file is overwritten.
Unique name. The file name is extended with a unique date and
time string. Existing data is not overwritten, since a new file is
created each time.
File name. Use Browse to enter a name for the file and to select the
target folder. The file can be saved as a text file (*.txt).
After selecting the folder, you can use {abc} to add a placeholder to the
file name of file path. Place your cursor in the File name field at the
position where you want to add the placeholder. The placeholder is
replaced with a current value when the file is created.
The format of the timestamp placeholder is yyyymmdd-hhmmss.
For example, to create a folder for each year: add the year placeholder
to the file path and separate it with the backslash (\) character.
The plate id placeholder always uses the plate name of the first plate in
naming the file or folder. It is mainly intended to be used with the
Automation Interface when only one plate is used.
Presenting results as a
report
94
You can create a detailed measurement and calculation data report in the
Reports view. For more information, see Chapter 13: Reports.
Chapter 11
Calculations
This chapter describes how calculations are added to and deleted from the
sessions. It also provides detailed information on the use and settings of the
calculation parameters.
Adding calculations
In the Results view, you can add and define calculations before or after
executing the measurement.
To add calculations:
1.
Select from the Results tree the result step to which you want to add
calculations. The calculation step has to be placed under the result step
that contains the required source data.
2.
Click the desired icon on the action panel or right-click in the Results
tree view, and select the calculation from the context menu.
Each added calculation appears after the selected item in the tree view.
95
Calculations
Note on sample names
If you want to perform several independent calculations for the same

result step, select the corresponding step from the Results tree view
each time before adding the calculation.
If a calculation step cannot be performed with a certain result step, its
icon is disabled.
3.
Define calculation parameters for the calculation step, and click Table
or List to view the results.
Each calculation step and its parameters are described in detail later
in this chapter.
The software checks the validity of the calculation and the previous
calculation step. If the calculation cannot be performed with the parameters
that have been set, the calculation step is displayed in red.
Deleting calculations
Note If you delete a calculation that has other calculations added
as substeps, those calculations will also be deleted.
You can remove calculations in several ways. Select a calculation from the
Results tree view and perform one of the steps below:
Note on sample names
Right-click it and select Delete from the menu.
Press Delete on your keyboard.
Click the Delete icon in the Results toolbar.
Some calculations require you to select the appropriate samples or replicates

for use in the calculation. In these cases, for example, the following
designations refer to sample averages or replicates as follows:
Ctrl_0001 refers to the measurement average for sample Ctrl_0001.
96
Calculations
Blank subtraction
Ctrl_0001 1/2 refers to the first replicate of sample Ctrl_0001.

Ctrl_0001 2/2 refers to the second replicate of sample Ctrl_0001.
Some calculation steps show samples and their replicates separately and
some show only the average.
Blank subtraction
Blank subtraction is used for subtracting the average blank value from all
the wells in the layout. If samples have specific blanks, these blanks are
subtracted from their own samples and no normal blank average is subtracted
from samples with specific blanks.
For blank subtraction, you can define the following parameters:
Blank type:
Examples of blank
subtraction
Average. The average of all nonspecific blanks in a group is calculated

and subtracted from all the samples in the same group (blanks,
calibrators, controls and unknowns). The blanks can be on the same
plate or on different plates, but they are all in the same group and they
are subtracted from all the samples belonging to the same group. See
Example 11-1, Average blank subtraction. Specific blanks are
subtracted from their own samples.
Plate blank. The average of all nonspecific blanks available on each

plate in each group is calculated separately. The average of the blanks
from each plate in each group is then subtracted from the samples on
each specific plate in the same group only. See Example 11-2, Plate
blank subtraction. Specific blanks are subtracted from their own
samples.
In this example, the measurement session consists of two plates. Blanks are
positioned in the first well on both plates:
97
Calculations
Blank subtraction
Example 11-1 Average blank subtraction

The blank average is: (0.010 + 0.020)/2 = 0.015
The blank subtracted data would then be (with an accuracy of three
decimals):
Example 11-2 Plate blank subtraction

The blank subtracted results calculated from the same measurement data
would be (with an accuracy of two decimals):
Blank subtraction in kinetic

measurements
98
You can use all modes of blanking in kinetic measurements as well. Normally
this means that the kinetic data is first reduced to rates, peak maximums,
integrals, and so on by using kinetic calculations (see Kinetics on page 106),
after which the blank subtraction is performed on the reduced data.
Calculations
Basic statistics
Consider, for example, a kinetic measurement with a plate containing one

blank, the rest being other samples, and an average rate calculation with
linear regression. The rate is calculated separately for all samples. The reduced
rate is then calculated by subtracting the rate of the blank sample from the
rates of the other samples.
Alternatively, you may specify point-wise kinetic blank reduction directly
from measurement data. In this mode, the raw blank signal at each point
in time is subtracted from raw sample signals at that specific time. This
produces reduced curves for all samples. Only then is the kinetic processor
applied to the reduced curves to determine the reduced rate, and so on.
Basic statistics
The basic statistics calculates the average (Avg), the standard deviation (SD)
and the coefficient of variation (CV%) of the replicates.
For basic statistics, you can define the following parameters:
Statistics Type:
Replicate. Calculates the statistics per dilution without combining data

from different dilutions of the same sample. It can be used to calculate
the statistics within each dilution in a dilution series.
Sample. Calculates the statistics per sample while combining data from
different dilutions and replicates into a single value. It can be used to
calculate the statistics within each sample in a dilution series.
99
Calculations
Basic statistics
If a dilution series has not been defined, both settings produce the same
result.
Dilutions:
With dilution factors. Results are first multiplied with the dilution
factor before calculating the average.
Without dilution factors. Dilution factors are not taken into account.
This option is not available if Sample is selected as the statistics type.
The standard deviation is calculated using the following formula:
In the formula, x is the measured value from a single measurement point,

m is the average of the measured replicate values, and n is the number of
replicates.
The average is displayed in both the table and list views and the SD and
CV% only in the list view.
100
Calculations
Pathlength correction
Pathlength correction is used to normalize absorbance measurement results
to correspond to a 10 mm pathlength. This makes it possible to calculate
sample concentrations from the absorbance values by using known
concentration factors or extinction coefficient values.
The use of pathlength correction in a microplate measurement requires a
suitable mathematical K-factor, which depends on the microplate and buffer
solution used in the measurement.
For more information on pathlength correction, see Chapter 12: Pathlength
Correction.
For pathlength correction, you can define the following parameters:
Wavelength. Select the wavelength of the measurement data for which

the pathlength correction is to be performed.
K-Factor or Cuvette pathlength. Select the K-factor in a microplate

measurement or the enter the actual cuvette pathlength in a cuvette
measurement.
Calculate concentrations: Tick to calculate concentrations.
Concentration equation. Select the appropriate concentration

equation and set the value for the coefficient. In the equation, C
refers to the concentration, A refers to the absorbance, and x and
refer to extinction coefficient.
101
Calculations
Spectral analysis
Use in subcalculations. Defines the data source for calculations

placed as substeps to the pathlength correction result step. Select
either the corrected absorbance values or calculated concentrations.
Ignore dilutions. Defines whether the dilution factors of the

unknown samples are taken into account in the concentration
calculation.
Spectral analysis
Spectral analysis is used to handle photometric spectrum scanning
measurement data. The wavelength range for spectral analysis is 2001000
nm.
Select the desired spectral analysis calculation type and define its options.
View the results by selecting the table or list view.
Spectral peak search
Spectral peak search locates the wavelengths with peak values with an
absorbance above the threshold value. You can set the start and end
wavelengths for the peak search.
A peak is defined by comparing the window count of adjacent measurement
values to a possible peak value. A true peak value is declared, if the
measurement values of the window count before and after the possible peak
are smaller.
Spectral peak search options:
102
Wavelengths. The start and end wavelengths for the peak search.
Calculations
Spectral analysis
Threshold. The intensity threshold for the peak search. Only values
above the threshold are considered.
Window. The number of adjacent measurements considered when

determining a peak value.
Spectral peak search with window count 1:
Spectral peak search with window count 2:
103
Calculations
Spectral analysis
Spectral maximum
Spectral maximum returns the maximum measured absorbance value in

each well.
Spectral maximum options:
Spectral minimum
Wavelengths. The start and end wavelengths for the maximum

absorbance search.
Threshold. The intensity threshold for the maximum absorbance search.

Only values above the threshold are considered.
Spectral minimum returns the minimum measured absorbance value in

each well.
Spectral minimum options:
Ratio within spectrum
104
Wavelengths. The start and end wavelengths for the minimum

absorbance search.
Threshold. The intensity threshold for the minimum absorbance search.

Only values above the threshold are considered.
Ratio within spectrum calculates the absorbance ratio between two

wavelengths in the same spectrum.
Calculations
Spectral analysis
Enter the wavelength values (1 and 2) that correspond to absorbances AbsWl1

and AbsWl2 in the following ratio equation:
Ratio = AbsWl1 / AbsWl2
Ratio within spectrum options:
Ratio between spectra
Wavelength 1. The wavelength of absorbance AbsWl1.
Wavelength 2. The wavelength of absorbance AbsWl2.
Ratio between spectra calculates a ratio curve over a wavelength range. All
the sample absorbances are divided by the reference sample absorbances of
the same wavelengths. The ratio between the spectra can be used, for
example, to calculate the signal to blank spectra.
The calculation uses the following formulas:
Ratio = SpectrumSample / SpectrumReference
Ratio between spectra options:
Select wavelength range
Wavelengths. The start and end wavelengths for the ratio calculation.
Group. Select the sample group.
Sample. Select the reference sample to be used as the base of the ratio
calculation. The spectra of all samples are divided with the spectrum of
this sample.
Select wavelength range allows you to select part of the measured spectrum
for viewing.
Enter the start and end wavelengths for the range.
Select single wavelength
Select single wavelength allows you to select a single wavelength for viewing.
Enter the desired wavelength.
105
Calculations
Kinetics
Kinetics
Kinetic calculations are used to reduce data from kinetic measurements.
For kinetic calculations, you can define the following parameters:
Average rate
Average rate is also known as normal rate. The average kinetic rate (slope
of the absorbance (Abs) vs. time curve) will be calculated by linear regression
(linear least squares method or LLS) using all the measurement readings
within the selected data and time range.
For average rate, you can define the following parameters:
106
Calculations
Kinetics
Maximum rate
Kinetic rate. Select to view the results either per second (s) or per minute
(min).
Ignore first (n) readings. Ignores a defined number of points (readings),

counted from the first reading.
Ignore last (n) readings. Ignores a defined number of points (readings),

counted from the last reading.
If the maximum rate is selected, the software searches the data for the
maximum rate that is found in each well. To obtain the maximum rate, a
series of linear curve fits will be performed for different segments of the
measurement value or absorbance vs. time curve (Figure 11-1). The first
segment starts at the first data point within the selected time and
measurement range, the second segment starts at the second data point, and
so on, until all the data points have been analyzed. All the rate calculations
are evaluated to determine the maximum rate. In other words, the LLS fit
of m span points are sequentially fitted through each of the n data points.
There will be n - m + 1 curves produced from this. You can specify the
number of data points in a segment with the Window (2...100) setting.
Figure 11-1. Determining the maximum rate with window value 2
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Calculations
Kinetics
For maximum rate, you can define the following parameters:
108
Reaction. Define whether the reaction is supposed to produce increasing

or decreasing signal levels. There are three options for this setting:
Undefined (default). The reaction can be increasing, decreasing or

both (for example, first increasing and then decreasing, that is,
peaking). The software does not produce any warnings in either
case. It searches for the absolute maximum rate. If the highest
absolute rate value is increasing, it is displayed as a positive value.
If the maximum rate is decreasing, it will be presented with the
prefix -.
Increasing. The software searches for the maximum increasing rate.

The rate is displayed per second or per minute. If no increasing rate
is found, the result is NaN (not a number).
Decreasing. The software searches for the maximum decreasing

rate. The rate is displayed per second or per minute. If no decreasing
rate is found, the result is NaN (not a number).
Kinetic rate. You can view the results either per second (s) or per minute
(min).


