MAN - MFG006 - RevD-Expression CMS User's Manual PDF

CMS Product Family User’s
Manual
Expression CMS User’s Manual
Contents
1. Introduction to expression CMS ........................................................................................... 5
1.1. Welcome to the expression CMS Manual ............................................................................. 5
1.1.1. Advion Contact Information ............................................................................................. 5
1.1.2. Warranty ........................................................................................................................... 6
1.1.3. Copyright Information....................................................................................................... 7
1.1.4. Trademarks ....................................................................................................................... 7
1.2. expression CMS Overview..................................................................................................... 8
1.2.1. Family of compact mass spectrometers ........................................................................... 8
1.2.2. expression CMS Capabilities ............................................................................................. 8
1.2.3. Safety Information ............................................................................................................ 9
1.2.4. Electrical and Environmental Compliance ...................................................................... 11
1.2.5. Environmental and European Union (EU) Standards Compliance .................................. 12
1.2.6. General Installation Requirements ................................................................................. 14
1.2.6.1. Lab Environment Requirements ................................................................................. 14
1.2.6.2. Electrical Requirements and Connections .................................................................. 16
1.2.6.3. Electrical Connections ................................................................................................. 16
1.2.6.4. Environmental Requirements ..................................................................................... 17
1.2.6.5. Gas Requirements ....................................................................................................... 17
1.2.6.6. Services and Solvents Requirements .......................................................................... 18
1.2.6.7. Computer System Requirements ................................................................................ 18
1.3. Introduction to Mass Spectrometry.................................................................................... 19
1.3.1. Mass Spectrometer ......................................................................................................... 19
1.3.2. Ionization Source ............................................................................................................ 19
1.3.3. Mass Analyzer ................................................................................................................. 20
1.3.4. Detector .......................................................................................................................... 21
1.3.5. Mass Spectrometry Analysis ........................................................................................... 21
1.4. Key Parts of the expression CMS System ............................................................................ 22
1.4.1. Ion Generation ................................................................................................................ 22
1.4.2. Electrospray Ionization (ESI) ........................................................................................... 23
1.4.3. Atmospheric Pressure Chemical Ionization (APCI).......................................................... 24
MAN_MFG006_RevD Original Instructions Page 2

1.4.4. Atmospheric Solids Analysis Probe (ASAP) ..................................................................... 25

1.4.5. Volatile APCI (vAPCI) ....................................................................................................... 26
1.4.6. Atmospheric Pressure Interface (API) ............................................................................. 28
1.5. Vacuum System ................................................................................................................... 32
1.5.1. Vacuum System Stages ................................................................................................... 32
1.5.2. Roughing Pump (External) .............................................................................................. 33
1.6. Calibrant System ................................................................................................................. 34
1.7. Human Machine Interface (HMI) ........................................................................................ 35
1.8. Physical Interfaces............................................................................................................... 36
1.8.1. Interfacing with Flash and Liquid Chromatography (LC)................................................. 36
1.8.2. Plate Express™ ................................................................................................................ 36
1.8.3. Rheodyne MRA100-000TM Splitter .................................................................................. 37
1.8.4. SSI LS Class binary Pump ................................................................................................. 38
1.8.5. SSI Series I+ isocratic pump............................................................................................. 39
1.8.6. Vici valve ......................................................................................................................... 40
2. Instrument Specifications ................................................................................................... 41
2.1. Performance Specifications ................................................................................................ 41
2.2. Hardware Specifications ..................................................................................................... 42
2.2.1. Electrical Specification .................................................................................................... 42
2.2.2. Input/output ................................................................................................................... 42
2.2.3. Internal Components of System ..................................................................................... 44
3. Software System ................................................................................................................. 46
3.1. Mass Express™ .................................................................................................................... 46
3.2. Data Express™ ..................................................................................................................... 47
4. Practical CMS Guidelines .................................................................................................... 48
4.1. Electrospray Mass Spectrometry Guidelines ...................................................................... 48
4.2. Sample Concentration Guidelines....................................................................................... 49
4.3. Typical ESI Parameters ........................................................................................................ 50
4.4. Typical APCI Parameters ..................................................................................................... 51
4.5. Sample Preparation Guidelines........................................................................................... 52
5. Maintenance ....................................................................................................................... 53
5.1. Troubleshooting .................................................................................................................. 53