Window (2...100). Select the number of consecutive readings to use

for evaluation. The highest reaction rate for each well is calculated by
Calculations
Kinetics
using a sliding window. The window defines how many measurement

points are included in the measurement calculations. The size of this
window is given in the Window parameter box. For example, if the
number of measurements is ten and the Window parameter is three,
the system will calculate the first rate by using measurements 1 to 3, the
second rate by using measurements 2 to 4, and so on up to measurements
8 to 10. The maximum rate will be the maximum value among these
calculated rates.
Time to maximum rate
The time to maximum rate is calculated similarly to the maximum rate, but
the result is reported as the time in seconds from the first reading to the
middle point of the sliding window where the maximum rate occurs. See
Figure 11-2.
Figure 11-2. Determining the time to maximum rate
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Calculations
Kinetics
For time to maximum rate, you can define the following parameters:
110
Reaction. Defines whether the reaction is supposed to produce

increasing or decreasing signal levels. There are three options for this
setting (see Maximum rate on page 107):
Undefined. Searches for the absolute maximum rate and returns

the corresponding time in seconds.
Increasing. Searches for the maximum increasing rate and returns

the corresponding time in seconds. If no increasing rate is found,
the result is NaN (not a number).
Decreasing. Searches for the maximum decreasing rate and returns

the corresponding time in seconds. If no decreasing rate is found,
the result is NaN (not a number).


Window (2...100). The number of consecutive readings to use for

evaluation. For more information on this parameter, see Maximum
rate on page 107.
Calculations
Kinetics
Time to maximum rate / 2
The time to maximum rate / 2 averages the time that is taken to reach half
of the maximum rate. The maximum rate is determined as it is described
in Time to maximum rate on page 109. This rate is halved and the data
is scanned to determine the first rate, which is equal or exceeds this rate.
The result is the time when this rate occurs.
For information on the available parameters, see Time to maximum rate
on page 109.
Time to change
The time to change parameter is used for calculating the time that is required
to reach a defined change in the signal (in each well).
First define the baseline value by entering the number of readings from the
beginning. The baseline value is the average of the results of the given
baseline count from the beginning or end of the results. Then select whether
the change from the baseline value is evaluated as a relative (%) or an
absolute value and define that percentage or value. This change is then added
to the baseline value to create a required change value. The measurements
are then compared to the baseline value by using a sliding window of
measurement values. The result is the exact interpolated time at which the
given change occurs. The required change is searched by starting from the
first measurement point (reading) following the last baseline reading.
For the time to change, you can define the following parameters:
Ignore readings:
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Calculations
Kinetics
From beginning. Ignores a defined number of points (readings), counted

from the first reading.
From end. Ignores a defined number of points (readings), counted from

the last reading.
Window (1...100). The number of consecutive readings to use for

evaluation. For more information on this parameter, see Maximum
rate on page 107.
Baseline points:
The baseline parameter is the number of initial readings that are used for
the baseline calculation.
From beginning. The number of initial readings is calculated from the

beginning of the measurement.
From end. The number of initial readings is calculated from the end
of the measurement.
Readings (0...100). The number of readings used for the baseline

calculation. The software calculates the average value of the readings
selected for the baseline. The average equals the baseline value. If From
end is selected, the change is extrapolated starting from the end of the
measurement. The baseline can also be zero, in which case the
comparison is made against zero.
Change (Absolute or Relative [%] ). The change from the baseline as a

relative or absolute change. The change in signal is specified in the Change
parameter and is compared to the baseline. The change can be positive or
negative. The value is positive when the signal increases from the baseline.
The value is negative when the signal decreases from the baseline. The
Window parameter averages the number of consecutive measurements which
should reach the change before the result is accepted.
Maximum of well (Peak)
112
The maximum of well calculation is used to search for the maximum

measurement value in each well. The maximum value can be searched from
a reading range by ignoring kinetic readings from the beginning or end with
the following parameters:
Calculations
Kinetics
Maximum - Minimum
(Change)


The minimum measurement value of each well is subtracted from the

maximum measurement value of each well.
For information on the available parameters, see Maximum of well (Peak)
on page 112.
Time to maximum (Peak)
The time to maximum is used to calculate the time elapsed before the
maximum measurement signal in each well (peak) is reached.
on page 112.
Time to maximum (Peak) /

2
The time to maximum / 2 equals the time to reach half of the maximum
value.
on page 112.
Select reading
Select reading is used to select a specific kinetic measurement point (reading).

You can define the following setting:
Ignore readings
Reading (-1000...1000). The number of the kinetic measurement

reading. With Multiskan GO, negative readings are not applicable.
Ignore readings is used to dismiss a selected number of readings from the

beginning or end of the measurement.
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Calculations
Kinetics

on page 112.
Integral
The integral calculation estimates the area under the measurement curve
(Figure 11-3). The range of readings can be limited with the Ignore readings
selection.
Figure 11-3. Integral calculation

on page 112.
Sum
Sum calculates the sum of the selected range of readings. The range of
readings can be limited with the Ignore readings selection.
In the example below (Figure 11-4), the kinetic processor sum gives the
result
(0.00 + 0.30 + 0.50 + 0.60 + 0.65 + 0.67) Abs = 2.72 Abs.
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Calculations
Kinetics
Figure 11-4. Example of an absorbance curve

on page 112.
Average value
Average value is used to calculate the average value of all kinetic readings.
Figure 11-5. Determining the average value of a kinetic measurement

on page 112.
Baseline subtraction
Baseline subtraction is used to transform the measured values to start from

0 by removing the measured baseline before the actual reaction. It subtracts
the average of a defined number of readings from the beginning or the end
of all other readings.
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Calculations
Kinetics
Figure 11-6. Determining the baseline subtracted kinetic curve

For baseline subtraction, you can define the following parameters:


Baseline:
The baseline parameter is the number of initial readings that are used for
the baseline calculation.
116
Readings (0...100). The number of readings used for the baseline

calculation. The software calculates the average value of the readings
selected for the baseline. The average equals the baseline value. If last is
selected, the change is extrapolated starting from the end of the
Calculations
Precalculation
measurement. The baseline can also be zero, in which case the

comparison will be made against zero.
First. The number of initial readings are calculated from the beginning
(first) of the measurement.
Last. The number of initial readings are calculated form the end (last)
of the measurement.
Precalculation
Precalculation offers a possibility to carry out simple calculations, such as
subtractions, ratios and multiplications. The step is automatically added to
the root level in the Results tree view. Therefore, both measurement and
calculated data can be used as a data source. The step can be used, for
example, in dual-wavelength measurements, in the subtraction of the
reference wavelength data from the assay wavelength data.
Calculation type:
Difference (A-B). The result data of the second data source is subtracted
from the result data of the first data source.
Ratio (A/B). The result data of the first data source is divided by the
result data of the second data source.
Scale (A*x). The result data of one data source is multiplied by the
determined value.
Data sources:
A & B. Select the name of the first and second data sources.
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Calculations
Graph
A & X. Select the name of one data source and the value by which it is
multiplied.
In multiple wavelength measurements, select the wavelength of the source

data.
Merge data
The Merge data calculation is used to combine measurement data and
measurement times from separate measurement steps into one kinetic data
set. Data can be combined from both endpoint and kinetic measurements.
Select the measurements whose data you want to combine. The combined
data is shown as a kinetic curve for each well in the Table view and as a
kinetic data list in the List view. You can also perform calculations on the
combined data by using calculations that are available for kinetic
measurements.
Graph
You can create graphs, such as kinetic curves or spectra, from the
measurement results.
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Calculations
Graph
Graph title, X axis title and Y axis title. Enter titles for the graph and
the X and Y axes.
X axis. Select which data you want to present on the X axis: the samples,
the readings (in kinetic measurements), the measurement time or
wavelengths (in spectral measurements).
Well/sample label. You can display the names of the samples according
to the sample names or the well position. This option is not available
for readings.
Wells and Readings. Select which wells and readings to display on the
graph by selecting the check boxes in question.
To view the graph, click the Graph step in the tree view and select the
Graph tab from the main window area. An example of kinetic absorbance
curves is shown in Figure 11-7.
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Calculations
Graph
Figure 11-7. An example of a graph with photometric measurement results
Viewing results as a graph
In the Results view, select a calculation from the Results tree view and select
the Graph tab. The calculation results are shown as a graph. The graph is
only available for certain calculations.
To view more options on how the graph is displayed, right-click on the
graph area under the Graph tab to display the menu.
120
Toolbar. Shows the graph toolbar that includes all the items of the
menu.
Data Editor. Displays the data points below the graph.
Legend Box. Creates a legend for the curve.
Calculations
Graph
Gallery. Opens a menu including different graph types.
Color. Opens a menu including different colors that can be selected for
the curve.
Edit title. Gives a title to the graph.
Point Labels. Displays the value of the data points.
Font. Determines the font for displaying the data in the graph.
Properties. Opens a dialog in which you can define more precisely what
the graph looks like.
To view more options on how the text and labels are displayed, right-click
in the label area under the Graph tab to display the menu.
Text color. Selects the color used for the text.
Font. Determines the font for the label text.
Edit title. Changes the title.
Staggered. Staggers the label values for the graph.
Vertical Labels. Turns the labels vertically.
Grid. Shows a grid underneath the graph.
Interlaced. Interlaces the graph horizontally or vertically.
Properties. Opens a dialog in which you can define more precisely what
the graph looks like.
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Calculations
Quality control (QC)
The same options are also available in graphs with curve fit and effective
dose measurement results. For more information, see Quantitative curve
fit results on page 132 andEffective dose on page 134.

The quality control calculation is used to check the validity of the assay with
known control samples. You can create several quality control rules using
one Quality Control calculation step. The Quality Control step is placed
under the step containing the source data.
Note If you want to use the Average, SD or CV calculations in the
quality control rule, the Quality Control step is not placed under
the Basic Statistics step but under the step in which each replicate
is situated.
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Wavelength. In multi-wavelength measurements, select the wavelength

of the source data.
Add. Opens a menu in which you can select the item from the list and
the relational operator. After making the selection, the Quality Control
rule is added in the form of a sentence to the Parameters view. After
this you can edit the rule and the underlined items, such as the value(s)
or sample(s), by clicking the item in question in the sentence. For
number values in the Quality Control rule, you can also click the
Advanced button, which opens a dialog for entering a formula by using
the operator buttons and number keys.
Calculations
Click the arrowhead to open the fields in which you can enter a text
string for each passed or failed quality control check and the color for
displaying each quality control check result.
In the List view, you can view the results for the quality control check.
The view shows one common result (Passed or Failed) for all samples
that are affected by the quality control rule. The result is interpreted as
passed only if the results of all the individual samples have passed.
Therefore, if even one of the samples fails, the result of the quality
control rule is interpreted as failed. By clicking the + sign beside the
result, you can view the value and interpretation of each sample
individually:
Note that the dilution factors of unknown samples are not taken into account
in quality control calculations.
Example of a Quality
Control calculation
In this example, the QC rules of the assay state that the average absorbance
value of blanks must be less than 0.15 and the absorbance of all control
sample replicates must be greater than 1.2.
The rules are defined as follows:
Quality control results for the example:

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Calculations
User-defined equation
A user-defined equation allows you to manually define calculations for
measurement or calculation results. In kinetic measurements, the calculation
is performed for each reading.
If you wish to use all the defined measurement and calculation steps in the
user-defined equation, place the User-Defined Equation step on the root
level (that is, select the session name from the Results tree and add the
User-Defined Equation step). If you wish to use data from only one step,
place the User-Defined Equation as a substep under the source step.
The equation is defined by first defining variables from measurement or
calculation data, and then entering the desired equation into the formula
field using the defined variables, mathematical operators and numbers.
1.
Click Add New to define a variable in the Variable Definition dialog:
124
Name. Enter a name for the variable. The first character of the
variable name must be a letter. This name is used when defining
the actual equation.
Calculations
Data Source:
Result. Select the result step that contains the data that you wish
to include in the calculation. The list includes all the available
steps. Note that spectral or kinetic data cannot be used as source
data. In multi-wavelength measurements, the list includes results
at the different measurement wavelengths.
Field. Select Time, Value, SD, or CV as the data type.
Result Selection:
Select which values of the selected data group (all, values of a certain
group or sample) are used in the calculation.
2.
Click OK to close the dialog.
3.
Define the formula by entering numbers, using the defined variables,

and selecting or entering calculations into the text field. The software
verifies the validity of the equation.
You can enter simple mathematical formulas directly into the text field
by using the defined variables, mathematical operators (e.g. +, -, *, /)
and numbers.
To enter more complex equations, click the desired operators above

the text field and enter the desired variables into the equation, that is,
into the parenthesis of the operators.
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Calculations
When selecting the operation, the following choices are available:
Simple function uses all the variable's result values.
By replicate forms separate result groups by replicates. The

calculation is performed separately for each replicate.
By sample groups results by individual samples. The calculation is

performed separately for each sample.
By dilution performs calculations separately for each sample

dilution.
By group utilizes predefined sample groups and performs the

calculations separately for each group.
The With dilutions setting defines whether dilution factors are taken into
account in the calculations.
Functions in a user-defined
equation
126
This section describes the mathematical operations that you can use in
user-defined equation.
Calculations
Quantitative curve fit
ABS. Calculates the absolute values of the selected values.
AVG. Calculates the average of the selected values.
SUM. Calculates the sum of the selected values.
SQRT. Calculates the square root of the selected values.

LOG. Calculates the base-10 logarithm of the selected values.
LN. Calculates the natural logarithm of the selected values.
EXP. Raises e to the selected power.
SD. Calculates the standard deviation of the selected values.
CV. Calculates the coefficient of variation of the selected values.
MAX. Determines the maximum of the selected values.
MIN. Determines the minimum of the selected values.

Quantitative curve fit is used for quantitative analysis. It calculates the
concentrations of the samples based on a standard curve that is made from
a series of calibrators with known concentrations.
Any dilutions defined for unknowns in the layout are taken into account
in the concentration calculations.
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Calculations
Note Curve fit requires that calibrators have been defined in the
plate layout. The minimum number of calibrators that are required
for different fit types is given in Table 11-1.

definition
Source:
Calibrators group and Unknowns group. Select the groups (assays)

for both the calibrators and the unknowns that are used.
Calibrators from saved data. You can use a calibrator series from
previously saved data (standard curve).
To save the data as a new standard curve for use in other sessions, follow
these steps:
1.
Select the groups for calibrators.
2.
Click Save. Enter a name and description for the curve in the Save
Curve dialog. For example, you can enter the wavelength and the assay
name as a description so that it is available for later use.
Click Save. For more information, see Saved curves on page 166.
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Calculations
Wavelength. Select the wavelength of the source data.
Concentration extrapolation. Select this if you want to enable

extrapolation. Enter the minimum and maximum concentrations for
extrapolation. Extrapolation is only available for the linear regression
fit type, as it is not mathematically reliable for other fit types.
Fit type. Select the quantitative curve fit type from the list. The curve
fit types are explained in sections Polynomial fit types on page 130
throughFour parameter logistic and Log-Logit on page 131. The
number of calibrators required for each curve fit type is shown in
Table 11-1.
Table 11-1. The minimum number of calibrators required in different curve
fit types
Curve fit type
Minimum number of calibrators
Linear regression (LLS)
1 (3 is recommended see the note in

Polynomial fit types on page 130)
Quadratic polynomial
Cubic polynomial
Quartic polynomial
Point to point
Cubic spline
Four parameter logistic
Log-Logit
Concentration transformation and Measurement transformation:
Linear and Logarithmic. Select the type of data transformation between

linear and logarithmic. The transformation means a change of scale to
improve the accuracy of statistical analyses.
The logarithmic concentration transformation cannot be selected for
the four-parameter logistic or Log-Logit fit types, since these algorithms
already use logarithmic transformations.
The logarithmic concentration or measurement transformation cannot
be selected, if the Force fitted curve through origin option is selected.
Note If the concentration range of the calibrators is more than
four decades, logarithmic transformation should be used to obtain
more precise curve fitting.
Markers:
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Calculations
Average. When you select this option, the averages of the measured
calibrator replicates are displayed in the curve.
Replicates. When you select this option, individual measurements

(replicates) are displayed in the curve.
Additional Options:
Polynomial fit types
Force fitted curve through origin. This option is available only for the
linear regression fit type and when the concentration and measurement
transformations are set to Linear. This option forces the fitted curve to
intercept the origin by following the equation y = ax. When this option
is active, the R2 value is not calculated.
The polynomial fit is determined as:

y = a + bx + cx2 ...mxn, where
n = 1, 2, 3 or 4,
a, b, ..., m = coefficients,
x = the concentration value, and
y = the measured signal.
Derived from the above equation:
y = ax + b for the linear regression (LLS) fit type. The minimum number
of calibrators is two.
Note If only one calibrator is used, the second point is assumed
to cross the origin (0,0).
At least three (3) calibrators should be used to increase the accuracy
of the result.
130
y = ax2 + bx + c for the quadratic polynomial fit type. The minimum

number of calibrators is three.
y = ax3 + bx2 + cx + d for the cubic polynomial fit type. The minimum
number of calibrators is four.
y = ax4 + bx3 + cx2 + dx + e for the quartic polynomial fit type. The
minimum number of calibrators is five.
Calculations
The coefficients of the functions are solved with matrix calculations by using
Gauss-Jordan elimination with a backsubstitution algorithm, except for
linear regression, where the linear least squares (LLS) method is used.
The roots of the polynomial, that is, the results, are calculated with an
iterative Laguerres method. If more than one root is found in the calibration
area, the software produces a warning (see Multiple roots on page 134).
Point to point
The point-to-point method connects the adjacent response-concentration

coordinates, that is, the calibration points, together by using a straight line
(see the equation below), which is different for each of the intervals. The
results are calculated by first searching for the correct interval, and then by
using the corresponding equation. The minimum number of calibrators for
this fit type is two.
yi = aixi + bi
Only the averages of the measured calibrator replicates are used in the
calculations. The replicates are visible in the graph but they are not used in
the calculations.
Cubic spline
This method is a smoothed point-to-point method where the adjacent

calibration points are connected together by using cubic polynomials (see
the equation below) and by optimizing the connecting points as smoothly
as possible to avoid sharp angles. The results are calculated by first searching
for the correct interval, and then using a bisectional method to find the
answer in the corresponding equation. The minimum number of calibrators
for this fit type is three.
yi = aixi3 + bixi2 +cixi + di
Only the averages of the measured calibrator replicates can be used, not the
individual replicate values.
Four parameter logistic and

Log-Logit
The four-parameter logistic and Log-Logit logistic methods use the same
fit model:
In the equation, y is the signal, x the concentration, a the minimum signal

(asymptote below), d the maximum signal (asymptote above), c the
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Calculations
concentration at the inflection point, and b a slope-related term at the

inflection point.
The minimum number of calibrators for these fit types is four.

results
Four-parameter logistic fit type. The coefficients of the function are

solved using the Levenberg-Marquardt method.
Log-Logit fit type. The a and d coefficients are treated as known,

otherwise it is the same as the four-parameter logistic (4PL) fit type.
The graph view displays the results of the curve fit. The table below the
graph shows the calibrators used in the curve fit. It includes the following
columns:
Concentration: The given concentration of the calibrator.
Original Abs: The measured absorbance of the calibrator.
Fitted Abs: The absorbance value calculated using the curve fit function
at the given calibrator concentration.
Residual: The difference between measured (Original Abs) and the

calculated (Fitted Abs) absorbance values.
The Parameters section lists the parameters of the curve fit function as well
as the correlation coefficient R2
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Calculations
The results marked in bold in the list are the average values of all the
replicates
You can select whether to display the data on linear or logarithmic X and
Y axes by selecting the corresponding lin and log buttons.
You can change the scale of the Y or X axis by placing the cursor on the
number in the axis, right-clicking and selecting Properties from the list.
Note If you wish to remove a calibrator or its replicate from the
calibrator curve, you can do so directly from the list under the
graph by right-clicking and selecting Disable <item> from the
menu.
The graph view shows the calibration curve and calibrator data. The table
and list views show the calculated concentrations of the unknown and
control samples. The samples that are shown in italics and in orange in the
list view are extrapolated.
The coefficient of determination, R2, is a statistical measure of how well
the curve fit represents the data, that is, its statistical reliability.
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Calculations
Effective dose
The R2 value is not calculated in the following cases: cubic spline fit,
point-to-point fit or linear regression with the force fitted curve through
the origin option.
Multiple roots
With certain fit types and data, the resulting curve is shaped in a way that
an absorbance hits the curve in two or more points. It means that the
absorbance corresponds to two different concentration values. This occurs
only if there is a maximum or minimum in the curve. In such a case, a curve
is drawn but no concentrations are calculated for unknown or control
samples. The following message is shown in the curve fit results graph: The
curve contains signal values with multiple possible concentration values (multiple
roots).
Multiple roots can occur in all fit types except for linear regression (LLS),
Four parameter logistic and Log-Logit.
If the message is shown, try to disable the calibrators that cause the curve
being shaped in a way that multiple roots occur.
Effective dose
The ED50 value is a concentration value in which 50% of the monitored
characteristic of the sample has been lost. Typically, the characteristic is cell
death or cell survival or certain enzymatic activity. This value is used to
demonstrate the efficiency (such as toxicity) of the sample. In addition to
ED50, other ED values are also counted, typically ED20 and ED80. The
ED20 value is a concentration where 20% of the activity is lost, and similarly,
ED80 is the value where 80% has been lost. An example of ED determination
is shown in Figure 11-8.
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Calculations
Effective dose
Figure 11-8. Effective dose (ED) determination

The curve values are defined according to the following equations:
X is a sample that is used as a reference value to which other samples are

compared. The sample selected as X either represents the value 0% or 100%.
All results (curves and ED values) are collected into one graph from the
selected assay. The calculated ED values are also shown in a list.
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Calculations
Effective dose
Wavelength. Select the wavelength of the source data.
ED. Select whether you want an inhibition curve (ED0) or an activity

curve (ED100).
Use series:
Select whether you want to base the effective dose calculation on Dilution
or on Concentration series.
Dilution. The Reference value selection can be made from Controls and
Unknowns.
Concentration. The Reference value selection can be made from Controls

and Calibrators. However, when Use maximum value is checked,
selection is made only from calibrators.
Reference value. Select a sample or a replicate, which acts as the ED100 or

ED0 value:
136
Use maximum value. The software selects the sample or the average of
its replicates with the highest value from the selected assay to be the
ED100 or ED0 value.
Calculations
Effective dose
Group. Selects the group from which the reference value is selected and
for which the ED values are calculated.
Sample. Selects an individual sample that is used as the reference value.