5.2. Replacing CMS Components ............................................................................................... 54

5.2.1. Removing the Ion Source Housing .................................................................................. 54
5.2.2. Reinstalling the Ion Source Housing ............................................................................... 55
5.2.3. Cleaning the Capillary ..................................................................................................... 55
6. Appendix ............................................................................................................................. 57

1. Introduction to expression CMS

Advion expression CMS User’s Manual
The information in this document is subject to change without notice. Advion, Inc. makes no
warranty of any kind with regard to this material, including, but not limited to, the implied
warranties or merchantability and fitness for a particular purpose. Advion, Inc. shall not be liable
for errors contained herein for incidental consequential damages in connection with furnishing,
performance, or use of this material.
1.1. Welcome to the expression CMS Manual
1.1.1. Advion Contact Information
Advion Worldwide Offices
North America
Advion, Inc.
10 Brown Road
Ithaca, N.Y. 14850 U.S.A.
Phone: 1-877-5ADVION (523-8466)
General Information Phone: (607) 266-9162 x 3
Technical Support Phone: 1-877-5ADVION (523-8466)
Order Management (placing orders) Phone: (607) 266-9162 x 1
Fax: (607) 257-5761
General Information Email: [email protected]
Technical Support Email: [email protected]
Order Management Email: [email protected]

Europe
Advion, Ltd.
Harlow Enterprise Hub
Kao Hockham Building
Edinburgh Way, Harlow
CM20 2NQ United Kingdom
General Information Phone: +44 (0)1279 311432
Fax: +44 (0) 1279 311433General Information Email: [email protected]
Technical Support Email: [email protected]
Worldwide Advion Distributors

http://www.advion.com/contact/distributors
1.1.2. Warranty
We warrant to you that title to all products sold to you is good and the transfer rightful, subject
to the paragraph entitled “SECURITY INTEREST.” We warrant to you that each product
manufactured by or for us will be free from defects in material and workmanship in normal use
and service for one (1) year from the date of delivery to you as the original purchaser. This
warranty does not cover, and no warranty is provided for, parts which by their nature are
normally required to be replaced periodically consistent with normal maintenance and use,
including, without limitation, syringes, air filters, lubricants, detectors, capillaries and
consumable products. If any product covered by this warranty is returned to the original
shipping point, transportation charges prepaid, within the applicable warranty period set forth
above and upon examination we determine to our satisfaction that such product was defective
in material or workmanship at the time of delivery to you, we will, at our option, repair or
replace the product or the defective part thereof or refund the original purchase price of the
product.
The foregoing notwithstanding, we will not be responsible for damage to any product resulting
from misuse, negligence or accident or resulting from repairs, alterations or installation made by
any person or firm not duly authorized by us in writing. We shall not be liable for failure to
comply with statutes relating to safety and health, including, without limitation, standards
promulgated under the Occupational Safety and Health Act (OSHA) of 1970, as amended, and
regulations issued pursuant thereto.

If, at any time during the period ending one (1) year after delivery of any product to you, you
report and document any error in any software provided with such product and developed by or
for us or any failure of any such software substantially to conform to our software description
that limits or prevents use of the product by you, we, at our option, will use reasonable efforts
to correct any such error or failure, will replace such software or will terminate your license to
use the software and refund the price of the related product. In connection with any such
termination and refund, you will return the related product to us forthwith upon request. This
warranty shall apply only to those portions of the software that were developed by or for us and
that incorporate all program corrections and modifications, if any, delivered to you. It shall not
apply to any error or failure due to machine error or to the misuse by or negligence of any
person or entity other than us or to any software which is modified by any person or entity
other than us.
1.1.3. Copyright Information
Contents of the publication may not be reproduced in any form or by any means, including
electronic storage and retrieval or translation into a foreign language without prior agreement
and written consent from the copyright owner.
Copyright© 2014 Advion, Inc.
Documented and printed in the United States of America.
All rights reserved.
1.1.4. Trademarks
expression™ is a trademark of Advion, Inc.