The average value of the selected sample (if replicates exist) will be used
in the calculation. This selection is only active if Use maximum value is
not selected. The sample selection shows either the unknown or
calibrator samples of that particular group and the control samples of
all the groups.
If you have selected Dilution in the User series selection, you can select
a Control or an Unknown sample.
If you have selected a Control, the same graph will display all the dilution
series of the unknown samples. If you select an Unknown, the graph
will only display the dilution series of that particular sample.
When you have selected Concentration, you can select a Control or a
Calibrator.
If you select a Control, the same graph will display all the concentration
series. If you select a Calibrator, the graph will display only the
concentration series to which that calibrator belongs.
ED value:
Up to three different ED values can be determined in one calculation. The
default values are ED20, ED50 and ED80, but you can set any three ED
values between 0 and 100.
Note All other selections are equal to quantitative curve fit
selections except for extrapolation which is not available. All
calculated ED values are between the lowest and highest dilution
or concentration given in the source data.
Fit type:
ED values are calculated based on the function generated by the quantitative
curve fit. With this function, the concentration/dilution values corresponding
to the required ED values are solved and listed as results. Select the curve
fit type from the list. The default fit type is Cubic spline. The curve fit types
are explained in Quantitative curve fit on page 127.
Concentration/Dilution and Measurement:
Linear and Logarithmic. Select the type of data transformation between

linear and logarithmic. The transformation means a change of scale to
improve the accuracy of statistical analyses.
137
Calculations
Data normalization
Note If the concentration range of the calibrators is more than

four decades, logarithmic transformation should be used to obtain
more precise curve fitting.
Markers:
Average. The averages of the measured calibrator replicates are displayed

in the curve.
Replicates. Individual measurements (replicates) are displayed in the

curve.
Data normalization
In data normalization the data of a certain group of samples is normalized
to a certain single sample of the same group.
Calculation. Select either Ratio or Inhibition.
The sample selected as B0 will represent the value 100%.
The sample selected as B0 will represent the value 0%.
Source. Select which sample is used as the B0 and the group that contains
that sample. The average value of the selected sample (if replicates do
exist) will be used in the calculation.
The B0 can be any sample type (calibrator, control, blank, or unknown),
and you can define which specific sample should be used as B0. The
138
Calculations
Qualitative classification
ratio or inhibition value is calculated for all the samples belonging to

the same group as the B0 sample.
Qualitative
classification
Qualitative classification categorizes the source data based on user-defined
limit values. The limit or boundary values can be defined as a number, a
specific sample, or a formula that can contain both samples and numbers.
These formulas can contain the mathematical operators, such as +, -, / and
*. Sample values that are less than the defined limit are placed into the lower
category, whereas samples that are equal to or higher than the limit are
placed into the higher category.
For example, to categorize samples into two sets (e.g. positive and negative),
you must define one limit value.
Any dilutions defined for samples in the layout are taken into account in
the calculations. You can also select to ignore the dilutions in the
calculations.
For qualitative classification, you can define the following parameters:
Source:
Group. Select which group is used as the source.
139
Calculations
Parallel Line Analysis
Wavelength. In multi-wavelength measurements, select the wavelength

of the source data.
Ignore dilutions. If you select this option, the dilutions are not taken
into account in the calculation.
Limit. Select the Limit check boxes for each desired category starting
from the bottom. The selected category becomes available and the dialog
is opened for entering the limit value.
Samples. Select a sample average or replicate to be used in the

formula.
Values. Enter the formula by using the operator buttons and number
keys. Use the backspace key to delete one character at a time.
Click OK to accept the formula. The value or formula is displayed in

the text box.
The Edit button is available for the selected categories. Click the
button to open the dialog for editing the formula.
Note To obtain correct limit values, it is important to update
formulas if the controls that are used in the respective formulas are
deleted or if all replicates are disabled.
Category label. Enter a text string to describe each category. The text
string, for example, + or Positive, will be displayed for the Cut-Off
result categories in the Table and List views.
Color. Select a color for each category in the Table and List views.
Click the arrow beside the color field to select the color from the list.
The result of the qualitative classification calculation is shown as category

text strings in the results in the Table and List views.

Parallel line analysis (PLA) is a statistical calculation method that analyzes
the parallelism of the standard curves of two different chemicals and
calculates the relative potency between them. It is used mainly for testing
140
Calculations
the efficacy of pharmaceutical compounds on biological or biochemical

systems. In SkanIt Software, the calculation is performed in compliance
with the European Pharmacopoeia guidelines (including a test for
parallelism).
The PLA calculation compares the effects of two chemicals that have been
tested with an identical test setup, but with a possibly different concentration
range. One chemical is refered to as the research compound and the other
is the reference compound.
Performing a PLA
calculation
To perform a parallel line analysis:

1.
Define the calibration series of the reference and research compounds

on the plate layout. This must be done by defining the two series to
different sample groups (see Group in Adding samples with the Fill
Wizard function on page 60).
2.
Perform the measurement.
3.
Define the quantitative curve fit separately for the reference and
research compounds.
PLA curve fits have the following requirements:
4.
Only linear regression (no extrapolation) can be used.
The concentration transformation must be logarithmic.
The measurement transformation must be linear.
Both calibrator series must have the same concentration unit.
Each curve fit has at least three calibrators.
Add the Parallel Line Analysis calculation and define the calculation
parameters.
141
Calculations
Results of the PLA
142
Reference data. Select the curve fit step with the reference
compound data.
Research data. Select the curve fit step with the research compound
data.
Confidence Level for Parallelism. Select the confidence level used

for validating parallelism. Based on the selected confidence level,
a corresponding t-distribution reference value is read from the
t-distribution table, according to the degrees of freedom.
After the parameters have been selected, the results are shown in the graph
view:
Calculations
T-test for parallelism

Prior to the calculation of the relative potency, a statistical t-test for
parallelism is performed. This test does not prove parallelism between the
two linear regressions, but evaluates the possibility that both data sets have
parallel linear regressions. In other words, whether the difference in the
slopes is insignificant.
If the calculated t-value is smaller than the t-distribution reference value
(the hypothesis of parallelism is statistically accepted), the t-test passes. In
this case, the common slope and relative potency are calculated.
If the calculated t-value is higher than the t-distribution reference value
(hypothesis of parallelism is not statistically accepted), the t-test fails and
no further calculations are performed.
Note If a PLA calculation is performed with statistically unreliable
curve fits (low R2 value), the t-test may pass, even though both
curve fits have linear regressions with very different slopes. This is
caused by non-linear data sets where removing or altering only one
data point may yield a significantly different linear regression
slope.
Relative potency is the relative difference between the concentrations of the
reference and research compounds that cause exactly the same effect.
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Calculations
The confidence level (or level of significance) is set by the user. The higher
the confidence level the greater the t-distribution reference value.
Degrees of freedom = (N1 2) + (N2 2), where
N1 is the number of calibrators in curve 1, and
N2 is the number of calibrators in curve 2.
The critical t-value is the value read from the t-distribution table based on
the selected confidence level.
Calculated t-value:
In the equation,
slope1 and slope2 refer to the slopes of the two regression lines,
s is the pooled standard error of estimate, and
SSxx1 and SSxx2 are the square sums of concentration from the two data sets.
Equations
If two linear regression lines are parallel, the slope of both curves is the same.
This slope is called the common slope and it is calculated from the data of
both data sets. When the common slope is known, new equations using the
common slope are inferred from the curve fits of both the reference and
research compounds. The curves of these common slope equations are shown
in the graph.
144
Chapter 12
Pathlength Correction
This chapter describes the use of pathlength correction in SkanIt Software.
Pathlength correction is used to normalize absorbance measurement results
to correspond to a 10 mm pathlength. This makes it possible to calculate
sample (for example, DNA) concentrations from the absorbance values by
using known concentration factors or extinction coefficient values.
With cuvettes, the actual cuvette pathlength can be used to normalize
measurement results. In microplate measurements, pathlength correction
requires the generation of a suitable correction factor (K-factor).
Note Pathlength correction is not recommended with 384-well
plates, as the calculations involved in creating the K-factor best suit
cylindrical wells and do not account for a conical well shape. In
very conical wells, this causes inaccuracy in the K-factor.
Note Pathlength correction is applicable only to water-based
solutions. There must be an aqueous solution in the well when you
measure pathlength correction.
Microwell pathlength
In microplate measurements, the measurement beam traverses each well

from bottom to top and the pathlength is determined by the liquid volume
in the well. A longer pathlength results in a higher absorbance value, that
is, absorbance measured from a standard 10 mm cuvette is greater than
when measured from a microwell. The pathlength correction factor or
K-factor is used to correct the results and to allow for direct comparison
between microplate and cuvette measurements.
The liquid pathlength in a microplate well can be measured by determining
the absorbance of the liquid in the well at a wavelength at which the solvent
absorbs and the photometric dye does not. This absorbance is used to correct
the actual measured absorbance for variation in well volume at the analytical
wavelength. The measurement results are normalized to correspond to a 10
mm pathlength.
A water-based buffer solution is usually used for photometric samples. The
absorbance of water at a far-infrared wavelength can be used for pathlength
correction. SkanIt Software performs the correction measurement at 900
nm and 975 nm. The 975 nm measurement is used for the calculation and
the 900 nm measurement is used as a background value in the 975
145
Creating a K-factor
measurement. The absorption at 975 nm is used to calculate the well

pathlength, which is then used to normalize the measurement data.
Note The pathlength correction factor or K-factor depends on

the buffer solution and the microplate type, and should be
determined separately for each combination.
Note Pathlength correction is not applicable to turbidometric
measurements.
Creating a K-factor
A suitable K-factor is necessary for performing pathlength correction in

microplate measurements.
To create a new K-factor:
146
1.
Click the New K-factor icon in the Home view.
2.
Select the appropriate 96-well plate template.
3.
Pipette the solution into the wells according to the Layout Description
field.
4.
Start the measurement.
5.
The Results view displays the calculated K-factor in the K-Factor step.
6.
Click the Save K-factor button to save the K-factor in the database.
Pathlength correction with microplates
Saved K-factors can be viewed on the K-Factors page of the SkanIt Software
Settings.
SkanIt Software checks the validity of the determined K-factor automatically
according to specific quality control rules. Select the K-Factor step in the
Results tree to view the results of the quality control rules.
Absorbance level: Small volume Av1 > 0.02, where Av1 is the
difference between the 975 nm and 900 nm measurements at Volume
1.
Absorbance ratio: Av2 / Av1 is between 1.5 and 2.1, where Av2 is
the difference in absorbance between the 975 nm and 900 nm
measurements at Volume 2.
CV%: The measurement creates four data sets: Volume 1 at 900 nm,
Volume 1 at 975 nm, Volume 2 at 900 nm and Volume 2 at 975 nm.
The calculated coefficient of variation (CV%) of each set must be within
5%.
Note A K-factor can be saved even if the validity check fails, but
using such K-factors produces unreliable results.
with microplates
To use pathlength correction in a microplate measurement:

1.
Create a new plate session and define the layout. Add at least one blank
sample to the layout.
2.
Select Use pathlength correction in the measurement step.
3.
Add a Pathlength Correction result step.
4.
Select the wavelength of the source data and K-factor to be used.

147
Pathlength correction with cuvettes
5.
Select Calculate concentrations and enter the parameters to calculate

the concentrations of unknown samples based on the corrected
absorbance values.
6.

SkanIt Software automatically adds a Pathlength Measurement step to
the protocol to perform the 900 nm and 975 nm measurements
required for pathlength correction calculations.
7.
The table and list views of the Pathlength Correction result step show
the corrected absorbance values and calculated concentrations.
In the list view,
Blank. Abs is the blank-subtracted absorbance.
Corr. Abs is the absorbance corrected to correspond to a 10 mm

pathlength.
Concentration is the concentration calculated with the selected

equation. If a dilution factor has been defined for unknown
samples, it is taken into account in concentration calculations.
Note Pathlength correction automatically performs blank

subtraction.
with cuvettes
148
Pathlength correction can be used in cuvette measurements to normalize

results when the actual cuvette pathlength is shorter than 10 mm. Pathlength
correction is not required with a standard 10 mm cuvette.
Note K-factors are not used with cuvette measurements.
To use pathlength correction in a cuvette measurement:
1.
Create a new cuvette session and define the layout and protocol.
2.
Add a Pathlength Correction result step.
3.
Enter the actual cuvette pathlength in millimeters.
4.
Select Calculate concentrations and enter the parameters to calculate

the concentrations of unknown samples based on the corrected
absorbance values.
5.
6.
The table and list views of the Pathlength Correction result step show
the corrected absorbance values and calculated concentrations.
149
150
Chapter 13
Reports
This chapter describes how you can create and edit reports with SkanIt
Software.
Measurement and
calculation reports
In the Reports view, you can create a detailed report from your measurement
and calculation results. The report can be printed or stored manually or
automatically each time a session is run.
Creating a report
In the Reports view, you can create a report to which you can add the
measurement and calculation results of your choice. The Add New button
creates a report including the general information, such as run information
and instrument parameters. The General Info part of the report is the same
as the Session Status Report in the Results view.
To add individual measurement and calculation results, click the arrow
beside the result format on the Add Module action panel, and select the
measurement or calculation result from the list. The list only includes the
result steps that exist in the results. The available result formats are:
151
Reports
Editing a report
Layout. Adds the current or the original layout to the report. Original
layout refers to layouts that have not been changed after execution.
Table. Adds the results to the report as a table.
List. Adds the results to the report as a list.
Note that some calculation steps are available only in either table or list
format and cannot be presented in both formats.
The tree view shows the created report with each calculation and
measurement as a separate item in the tree view. The icon beside the item
in the tree view shows the data format (table or list). Note that adding the
table, list or layout also adds the General Info part of the report if you have
not added it earlier with the Add New function.
Note When adding kinetic or spectral result data in table format
to a report, it is advisable to activate the Spectral export or Kinetic
export feature in the Edit dialog to produce an organized result
table in the report.
Editing a report
152
You can also rename, delete and reorganize the result steps of a report in
the Reports tree view by using the toolbar buttons beside the Reports title.
Reports
Editing a report item
Editing a report item
Click the desired result step in the Reports tree view and use the
Up and Down arrow keys to change the order of the result steps in the
report.
Select the result step from the Reports tree view and click Rename
to enter a new name for the step.
Select the result step from the Reports tree view and click the icon
to remove it from the report.
You can change the appearance of a report item by selecting the information
that is displayed in the report.
1.
Select the calculation or measurement result from the Reports tree view.
2.
Click Edit to open the dialog that displays all settings and items in the
report. The selection depends on the calculation and measurement
type and the result format (table or list).
153
Reports
Exporting the report
3.
Exporting manually
Click the check box beside an item to select or to clear it, and then
click OK to confirm the selections.
You can export the measurement and calculation report either automatically
each time the session is run or manually afterwards for use outside SkanIt
Software.
In SkanIt Software you can export the report manually by opening the
report as a Microsoft Excel file or exporting it to another file format.
Open in Excel
You can open the report as a Microsoft Excel file (*.xls) (SkanIt Software
supports Microsoft Excel 2003 and 2007).
To open a report in Microsoft Excel, click Open in Excel in the Reports
view. The Microsoft Excel file is sorted into separate worksheets based on
the result steps. In this format you can, for example, edit, delete or add new
information to it and save it manually.
Exporting data
You can also export a report with the Export function.
To export data:
Exporting automatically
154
1.
In the Reports tree view, select the report that you want to export.
2.
Click Export to open the Save As dialog.
3.
In the Save As dialog, select the folder in which the file will be saved.
You can save the file as a Microsoft Excel file (*.xls), an Adobe Acrobat
Portable Document Format file (*.pdf) or a text file (*.txt).
4.
Click Save.
In the Reports view, you can set SkanIt Software to export the report as a
file automatically each time the session is run. Note that the setting applies
only to the session and report that is currently open. You have to add the
setting to each session and report separately.
Reports
To save the report:

1.
In the Reports tree view, select the root step or scroll to the top of the
report. The After Execution dialog is displayed.
2.
Select Save to file. The software suggests a file name. You can accept
it or use Browse to enter a name for the file and to select the target
folder.
The file can be saved as a Microsoft Excel file (*.xls), an Adobe Acrobat
Portable Document Format file (*.pdf) or a text file (*.txt) if you choose
Overwrite or Unique name as the save mode. If you choose Append as
the save mode, you can only save the file as a text file (*.txt).
After selecting the folder, you can select with the {abc} button a
placeholder which is affixed to the file path or to the file name. The
placeholder is replaced with a current value when the file is created. If
you separate the placeholder with a backslash (\) from the file name,
you can create new folders. For example, if you add the year and the
month placeholders to the file path and separate them with the backslash
as in the example below, two folders are created in hierarchical order
in the SkanIt Export folder: (for example: C:\SkanIt Export\2010\08,
if a session is run in August 2010).
155
Reports
If you add a placeholder to the file path without a backslash, the

placeholder is added to the file name and no folder is created. For
example, in the example below, two folders in hierarchical order are
created (for example, C:\SkanIt Export\2010\08), and in the 08 folder
is saved a file with the name <plate name> + SkanIt Export.txt. With
this selection you can, for example, add the bar code of the plate to
the file name.
3.
Select the save mode:
Append. The data is added to the existing (text) file after the last
saved data. If you select this save mode, you can only save the file
as a text file (*.txt).
Overwrite. The data in the existing file is overwritten.
Unique name. The file name is extended with a unique date and
time string. Data is not overwritten, as a new file is created at each
save.
You can remove the automatic setting by clearing the Save to file check
box in the dialog.
156
Reports
Printing a report
Printing a report
You can print a report either manually or set SkanIt Software to print it
automatically each time a report has been created.
Printing a report manually

To print a report manually, click the icon to open the Print dialog for
defining the printing settings and printing the report.
Printing a report
automatically
You can set SkanIt Software to print the report automatically with the
default printer each time after a session is run. Note that the setting only
applies to a session that is currently open. You have to add the setting to
each session separately.
To print a report automatically:
1.
In the Reports view, click Add New to create the report, and then
click the report name that you want to print. The After execution dialog
is displayed.
2.
Select Print to default printer.
You can remove the automatic setting by clearing the Print to default
printer check box in the dialog.
Sending a report via email
You can set SkanIt Software to send the report as an email message after
each execution.
To define automatic reporting via email, for the desired report check the
Send via email to box and enter the recipients email address.
Note that for email-reporting to be possible, you must define the outgoing
email server and the sender address. This is accomplished in the Reporting
dialog of SkanIt Software settings. See Reporting on page 162
157
Reports
Printing a report
158
Chapter 14
Settings
In the Home view, click the Settings icon to open the Settings menu. The
Settings menu is divided into three categories: Options, with software
settings; Instruments, with instrument related settings; and User
Management, with settings for controlling software user and user group
access rights.
Options
General
The Options category contains settings for SkanIt Software.
In the General dialog, you can define settings that are related to the default
connection, plate position and locking the software.
Language. You can select the language used in SkanIt Software. The
available languages are Chinese, German, English, Spanish, French,
Japanese, Portuguese and Russian. After changing the language, the
software must be restarted for the change to take effect.
Items shown in recently used session list. This selection determines

the number of sessions displayed in the Recent Sessions list in the Home
view.
159
Settings
Options
Database
Auto lock software after no usage. You can select the time after which
the user interface requires a new login, if SkanIt Software has not been
used. When the user gives the correct user name and password, the
software will be available in the state in which it was last used.
Connect to default instrument at startup. When selected, the software

connects to the default instrument (see Instruments on page 169) at
startup. Otherwise, the instrument is not connected and the user has
to establish the connection manually by selecting Connect.
Leave plate in after execution. When selected, the plate is left inside
the instrument after the measurement has finished. Otherwise, the plate
is always run out of the instrument.
Run plate in on disconnect. When selected, the plate is run into the
instrument when the instrument is disconnected.
In the Database dialog, you can check and change the working database
used by SkanIt Software (see Appendix A: Database Maintenance).
Database server name. The SQL database server where the working
database is located.
You can change the database server. Only the databases connected to
the selected database server can be selected. When you change the SQL
server instance, the Database field is updated.
160
Settings
Options
Database. Shows the database which is currently in use by SkanIt

Software. If you want to change the working database, select the new
database from the drop-down menu. Note that you can only connect
to the database with a user name that was created for that particular
database.
User name. Shows the name of the user that is currently logged in.
Password. The password that has been defined for the user.
Test connection. Click this button to allow the software to test the
connection to the database. You will receive a message which informs
you whether the connection succeeded or not. Click OK.
Click Save to change the database and restart SkanIt Software in order to
use the new database.
If you wish to copy and use sessions from an archived or restored database:
Connect to the database in question, restart SkanIt Software, export the
sessions as described in Exporting sessions on page 47, connect back to
your working database, restart SkanIt Software, and import the sessions as
described in Importing sessions on page 50.
Results
In the Results dialog, you can select the number of decimals or significant
digits that is shown for measurement raw data and calculated data in the
results and reports. The original accuracy of the data is retained in the
memory and used for the calculations.
161
Settings
Options
Select the number format for presenting data:
Reporting
162
Photometric data. The number of decimals shown for raw measurement

data. The instrument measures the absorbance with four decimals. By
default, raw data is presented in SkanIt Software with three decimals.
However, all measured decimals are used in further calculations.
Calculated data. The number of decimals or significant digits shown

for calculated data. The calculated results are by default presented with
three decimals.
In the Reporting dialog, you can define the email settings. The settings are
needed, if you want to send, for example, measurement and calculation data
reports to an email address after executing a session automatically. For more
information, see Sending a report via email on page 157.
Email server name. Enter the name of the email server. If the server
requires authentication, it is not possible to send an email outside the
SMTP server.
Sender address. Enter the email address of the sender.
Settings
Options
Colors
In the Colors dialog, you can change the color theme of the user interface
and the default layout colors for sample types (blanks, calibrators, unknowns,
controls and empty wells) to display them in the plate layout and in the
Results table view.
To change the color theme of the user interface:
Click the desired color theme. The user interface changes the color after
you have closed the window.
To change the color of a sample type:
Plate Template
Click the arrow beside a sample type, and then select a new color from
the list.
In the Plate Template dialog, you can change the default plate template, and
create, edit and delete plate templates.
Note You cannot edit plate templates created by Thermo Fisher
Scientific. You can only view the settings. If you want to edit an
existing plate template, make a duplicate of it and save it with a
new name.
163
Settings
Options
Close. Closes the dialog.
Setting a plate template as default

You can set the selected plate type as the default template. The default plate
type is used for new sessions (see Creating a new session on page 44).
1.
In the Plate Template dialog, select the desired plate template from the
list.
2.
Click Set As Default. The selected plate is now set as default in the
Layout view.
Creating a new plate template

You can create a new plate template by making a duplicate of an existing
plate template.
164
1.
In the Plate Template dialog, select a plate template from the list. Select
a plate template that is as similar as possible to the one you want to
create.
2.
Click Duplicate.
Settings
Options
3.
In the New Plate Template dialog, enter a name for the new plate
template and click OK. The duplicate plate template is saved and
displayed in the list of plate templates.
4.
Select the new plate template from the list of plate templates, and click
Edit to open the Plate Template Editor dialog.
5.
Edit the dimensions of the plate template if necessary (see section

Editing a Plate Template).
6.
Click OK to save the changes.
Editing a plate template

Except for the predefined templates, you can view and edit the settings of
existing plate templates.
1.
In the Plate Template dialog, select the plate template from the list and
click Edit to open the Plate Template Editor dialog.
Preview shows a model of the plate.
165
Settings
Options
The plate view at the bottom of the dialog is a visual aid showing the
selected distance on a plate.
2.
Click the desired parameter(s) in the list and enter the new
dimension(s).
3.
Click OK to save the changes.
4.
Close the editor by clicking Close. If you have unsaved changes, you
can save or ignore them.
Deleting a plate template

To remove the selected plate template from the database, click Delete.
The software requests you to confirm the deletion. Click Yes to confirm it.
Saved curves
In the Saved Curves dialog, you can view the saved standard curves used in
quantitative analysis and edit their descriptions. You can save standard curves
from an executed session and use them in other sessions. You can also remove
them. For more information about quantitative analysis, see Quantitative
curve fit on page 127.
When you export sessions, the saved standard curves related to them are
also exported. For more information, see Exporting sessions on page 47.
166
Settings
Options
Saved Curves:
Name. Name of the standard curve given when the curve was saved.
Select a saved standard curve to view its properties in the sample list.
Group. Sample group name.
Wavelength. Measurement wavelength of the standard curve.
Creator. Name of the creator.
Creation Time. Date of the saved curve.
Imported. When ticked, the curve is from an imported session.
Sample list:
Name. Name of the calibrators of the selected standard curve.
Value. Value of each calibrator.
Concentration. The concentrations of each calibrator.
Description. Shows the description of the selected curve.
Edit. Opens the Edit description dialog. Enter or change the description
and click OK.
167
Settings
Options
Delete. Removes a curve from the list of saved curves. Select the curve
you want to delete and click the button.
Note You can only delete curves that are not in use.
K-Factors
Close. Saves the changes and closes the dialog.
K-factors are mathematical factors used for pathlength correction in

microplate measurements. The K-Factors dialog allows you to view, add and
remove saved K-factors.
K-factors are created with the New K-factor session in the Home view. You
can also add known K-factors to the list manually, without performing the
K-factor measurement.
For more information on pathlength correction and K-factors, see
Chapter 12: Pathlength Correction.
Select a template in the Plate templates list to view the K-factors stored for
it. For each template, you can add a new K-factor by pressing the Add
168
Settings
Instruments
K-factor button and remove a stored K-factor by pressing the Remove