Mass Express™ is a trademark of Advion, Inc.
Data Express™ is a trademark of Advion, Inc.
Plate Express™ is a trademark of Advion, Inc.
Microsoft® is a registered trademark of Microsoft Corporation.

Windows® Windows® XP, Windows® Vista, Windows® 7, Excel®, and Word® are registered
trademarks of Microsoft Corporation.
ASX-7000® Series Auto-sampler is a registered trademark of CETAC Technologies.
Mass Rate Attenuator MRA® 100-000 Splitter is a registered trademark of Rheodyne.
SSI LC Class Pump® is a registered trademark of Scientific Systems, Inc.

1.2. expression CMS Overview
This chapter provides an overview of the expression CMS system and hardware as well as the
data acquisition software (Mass Express™) and data analysis software (Data Express™).
The following user’s manual shall cover all three expression CMS systems and unless specified
the content is assumed to apply to all expression CMS systems.
1.2.1. Family of compact mass spectrometers
Based upon over 20 years of mass spectrometry and chemistry experience, Advion, Inc. offers a
family of single quadrupole compact mass spectrometers (CMS) designed specifically for
chemists. While chemists generally require the same basic features, different applications
require different specifications. The latest releases of CMS, the expression S and expression L,
offer enhancements not available with the first generation expression CMS that include polarity
switching during a single analysis to ensure detection of the greatest range of compounds, fast
mass scanning (10,000 m/z units/s) for compatibility with UPLC, SFC and where multiple
compounds need to be monitored simultaneously with SIM, as well as higher flow rates of 1-2
ml/min for simpler interfacing with standard chromatographic conditions.
The difference between the –S and –L models of the second generation CMS is related to the
mass range specification. The –L is better suited for chemists working with larger molecule
applications, while the –S is for small molecule applications. The –S, –L and 1st generation
expression all feature a flexible, transportable mass detector that is easy to use for all levels of
experience.
1.2.2. expression CMS Capabilities
The expression compact mass spectrometer (CMS) is a single quadrupole mass analyzer with an
atmospheric pressure interface. It provides both electrospray ionization (ESI) and atmospheric
pressure chemical ionization (APCI) capabilities with positive and negative polarity switching
within a single analysis (-S and –L models only). The CMS provides mass measurements with unit
mass resolution over a mass range 0 – 1200 m/z units (base and –S models) or 0 – 2000 m/z
units (-L model). It is compact enough to fit in a fume hood and offers organic synthetic and
medicinal chemists direct access to identify, monitor and confirm compounds rapidly as they are
produced in the reactor. In addition, the expression CMS allows for rapid compound
confirmation and identification in normal and reverse phase chromatographic applications. The
expression CMS also offers mobility in space-restricted laboratories by installing in a cart and
transporting from one reaction/application to another.

1.2.3. Safety Information
Safety Conventions
READ THIS SECTION CAREFULLY!

The following graphic symbols and special text formats used throughout this manual and labeled
on the instrument are used to emphasize important safety information.
Warning A warning indicates an operation that could cause

personal injury if precautions are not followed.
In addition, a warning indicates an operation that will
result in sample loss if instructions are not followed.
Caution A caution indicates an operation that could cause

instrument damage if precautions are not followed.
High Voltage A high voltage symbol indicates the danger of electric

shock, if precautions are not followed, due to the
presence of high voltage.
Hot Surface A hot surface symbol indicates the danger of burning, if
precautions are not followed, due to exposed
instrument parts that are hot.
Corrosive A corrosive substance is one that will destroy and

Materials damage other substances with which it comes into
contact.
Flammable To prevent the ignition of solvent vapors or

Material accumulated solvent inside the source, maintain
constant nitrogen flow and when possible connect the
source exhaust.