K-factor button.
Instruments
Instrument Setup
The Instruments category includes the following dialogs: Instrument

Setup and Instrument Settings.
In the Instrument Setup dialog, you can define the default instrument, and
add, edit and delete instruments from the software. You can also create an
instrument report.
Set As Default. Sets the selected instrument as default. See Setting the
default instrument on page 170.
Find New. Searches for new instruments via a USB port. See Adding
an instrument to the SkanIt Software database manually on page 170.
Setup. Opens a dialog for editing the setup parameters of an existing

instrument.
Delete. Removes the selected instrument from the database.
Report. Creates an Instrument Report for the selected instrument.
Close. Closes the dialog.
169
Settings
Instruments
Note The default instrument cannot be deleted. To delete this

instrument, first set another instrument as default, and then delete
the instrument.
Setting the default instrument
To define the default instrument, click the desired instrument in the list
and click Set As Default.
The software will try to connect to the default instrument every time it is
started if you have selected Connect to default instrument at startup in
the General dialog in the Options menu (see General on page 159).
Adding an instrument to the SkanIt
Software database manually
Before you can add a new instrument, the PC must be connected to the
instrument through a USB cable. Each time you connect a USB cable to
the instrument, the software searches for new instruments automatically. If
you do not wish to add a new instrument to the PC at that stage, you can
also create the connection manually in the Instrument Setup dialog.
1.
In the Instrument Setup dialog, click Find New. The New Instrument
dialog opens.
2.
Select the desired instrument from the list and click OK.
The new instrument appears in the instrument list in the Instrument
Setup dialog.
3.
170
The new instrument is automatically set as a default instrument if you

have not connected any instruments to the PC earlier. If you have
already set another instrument as the default instrument, you can set
the new instrument as the default instrument: In the Instrument Setup
Settings
Instruments
dialog, select the new instrument from the list, and click Set As
Default.
Note To change the default instrument, you must first disconnect
from the current default instrument.
4.
Click Close to exit.

The new instrument is immediately available.
Creating an instrument report

In the Instrument Setup dialog, you can create an instrument status report.
The instrument report describes the parameters of the instrument and it is
useful especially for troubleshooting.
To create an instrument report, select an instrument from the list, and click
Report.
An Instrument Report is created which includes, for example, information

on the firmware version and instrument capabilities.
171
Settings
Instruments
Print. Opens the Print dialog for printing the report with the default
printer.
Export. Opens the Save As dialog for saving the report as a text file
(*.txt), an Adobe Acrobat Portable Document Format file (*.pdf) or a
Microsoft Excel file (.*.xls).
Instrument Settings
In the Instrument Settings dialog, you can set the instrument temperature
and control the Power Save feature.
Instrument temperature
Use instrument temperature. When this function is selected, the instrument

incubator is turned on when the instrument and the software are switched
on and connected. The incubator is heated up to the selected temperature
and will be kept at that temperature throughout its use. Note that incubation
steps in the protocol override this temperature setting.
To set the instrument temperature, move the slider to the desired
temperature. The temperature range is from ambient/10.0C to 45.0C.
Note that the instrument temperature is approximately 4C higher than
the ambient temperature.
The temperature set in the instrument's internal software is automatically
updated to SkanIt Software on connection.
172
Settings
User Management
If necessary, you can speed instrument cooling by setting the instrument

temperature to a low value, which activates the instrument's fan.
Power Save
The Multiskan GO has a Power Save feature, which decreases power

consumption when the instrument is idle.
Tick Power Save On to activate the feature.
Use the time control to set the delay before activating Power Save.
Note that when the instrument enters the Power Save mode, the instrument
incubator is switched off.
User Management
SkanIt User Management includes the following dialogs:

Password Options, Users, Groups and Laboratory Information.
In the User Management menu, you can add users, change passwords and
other user settings. The rights in the software and the user management
depend on the security group to which the logged-in user belongs.
All users can view all settings items but only an administrator can view and
modify all items. Only the administrator may add and remove users and
user groups and assign rights for them. The administrator can also change
passwords for other users (see Changing the login password on page 177).
Other users with more limited access rights can use the User Management
menu to change their login and passwords as well as the laboratory
information. Basic operators cannot modify settings at all.
173
Settings
User Management
Delete sessions
Load sessions and runs
Execute sessions
Generate, save and print reports
Export results data
Import and export sessions
Instrument configuration
Create, delete or modify plate templates

(and trays)
Create, delete or modify user accounts
Create, delete or modify user groups
Modify settings
Modify company settings
174
Service
Advanced
Operators
Operators
Administrators
Create and modify sessions
Rights
Password Options
Basic Operators
Table 14-1. Rights of the different security groups
In the Password Options dialog you can view and modify general login and
password settings. Only users with administrator rights can modify these
settings, other users may only view them.
Settings
User Management
Users
Expiration period. The number of days the password is valid. If

Password never expires is selected in the User Properties dialog, this setting
is not valid (see Users on page 175).
Entry attempts count. The number of failed password entry attempts.

If the user fails to enter the correct password in the allowed number of
attempts, the user account is locked and only an administrator can
unlock it by changing the user's password.
In the Users dialog it is possible to change user names and passwords. Users
with administrator rights can also create new users, edit user properties and
delete users.
The Users dialog displays the list including the current users and their user
groups that are defined in the database.
Adding a new user
Only an administrator can add new users. Other users may only view the
list of the different users in the Users dialog.
1.
In the Users dialog, click New User.
175
Settings
User Management
2.
176
Enter the user properties in the fields.
User name. The login name of the user. This is the name that is
entered when logging into SkanIt Software.
Full name. The full name of the user. It is displayed as the creator
name in session, protocol and plate layout lists and is shown on
the status bar.
Description. An optional description of the user.
Member of. The security group(s) to which the user belongs. The
rights of the different security groups are listed in Table 14-1.
User must change password at next login. If this is selected, the

user is asked to change the password when logging into the software
for the first time.
Password never expires. If this option is selected, the password

does not expire. Note that this option cannot be removed from a
user with administrator rights.
Settings
User Management
Change Password. Click the button to open the Change Login

Password dialog. See Changing the login password on page 177.
To exit the dialog and accept the changes, click OK.

3.
Click OK. The new user can log into SkanIt Software the next time
the software is started.
Viewing and editing user

information
All users can view their own user information, but only an administrator
can edit user information.
In the Users dialog, select the desired username and click Properties.
The User Properties dialog opens in which you can view and edit user
information. For more information on the content of the user properties,
see Adding a new user on page 175.
Changing the login password
All users can change their own password. Users with administrator rights
can also change other users' passwords.
1.
In the Users dialog, select the desired user name from the list.
2.
Click Properties or double-click the user name. The User Properties

dialog opens.
177
Settings
User Management
3.
Click Change Password to open the Change Login Password dialog.

Note that the password of an administrator can never expire, and
therefore if you are a user with administrator rights you cannot clear
this check box.
4.
Enter your current password in the Old password field and the new
password in both the New password and the Confirm password fields.
Note The login password is case-sensitive.
178
Settings
User Management
5.
Groups
Click OK. Your new password is valid the next time you log into
SkanIt Software.
Only an administrator can add new user groups and modify their rights.
Other users may only view the group list.
Adding a new user group

Only a user with administrator rights can add new user groups. Other users
can only view the groups in the Groups dialog.
1.
In the Groups dialog, click New Group. The Create Group dialog
opens.
179
Settings
User Management
2.
3.
Enter the following information in the dialog:
Name. Enter a name for the new user group.
Description. Enter a description for the new group. This

information is not obligatory.
Select rights. Select from the list the rights for the group.
Click OK to accept the choices and create the new group.
Viewing and editing group

information
Only a user with administrator rights can view and edit group information.
Other users may only view the groups in the list.
To view and edit group information, follow these steps:
1.
180
In the Groups dialog, click the desired group in the list, and then click
Properties. The Group Properties dialog opens.
Settings
User Management
Laboratory information
2.
Here you can view and edit the group properties: Name, Description
and Rights.
3.
Click OK to accept the changes.
Only a user with administrator rights can enter information on the laboratory
that is performing the measurements. Other users may only view the
information in the Laboratory Information dialog. The information will be
displayed in the reports (see Measurement and calculation reports on
page 151).
Enter the following information in the dialog:
Laboratory name, Telephone, E-mail and Address. Enter the name

and contact information of the laboratory.
Close. Click the button to save the information.
181
Settings
User Management
182
Chapter 15
Using Help
To open the Help, click the Help icon in the Home view or in the
Application menu, or press the F1 key on your keyboard.
Note The Help is only available in English.
The Help toolbar buttons are:
Hide. Hides the navigation pane. To display the navigation pane again,
click the Show button that appears instead of the Hide button.
Back. Takes you back to the previous view in your view history.
Forward. Takes you to the next view in your view history.
Print. Prints a single topic or multiple topics.
You can access the help content in different ways by selecting one of the
following tabs:
Contents. You can browse the help topics by subject.
Index. Type in the keyword or browse all keywords to find a specific

topic. Select the topic from the list, and click Display to view it.
Search. Enter a word or phrase to search in the help content. Click List
Topics to view the help topics. Select the topic that you want to view,
and click Display.
Favorites. Adds a shortcut to help topics of your choice.
183
Using Help
184
Chapter 16
Multiskan GO Simulator
If you do not have an instrument connected when you are installing SkanIt
Software, the software will use the simulator mode automatically until an
actual instrument is connected.
With the simulator you can create sessions that can also be used when the
software is connected to an actual instrument. You can create both plate
and cuvette layouts with the simulator. Note, however, that when you create
sessions including a cuvette layout, the instrument must support this feature.
Otherwise you are not able use these sessions with the real instrument.
You can also start a session with a simulator, but the simulator only gives
random results.
If a session has been run with a simulator, the result reports show Multiskan
GO Simulator as the instrument name.
To change the mode between the simulator and an actual instrument, first
disconnect the simulator or instrument by clicking Disconnect on the
toolbar or on the action panel. Then click the arrow beside the Connect
button on the toolbar or action panel, and select from the list either the
instrument or the simulator to be connected.
185
Multiskan GO Simulator
186
Chapter 17
Troubleshooting Guide
Note Do not use the instrument if it does not function properly.
When an error is detected, the current operation is terminated. After an

error, it is best to abort the current run and restart it from the beginning
after the problem is fixed.
The run log shows the error and warning messages that occur during the
run. For their explanations, see the Multiskan GO User Manual (Cat. no.
N10588).
If the software installation fails, SkanIt Software will be removed but third
party components (SQL server and Microsoft .Net) may remain installed.
The installation detects this and takes it into account when reinstalling
SkanIt Software.
The computer cannot communicate with the instrument:
Check the following things:
The USB cable is securely connected to the computer and instrument.
The instrument is defined in the database (see Connecting an

instrument on page 27).
The instrument you are using is set as a default instrument (see Setting
the default instrument on page 170).
You can also try switching the instrument OFF and ON again.
The measurement is aborted
Check that the computer has enough internal RAM memory. There
should be at least 2 GB of internal memory when making long kinetic
measurements that include a lot of data. For example, a 384-plate and
100 readings/well require approximately 80 MB/result list measurement
or calculation step.
187
Troubleshooting Guide
188
Appendix A
Database Maintenance
SkanIt Software uses Microsoft SQL Server 2008 R2 Express as the database
engine. The database names must comply with SQL Server 2008 R2 rules
for identifiers. For more information, visit the Microsoft website at
http://msdn.microsoft.com/en-us/library/ms175874.aspx.
With Database Maintenance the database administrator can archive previous
database content, make a backup file of the database, restore a backup file
as a working database, or create a new empty database. The Backup/Restore
pair is used to make backup copies of databases and to restore them.
Note In Windows Vista or in Windows 7, Database Maintenance
must be run with administrator privileges.
Selecting the database

in SkanIt Software
Starting Database
Maintenance
Before you start Database Maintenance, and start any database maintenance
operations, ensure that the correct database is selected in SkanIt Software,
and change it if necessary.
1.
Close Database Maintenance if it is running.
2.
Start SkanIt Software.
3.
Select Settings > Options > Database. Follow the steps as described
in Database on page 160.
4.
Exit SkanIt Software.
Start Database Maintenance according to the following instructions.
Note Close SkanIt Software before you start Database