Electrical Hazards and Precautions
Do not attempt to make adjustments, replacements, or repairs to this instrument except as

described in this User’s Manual. Only an Advion, Inc. service representative or similarly trained
and authorized person should be permitted to service the instrument. This instrument is not to
be used in a manner not specified by Advion, Inc.
High Voltage Do not operate the instrument with the cover or other
parts removed due to a danger of electric shock from
components carrying high voltage.
Capacitors inside the instrument may still be charged even if the instrument is turned off.
Only use fuses with the required current rating and of the specified type for replacement.
The supplied power cord must be inserted into a power outlet with a protective earth contact
(ground). When using an extension cord, make sure that the cord also has an earth contact.
Always disconnect the power cord before attempting any type of maintenance.
Lifting and Handling Hazards
The expression CMS and the rotary pump are too heavy and/or sized for one person to lift or
maneuver safely. A team of two or more people must be used during installation and initial
setup. If the instrument is repositioned or moved after initial installation by someone other than
Advion personal, the “team” approach must be used to prevent personal injury.

Other Hazards
Warning Liquids may be under high pressure; wear protective

eye equipment as necessary.
Caution The expression CMS system is a precision instrument

and instrument damage and damage can occur if the
system is mishandled.
Hot Surface Parts of the mass spectrometer that are hot may be
exposed when the expression CMS top lid is opened. Do
not touch hot parts of the mass spectrometer or burns
may occur.
Warning Two or more people are required to lift the expression

CMS due to the weight of the instrument.
1.2.4. Electrical and Environmental Compliance
Any changes that are made to the delivered system may void compliance with one or more of
the Safety or EMC Standards. Only Advion approved parts may be used or substituted during
the life-cycle of this product. Additionally Advion has design safety interlocks at various
locations within the system; defeating any of the safety interlocks will void safety certifications
and potentially result in personal injury.

1.2.5. Environmental and European Union (EU) Standards

Compliance
RoHS Compliance

EC Declaration of Conformity

FCC Compliance
This equipment has been tested and found to comply with the limits for a Class A digital device,
pursuant to Part 15 of the FCC Rules. Operation is subject to the following two conditions: (1)
this device may not cause harmful interference, and (2) this device must accept any interference
received, including interference that may cause undesired operation.
These limits are designed to provide reasonable protection against harmful interference when
the equipment is operated in a commercial environment. This equipment generates, uses, and
can radiate radio frequency energy and, if not installed and used in accordance with the User’s
Manual, may cause harmful interference to radio communications. Operation of this equipment
in a residential area is likely to cause harmful interference in which case the user will be
required to correct the interference at his/her own expense.
Warning: Changes or modifications to this unit not expressly approved by the party responsible
for compliance could void the user’s authority to operate the equipment.
Note: Shielded cables must be used with this unit to ensure compliance with the Class A FCC
limits.
1.2.6. General Installation Requirements
1.2.6.1. Lab Environment Requirements
The following is a footprint of the complete expression CMS system including the CMS, PC, and
external roughing pump.
Note: Do not place the MS detector near air ducts, windows or heating and cooling systems.

The dimensions below do not include spatial requirement for additional system options
including a liquid chromatography (LC) system.
System Weight Dimensions

Component (H x W x D)
expression CMS 120 lbs. (54 kg) 26”x 11” x 22”