Maintenance.
Select Start > Programs > Thermo SkanIt Software > SkanIt for Multiskan
GO > SkanIt for Multiskan GO 3.2 Database Maintenance.
The Database Maintenance dialog opens.
189
Appendix A Database Maintenance

Restoring a backup file
SkanIt Database Maintenance connects automatically to the database selected

in SkanIt Software. The database engine name is displayed in the Connected
to field.
Creating a backup file
The Backup function creates a copy of the working database used by SkanIt
Software. The backup file should be stored on permanent and secure media.
Note that the backup cannot be made to a network folder.
Caution You must make a separate backup file of the SkanIt
Software database. A general company backup does not backup
the SkanIt Software database because the SQL server does not give
access to the SkanIt Software database.
Note It is the responsibility of the user to make a backup file of
the database.
Note Do not backup files while the instrument is performing a
measurement.
1.
Ensure that the working database is correct. See Selecting the database
in SkanIt Software on page 189.
2.
Click Browse to enter a name to the backup file and a full file path in
the Backup file field. It is recommended to use the default folder (data)
which was automatically created in the installation folder of SkanIt
Software during the installation. The file path can be, for
example:C:\Program Files\Thermo\SkanIt for Multiskan GO 3.2\data\.
3.
Click the Backup button.

You will receive a message when the backup file is ready.
Restoring a backup file
You can restore a backup file as a database. The Restore function returns a
file created with the Backup function to a new database.
Note that the restore cannot be performed from a network folder.
1.
190
Click the Restore tab.

Archiving sessions
2.
Browse to the backup file or enter its full file path in the Backup file
field. Using the default folder (data) is recommended. It was created
automatically in the SkanIt Software installation folder during the
installation. The file path can be, for example:C:\Program
Files\Thermo\SkanIt for Multiskan GO 3.2\data\.
3.
Enter a name for the new database in the Restore as database field.
The new database name can, for example, be SkanIt_1. If the name
is the same as an existing database, or the database name does not
comply with Microsoft's naming conventions, you will be notified of
it, and you will be asked to give a new name.
4.
Click the Restore button. The Specify Default Password dialog is

displayed.
5.
Enter a new login password for the users in the Default password field.
Note The database backup file includes the SkanIt Software login
usernames, but the login passwords of the users not found in any
of the databases of the working database engine instance are not
retained. This is the case when you restore a backup file on a
computer from which you originally did not take it, or on which
the database has not been installed before.
The new password will be the same for all of these users, and they
must therefore change it as soon as possible in the Settings menu
of SkanIt Software (see Changing the login password on
page 177).
6.
Retype the password in the Confirm default password field.
7.
Click OK.
You will be notified when the database has been restored.
To use the restored database, change the working database in SkanIt

Software. See Selecting the database in SkanIt Software on page 189.
Archiving sessions
In the archiving process, the sessions that have been run before the specified
date will be transferred from the working database to the archive database.
Note that the size of the data file must not exceed the amount of the free
disk space on the hard disk.
191

Creating a new database
All sessions that have been run after the specified date will remain in the
working database. The sessions without results will be present in both
databases, and can be manually deleted from the working database if desired.
The archive database is read-only and cannot be altered. Sessions can be
exported from the archive database, and then imported into the working
database, if needed.
Note You cannot archive sessions while the instrument is
performing a measurement.
1.
Ensure that the working database is correct. See Selecting the database
in SkanIt Software on page 189.
2.
Click the Archive tab.
3.
Choose the date up to which all the data will be archived (the selected
date included) in the Up to and including date field.
4.
Name the archive database in the Archive to database field.

If the name is the same as an existing database, or the database name
does not comply with Microsoft's naming conventions, you will be
notified, and you will be asked to give a new name. Record the database
name so that you can retrieve it later.
5.
Click the Archive button.
To use the archive database, change the working database in SkanIt Software.
See Selecting the database in SkanIt Software on page 189.
Creating a new
database
192
You can create a new database locally on the computer for use with SkanIt
Software.
1.
Click the New Database tab.
2.
Name the new database in the Database name field.

Deleting the database
The new database name could, for example, be SkanIt_1. If the name
is the same as an existing database, or the database name does not
comply with Microsoft's naming conventions, you will be notified,
and you will be asked to give a new name.
3.
Click the Create button.
Database creation may take up to 15 minutes depending on your

computer. During this time, the SkanIt Database Maintenance may
appear to stop working but you should wait patiently. You will be
notified when the database has been created.
To use the new database, you have to change the working database in SkanIt
Software. See Selecting the database in SkanIt Software on page 189.
Note that users and passwords of the old database are not transferred to the
new database. The newly created database has only one user (admin without
a password) as default. You have to create all other users separately in User
Management (see Adding a new user on page 175).
Deleting the database
The Delete function allows you to permanently remove a database. However,

you cannot delete the working database.
Caution Deleting a database will permanently destroy all
information stored in the database and all files associated with it.
Therefore, it is highly recommended that you create a backup of
the database before deleting it.
1.
Click the Delete tab.
2.
Select the database you want to delete in the Database name field.
3.
Click Delete.
193

Attaching the database
4.
Click Make Backup or Delete without Backup to proceed.
5.
You are given a final warning.
Click Delete Database to confirm the deletion.
This functionality is useful, if the SkanIt Software database files (.mdf and
.ldf) that are linked to an SQL server need to be used with another SQL
server, for example, on another computer.
Note The database files can normally be transferred between
computers by creating a database backup file (.bak) and restoring
the backup via SkanIt on the target computer. If, however, a backup
file does not exist or one can no longer be created, the Attach
functionality can be used.
To attach a database:
194
1.
Stop the SQL server on the source computer.
2.
Create a copy of the database files.
3.
Transfer the database files on the target computer.
4.
Click the Attach tab.
5.
Click Browse to select the database file (.mdf).

6.
Click Attach. The Specify Default Password dialog is displayed.
7.
Enter a new login password for the users in the Default password field.
Note The database file includes the SkanIt Software login
usernames, but the login passwords of the users not found in any
of the databases of the working database engine instance are not
retained. This is the case when you attach a database file on a
computer from which you originally did not copy it.
The new password will be the same for all of these users, and they
must therefore change it as soon as possible in the Settings menu
of SkanIt Software (see Changing the login password on
page 177).
8.
Retype the password in the Confirm default password field.
9.
Click OK.
You will be notified when the database has been attached.
195

196
Appendix B
Registering SkanIt Software

You have to register SkanIt Software in order to receive the installation code.
1.
Navigate to our website at http://www.thermoscientific.com/skanit.
2.
On the main page, click the link Click here to register your software.
3.
The Thermo Scientific Sign In dialog opens. If you have not registered
earlier, click Register.
If you have registered earlier, you can sign in with your email address
and password that you have created during the registration, and click
Submit. After this you will continue with Step 6.
4.
In the Account Registration dialog, fill in at least the fields that are
marked with an asterisk (*), and click Submit. You will receive a
confirmation e-mail message after a successful registration.
197
Appendix B Registering SkanIt Software
198
5.
Navigate back to http://www.thermoscientific.com/skanit, and click

Click here to register your software.
6.
Enter the instrument serial number and SkanIt installation CD serial

number in the fields, and click Submit.
7.
You will receive a confirmation message telling you that the installation
code has been sent to your email.
Glossary
Abs See absorbance (optical density).
absorbance (optical density) (Abs) A logarithmic
function of the transmission of a wavelength of
light through a liquid.
log (I/I0), dimension [Abs]
effective dose Statistically derived dose expected to
produce a certain desired effect. For example,
ED50 represents the concentration that causes
half-maximal (50%) effect on the test system.
extrapolation Extrapolation is the process of
constructing new data points outside a discrete
set of known data points.
kinetic measurement Continuous or frequent
monitoring of the readings in a chemical reaction
to determine its rate.
photometry The measurement of the properties of
light, particularly its intensity.
protocol A sequence of steps that perform
predefined functions.
self tests Initialization tests and adjustments that
the instrument performs prior to operation as
well as autocalibration.
step A protocol consists of a number of steps. One
step performs a specific function, such as
measuring, shaking, and so on. Each step also
has a number of parameters according to which
the step is carried out.
strip A strip of wells in a row or column.
transmittance The ratio of transmitted (I) and
incident light (I0), I/I0.
well An individual reaction vessel in a plate.
zeroing Setting the baseline level (0.000 Abs) for
absorbance measurements.
199
Glossary
200
Index
A
aborting a run 84
absorbance 73
activation code 198
adding
a new plate 66
an instrument to the SkanIt Software database 170
calculations 95
concentration series for calibrators 64
instruments to the database 169
laboratory information 181
plate templates 163
protocol steps 70
samples 60
user groups 179
users 175
Alt key 41
archiving the database 191
area definition 76
attaching a database 194
auto lock 159
average rate 106
average value 115
B
background shaking 78
backup database 190, 190
baseline subtraction 115
basic statistics 99
blank sample 53, 60
blank subtraction 97, 98
examples of 97
in kinetic protocols 98
boundaries to categories 139
buttons
in the Cut-Off limit wizard 140
C
calculation results 87
calculation steps
adding 95
calculations 95
adding 95
basic statistics 99
blank subtraction 97
data normalization 138
deleting 96
effective dose 134
exporting results 92, 154
graph 118
kinetics 106
merge data 118
parallel line analysis 140
PLA 140
precalculation 117
qualitative classification 139
quality control 122
quantitative curve fit 127
results as graph 120
user-defined equation 124
calibrator 53, 60, 166
CD serial number 21, 198
change 113
changing
password 177
sample type colors 163
working database 189
clearing layout 66
colors
in graph 118
in plate layout 163
concentration 166
concentration series 60
concentration values
multiple roots 134
connecting
instrument via USB 27
simulator 185
connecting to default instrument at startup 159
context menus 41
control sample 53, 60
copying a sample 66
creating
a formula for user-defined equation 124
a new session 44
a simple layout 55
backups 190
folders 51
instrument report 171
new database 192
plate template 163, 164
report 151
reports 93
user groups 179
Ctrl key 41
cubic polynomial fit type 130
cubic spline fit type 131
curves
kinetic results 88
customer information 24, 25
cut-off 139
D
data handling 92, 93, 93, 154
exporting 92, 93, 93, 154, 154
opening in Excel format 92
data normalization 138
data reduction
blank subtraction in kinetic protocols 98
kinetic calculations 106
201
Index
data source 189

database 160
archive 191
attaching 194
changing 189
creating new 192
deleting 193
removing an instrument 169
database configuration 24, 25
database engine 30
database maintenance 196
database server name 189
decimal symbol 93
decreasing reaction 107
default plate template 163
defining
a protocol 69
calculations 95
deleting
a plate 66
a session 47
calculations 96
database 193
folders 51
instruments from the PC database 169
plate template 166
protocol steps 71
samples 66
demo sessions 32
dilution series 60
dimensions of the plate 163
disabling values from raw data 89
duplicating plate template 164
E
ED 134
editing
a plate layout 54, 60
a plate template 165
a protocol 69
a report 152
a report item 153
a session 44
group information 180
instrument setup 170
plate template 163
sample 65
standard curve 166
user information 177
effective dose 134
email
address of sender 162
server name 162
settings 162
empty well 53, 60
end user license agreement 25
example of
a quality control calculation 123
202
adding a concentration series for calibrators 64