(66 x 28 x 56 cm)
Rotary Pump 66 lbs. (30 kg) 10" x 9" x 18"
(26 x 23 x 46 cm)
Optional - Laptop 5 lbs. (2.2 kg) 10” x 16” x 11”
(PC) (26 x 41 x 28 cm)
Optional – HPLC 15 lbs. (7 kg) 7” x 10” x 16”
Pump (18 x 26 x 41 cm)
Optional – MRA 5 lbs. (2.2 kg) 6” x 3” x 9”
splitting valve (15 x 8 x 23 cm)
The expression CMS requires a flat, vibration free and clean bench space / fume hood which is
strong enough to support the weight of the system and selected accessories.
Install the rotary pump underneath the bench or fume hood when possible. Provide a firm,
level platform for the pump. Locate the pump so that the oil-level sight-glass is visible and the
oil filler-plug, oil drain-plug, mode selector and gas-ballast control are accessible. Minimize the
rotary pump vacuum hose (<5ft, around 152 cm). If the rotary pump is installed on a shelf that
holds the expression CMS, vibration and heat isolation is required.
The laptop (PC) shall be connected to the CMS with a USB cable not to exceed 12 ft. (4 m).
Additional space considerations (air circulation, vacuum hose, gas line, I/O connections and
maintenance):
 The expression CMS requires 1 inch (2.5 cm) on the rear and 1 inch (2.5 cm) on the left
side panel for air circulation.
 If the rotary pump will be located inside an enclosure or cabinet, ensure that there is
adequate ventilation at both ends of the pump, so that the ambient temperature
around the pump does not exceed 40 °C. There must be a minimum space of 1 inch (2.5
cm) between the pump and the enclosure walls.

1.2.6.2. Electrical Requirements and Connections
The quality of line power is critical for the longevity and performance of your expression CMS.
To ensure the highest level of performance, reliability and confidence it is recommended that
one or more of the following conditioning devices be used:
 Line conditioner
 Noise suppression transformer
 Uninterrupted Power Supply (UPS) – highly recommended ( 1000 VA)
Electrical Requirements
Power consumption:
System Component Power Consumption
expression CMS 600VA maximum

expression CMS while in stand-by 200VA Typical
expression CMS while in operate 400VA Typical
Rotary Pump 550VA maximum
Optional - Laptop (PC) 65VA Typical
Optional – HPLC Pump 100VA maximum
Optional – MRA splitting valve 50VA maximum
1.2.6.3. Electrical Connections
Outlet Requirements: (Recommended to have 5 dedicated outlets available.)

 Laptop (PC) – 1 outlet
 Typical (MS and rotary pump) – 2 outlets on 15A (minimum) dedicated circuit
 Typical accessories (LC pump, syringe pump and/or splitting valve) – 2 additional outlets
Warning: Never operate instrument(s) from a power outlet that has does not have a ground
connection. Never use a power cord other than the power cord designed for your region.

Type Specification Comments

Power Plug NEMA 5-15 (15A / 125V grounded) North America
CEE 7/7 (16A / 250V) Europe, England, UK
BS1363 (UK) (13A / 250V) All other countries
IEC60320-13 (Customer supplied)
Line Voltage 100 – 240VAC Nominal +/-10%
Line Frequency 47 – 63HZ Nominal +/- 3HZ
1.2.6.4. Environmental Requirements
The expression CMS may be operated in environments with the following limits and is only
intended for indoor use:
 Temperature: 21 °C +/- 3°C
 Operating Pressure (Altitude): 6560 feet (2000 meters)
 Operating Humidity: 40 to 60% RH (non-condensing)
 Storage and Transport Temperature: -20 °C and 60 °C
1.2.6.5. Gas Requirements
The delivery gas will normally be supplied via the main nitrogen gas supply from within your
facility. The end user must provide a regulated supply, terminated with a fitting for 1/4" or 4mm
tubing to make the required connection to the expression CMS. Your Advion Field Service
Engineer will discuss this with you prior to installation.
o Gas: Nitrogen (N2) 98% pure
o Pressure: 4.1 – 6.9 Bar (60-100 psi)

1.2.6.6. Services and Solvents Requirements
Type Specifications Comments

CMS Exhaust 1L/min source exhaust Recommended for optimal
performance and high
temperature desolvation gas
Rotary Exhaust 1L/min source exhaust
Gas Supply Nitrogen (N2) 98% pure 4mm OD or ¼”line required
4.1 - 6.9 Bar (60-100 psi)
Gas Consumption 8L/min
Solvents Clean / HPLC grade solvents
Solvent Waste Approved and labeled Source and sample waste
Container
1.2.6.7. Computer System Requirements
Operating System compatibility for Mass Express versions below v3.0:

Microsoft Windows XP SP3 (32 and 64-bit), Windows 7 (32 and 64-bit) and Windows 8 (64-bit)
Computer System Requirements (minimum) for Mass Express / Data Express:
 Dual Core processor: 2.0 GHz minimum
 Memory: >4GB RAM
 Hard Disk: >200 GB hard drive and CD ROM drive
 Display: VGA and monitor capable of 1024 x 728 resolution and 65536 colors
 Ports: >2 USB 2.0
Note: For best results the computer should be modern (i.e. manufactured within the last 2 years).
Operating System compatibility for Mass Express versions above v3.1:

Microsoft Windows 7, 8 and 10 (64-bit only)
Computer System Requirements (minimum) for Mass Express / Data Express:
 Dual Core processor: 2.0 GHz minimum
 Memory: >4GB RAM
 Hard Disk: >200 GB hard drive and CD ROM drive
 Display: VGA and monitor capable of 1024 x 728 resolution and 65536 colors
 Ports: >4 USB 2.0 (or USB hub)

1.3. Introduction to Mass Spectrometry
Mass spectrometry (MS) is the technique used to measure the mass-to-charge ratio of individual
molecular entities (compounds) that have been ionized and converted to the gas phase. There
are different types of mass spectrometers available, namely single-quadrupole (SQ), triple-
quadrupole (QQQ), ion trap (IT), time-of-flight (TOF) and Fourier transform ion cyclotron
resonance (FT-ICR) as well as hybrid instruments. The Advion expression compact mass
spectrometer (CMS) uses a single-quadrupole mass analyzer.
1.3.1. Mass Spectrometer
The Advion expression CMS consists of an ionization source, an atmospheric pressure interface,
hexapole ion transfer region, mass analyzer and a detector.
1.3.2. Ionization Source
The choice of ion source in a mass spectrometer depends on the type of analysis to be
performed. The expression CMS uses atmospheric pressure ionization - electrospray ionization
(ESI) and atmospheric pressure chemical ionization (APCI) with positive and negative polarity
switching within a single analysis (–S and –L models) or sequential analyses (base model).
Summary Features of Electrospray Ionization (ESI) with CMS:
 Optimal for polar compounds

 Chemical compound should have a heteroatom in its structure, e.g. nitrogen, oxygen,
sulfur, phosphorus, chlorine, bromine, and iodine
 Any molecular weight within m/z 10-1200 for base model and S systems, 10-2000 for L
systems.
 Provides molecular weight information via proton attachment (M+H)+ in positive ion
mode and proton removal (M-H)- in negative ion mode, as well as other adducts.
 Suitable solvents should be volatile, pure (>99% HPLC grade or better), low surface
tension such as methanol and acetonitrile and the ability to produce very small droplets.
 Analytes are typically polar, ionizable, acidic or basic (no limit to molecular weight)
 Additives (salts) should be kept to below 20 mM volatile salts, not inorganic.
 Water tends to produce less stable ion current which leads to less sensitivity.
 Lower eluent flows afford better sensitivity: flow rate of 0.05 – 0.40 mL/min are ideal.
 Sample matrix effects can be a problem. Minimize high levels of co-eluting matrix and
salt components.
 Analyte dynamic range is typically 500 – 1000. Response becomes non-linear at high
concentrations.