examples of
Excel file
opening a report 154
Excel file type 92, 93
executed sessions
importing 48
export options 93
exporting 93, 93
a report 154
a report manually 154
an instrument report 171
data 154
data automatically 93, 154
data manually 92, 93, 154
measurement and calculation results 92
reports 154
result data 93
results 154
sessions 47
exporting and importing sessions 47
exporting automatically
reports 154
exporting manually
a report 154
extrapolation 127, 128, 128
F
features
instrument 17
software 17
file types 60
html 93
mdf 29
msz 47, 48
pdf 67, 154, 154
txt 67, 93, 93, 154, 154
xls 67, 92, 93, 154, 154, 154
fill with 55
fill wizard 60
example 64
filling
order 60
fit types 127, 128
cubic spline 131
four parameter logistic 131
in effective dose 134
log-logit 131
point to point 131
polynomial fit types 130
folders 51
creating 51
deleting 51
in the tree view 51
managing 51
moving 51
renaming 51
Index
formula 124
four parameter logistic fit type 131
functions
in a user-defined equation 126
hardware requirements 21
Help 183
HTML file type 93
ignore readings 113

integral 114
maximum - minimum (change) 113
maximum of well (peak) 112
maximum rate 107
select reading 113
sum 114
time to change 111
time to maximum (peak) 113
time to maximum (peak) / 2 113
time to maximum rate 109
time to maximum rate / 2 111
kinetic loop 75
kinetic measurements 75
viewing measurement and calculation results as curves 88
kinetic protocols
kinetics 106
G
general 159
graph 118
graph view 120
groups 179
ID 60
ignore readings 113, 115
importing
executed sessions 48
sessions 48
increasing reaction 107
incubate 80
incubation time 80
inhibition 138
installation code 21, 24
installing
SkanIt Software 21
SkanIt Software for different instruments 29
instrument 17
adding to the SkanIt Software 170
deleting from the PC database 169
serial number 169, 170
setting as default 170
settings 159, 169
temperature 80
type 169, 170
instrument report 171
creating 171
exporting 171
printing 171
instrument serial number 21
Instrument Temperature 172
integral 114
interval
shaking 78
K
K-factor 145, 168
keyboard shortcuts 41
kinetic calculations 106
average value 115
baseline subtraction 115

language 17, 32
layout 53
layout view 37
leave plate in after run execution 159
limit wizard 139
limits to categories 139
linear regression (LLS) fit type 128, 130
liquid temperature 80
list order 89
log-logit fit type 131
login password 177
login password options
settings 174
M
making a new session 44
markers 127
maximum - minimum (change) 113
maximum of well (peak) 112
maximum rate 107
measurement 83
exporting results of 92
photometric 73
reports 154
starting 83
measurement mode 73
measurement results
results 87
measuring 83
merge data 118
microplate 163
shaking 78
Microsoft SQL Server 2005 Express 23
modifying
instrument setup 169, 170
plate dimensions 165
203
Index
plate template 163, 165

moving
folders 51
MSZ file type 47, 48
multiple roots
concentration values 134
multiple wavelengths 73
Multiskan GO 17
Multiskan GO simulator 185
N
name
of email server 162
of the instrument 170
of the user 24, 25
name of the laboratory 181
name of the user 175
naming a session 44
new plate
creating 163, 164
nonspecific blanks 97
normal rate 106, 106
number format 93
number formats 161
O
opening
a session 46
demo sessions 32
SkanIt Software 31
opening a report in Excel 154
options 159
instrument temperature 172
organizing the protocol step tree 70
original layout
viewing 67
P
parallel line analysis 140
password 177
changing 177
password options
login 174
pathlength correction 101, 145
pause 77
PC requirements 21
PDF file type 67, 154, 154
peak 112
Photometric measurement step 73
photometric spectrum 74
PLA 140
placeholder 93
plate 163
adding 66
deleting 66
in 81
out 81
204
renaming 66
type 54
plate dimensions 165
plate layout 53
adding samples 60
deleting 47
editing 54, 60
exporting 47
fill with 55
fill wizard 60, 60
importing 48
previewing 67
sample type colors 163
plate template 163, 163, 164, 165, 166
creating 164
deleting 166
editing 165
editor 163
importing 48
modifying 165
plate type 163
point to point fit type 131
polynomial fit function 130
Power Save 173
predefined calculation 117
previewing
a plate layout 67
printing
a report automatically 157
an instrument report 171
printing manually
a report 157
protocol
editing 69
protocol properties 69
protocol step
renaming 71
protocol steps 70
area definition 76
incubate 80
kinetic loop 75
pause 77
Photometric measurement 73
plate in 81
plate out 81
shake 78
protocols 69, 69, 70
adding steps 70
deleting 47
deleting steps 71
exporting 47
importing 48
saving 44
Q
QC 122
quadratic polynomial fit type 130
Index
qualitative classification 139, 139

qualitative cut-off analysis 139
quality control 122
quality control calculation
example of 123
quantitative analysis 166
quantitative curve fit 127, 128, 132, 166
quantitative curve fit results 132
quantitative curve fit types 130, 131, 131, 131
cubic spline 131
four-parameter logistic 131
log-logit 131
point to point 131
quartic polynomial fit type 130
R
ratio 138
raw measurement data 87
reaction 107, 109, 111, 111
reading 113, 113, 115
average 115
ignoring 113, 115
selecting 113
registering SkanIt Software 21, 198
reinstalling SkanIt Software 30
removing
a session 47
calculations 96
instrument from the PC database 169
plate template 166
protocol steps 71
samples 66
renaming
a plate 66
a protocol step 71
folders 51
result steps 152
repairing
SkanIt Software 30
replicates 53, 60
report
adding results 151
creating 151
editing 152
general information 151
report item
editing 153
reports 151
creating 93
exporting 154
exporting automatically 154
exporting manually 154, 154
printing automatically 157
printing manually 157
restoring a database 190
results 87, 87, 87, 120, 132
exporting 93, 93
exporting manually 92
number formats 161
tree 95
rights of users 173
run 83
run plate in on disconnect 159
running a session 83
S
sample
copying 66
editing 65
sample ID 60
sample types 53
colors 163
samples 53
temperature 80
save mode
results 93
saved curve
editing 166
saving
a session 44
select reading 113
selecting
plate type 54
wavelength 73
serial number 21, 198
session
creating 44
deleting 47
editing 44
exporting 47
exporting results 92, 154
importing 48
opening 46
saving 44
starting 83
structure 43
sessions 51
setting
color themes 163
default plate template 163
setting default
instrument 170
settings 159
adding a new instrument 170
adding a new user 175
colors 163
database 160
default instrument 170
email settings 162
general 159
groups 179
instrument setup 169
instrument status report 171
instrument temperature 172
instruments 169
205
Index

login password options 174
number formats 161
options 159
options menu 159
password 177
plate template 163
reports 162
results 161
saved curves 166
user management 173
users 175
shake 78
shaking interval 78
shaking speed 78
shaking time 78
shortcuts 41
show graph 88
show original 67
signal level 109, 111, 111
simulator 185
SkanIt data file 47, 48
SkanIt Software 17, 31
for different instruments 29
language 17
reinstalling 30
repairing 30
starting 31
uninstalling 29
SkanIt Software registration 21, 198
SkanIt Software Setup 23
SkanIt User Management 173
adding a new user 175
groups 179, 179, 180
login password 177
password options 174
users 175
SkanIt User management
software 17
installation 21
software options 159
software prerequisites 23
software serial number 24
sorting list 89
specific blanks 97
adding to the plate layout 60
spectral analysis 102
spectrum 74
SQL Server 23, 25
standard 166
standard curve 127, 166
editing 166
importing 48
starting
a measurement 83
a session 83
206
SkanIt Software 31
startup options 159
step tree 70
steps
adding new protocol steps 70
area definition 76
defining calculations 95
deleting protocol steps 71
incubate 80
kinetic loop 75
pause 77
Photometric measurement 73
plate in 81
plate out 81
shake 78
stopping the protocol 77
sum 114
T
target temperature 80
temperature 80
at startup 172
temperature range 172
time to change 111
time to maximum (peak) 113
time to maximum (peak) / 2 113
time to maximum rate 109
time to maximum rate / 2 111
transformation of statistical data 127
tree view 51, 70
results 95
steps 70
TXT file type 67, 93, 93, 154, 154
type
of sample 53
of the instrument 170
U
undefined reaction 107
uninstalling
database engine 29
uninstalling SkanIt Software 29
unknown sample 53, 60
USB cable 27, 170
user groups 179
adding 179
creating 179
user management 173
groups 179, 179, 180
password options 174
users 175
user properties 177
functions 126
users 175
adding 175
Index
login password 177

rights 173
settings 175
viewing and editing user information 177
V
viewing
calculation results 87
kinetic results as curves 88
measurement results 87
original layout 67
quantitative curve fit results 132
results in graph format 120
W
wavelength 73
well 163
dimensions 163
well plate 54
working database
changing 189
X
XLS file type 67, 92, 93, 154, 154, 154
207
Thermo Fisher Scientific Oy

Ratastie 2, P.O. Box 100
FI-01621 Vantaa
Finland
www.thermoscientific.com
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Thermo Scientific

SkanIt Software 3.2

Installing SkanIt Software ................................................................ 21

Getting Started .................................................................................... 31

User Interface ..................................................................................... 33

Step Parameters .................................................................................. 73

Starting a Session ............................................................................... 83

Pathlength Correction ....................................................................... 145

Reports .............................................................................................. 151

Settings ............................................................................................. 159

Using Help ......................................................................................... 183

Multiskan GO Simulator .................................................................... 185

Troubleshooting Guide ...................................................................... 187

Database Maintenance ..................................................................... 189

Registering SkanIt Software ............................................................. 197

Thermo Fisher Scientific

Thermo Scientific SkanIt Software 3.2 for Multiskan GO User Manual

Thermo Fisher Scientific

Installing SkanIt Software ................................................................ 21

Getting Started .................................................................................... 31

User Interface ..................................................................................... 33

Editing and saving a session ................................................................. 44

Step Parameters .................................................................................. 73

Starting a Session ............................................................................... 83

Thermo Scientific SkanIt Software 3.2 for Multiskan GO User Manual

Thermo Fisher Scientific

Exporting manually ........................................................................... 92

Thermo Fisher Scientific

Point to point .................................................................................. 131

Pathlength Correction ....................................................................... 145

Reports .............................................................................................. 151

Settings ............................................................................................. 159

Thermo Scientific SkanIt Software 3.2 for Multiskan GO User Manual

Thermo Fisher Scientific

Creating an instrument report ....................................................... 171

Using Help ......................................................................................... 183

Multiskan GO Simulator .................................................................... 185

Troubleshooting Guide ...................................................................... 187

Database Maintenance ..................................................................... 189

Registering SkanIt Software ............................................................. 197

Thermo Fisher Scientific

Thermo Scientific SkanIt Software 3.2 for Multiskan GO User Manual

Thermo Scientific SkanIt Software 3.2 for Multiskan GO User Manual

Thermo Fisher Scientific

Thermo Fisher Scientific

Multiskan GO with cuvette spectrophotometer .................. 18

Thermo Scientific SkanIt Software 3.2 for Multiskan GO User Manual

Thermo Scientific SkanIt Software 3.2 for Multiskan GO User Manual

Thermo Fisher Scientific

Thermo Fisher Scientific

Minimum PC requirements ............................................... 22

Thermo Scientific SkanIt Software 3.2 for Multiskan GO User Manual

Thermo Scientific SkanIt Software 3.2 for Multiskan GO User Manual

Thermo Fisher Scientific

About the User Manual

For more information

For instrument-related issues, refer to the Thermo Scientific Multiskan GO

Thermo Fisher Scientific

The language versions of the Thermo Scientific SkanIt Software Multiskan