Summary Features of Atmospheric Pressure Chemical Ionization (APCI) with CMS:
 Optimal for polar chemicals and some non-polar chemicals

 Chemical compound should have a heteroatom in its structure, e.g. nitrogen, oxygen,
sulfur, phosphorus, chlorine, bromine, and iodine
 Any molecular weight within m/z 10-1200 for base model and S systems, 10-2000 for L
systems.
 Provides molecular weight information via proton attachment (M+H)+ in positive ion
detection mode and proton removal (M-H)- in negative ion detection mode
 Does not display other adducts
 Chemical ionization (solvent mediated) mass spectra is produced via gas phase
processes at atmospheric pressure (charge transfer from solvent to analyte using a
constant current discharge needle).
 Mild ionization technique but thermal degradation possible for thermally labile
compounds.
 Can accept HPLC flows up to 2 mL/min (1mL/min for base model).
 Analytes must have sufficient proton affinity to be protonated or poor sensitivity may
result.
 Less susceptible to matrix suppression than electrospray.
 Limits of detection are similar to electrospray.
 Mass-flow sensitive detection.
1.3.3. Mass Analyzer
The Advion expression CMS uses a single-quadrupole mass analyzer. The quadrupole consists of
four parallel rods that use electric fields (RF and DC voltages) to filter ions based on their mass-
to-charge ratio. The electric fields are adjusted on the quadrupole (mass filter) based on m/z.
The expression CMS has a mass range of m/z 10 – 1200 for S systems, 10 – 2000 for L systems,
and a maximum scan rate of 10,000 m/z units sec-1. Mass spectra may be acquired using scan
(defined mass range) or selected ion monitoring (SIM) mode.

1.3.4. Detector
The expression CMS uses an electron multiplier with a high energy conversion dynode detector.
A positive ion entering the detector impacts the conversion dynode (which is set to -10kV) and
generates secondary electrons which are focused into the electron multiplier and are
subsequently amplified (i.e., each electron impact event on the surface of the electron
multiplier produces multiple electrons, resulting in a cascading/amplification effect).
A negative ion entering the detector impacts the conversion dynode (which is set to +10kV) and
generates secondary electrons which are focused into the electron multiplier and generates
electrons which are subsequently amplified (through the same cascading effect described
above).
The amplified electron current is measured at a collection plate, converted from an analogue-to-
digital signal and displayed as a mass spectrum in the software. (Refer to the Mass Express and
Data Express manuals.)
1.3.5. Mass Spectrometry Analysis
Mass spectrometry measures the mass-to-charge ratio of molecules that have been ionized and
converted to the gas phase. A mass spectrum is graphically represented with mass-to-charge
ratio (m/z) on the x-axis and intensity or relative abundance on the y-axis. The largest peak in
the mass spectrum is referred to as the ‘base peak’. All other peaks in the mass spectrum are
standardized (%) to the base peak. If the ions produced by using electrospray or atmospheric
pressure chemical ionization have a single charge, the m/z is equal to the mass of the ion.

1.4. Key Parts of the expression CMS System
The Advion expression compact mass spectrometer (CMS) consists of multiple regions. In simple
terms, ions are generated by either ESI or APCI, focused through electric fields (API, hexapole
and quadrupole) and detected. A detailed description of each region and function will be
described below.
1.4.1. Ion Generation
The source housing block is where the sample gets introduced into the CMS. There are two
types of source housing, electrospray ionization (ESI) and Atmospheric Pressure Chemical
Ionization (APCI), with positive and negative polarity analysis. Each ionization technique offers
different benefits and features that may be better suited to the analysis being performed.
The ionization mechanism of each technique will be described below.
Source
Housin

1.4.2. Electrospray Ionization (ESI)
Electrospray ionization (ESI) involves the nebulization of samples using nitrogen to form a very
fine spray and applying a high voltage (typically in the range of 1000 – 5000V) to the tip of the
ESI probe to facilitate ionization of the molecule. The electrostatic gradient (voltage differential)
between the tip of the ESI probe and the inlet cone aids the air flow in drawing ions into the
atmospheric pressure interface.
Electrospray relies on solution-phase chemistry – in positive ionization mode the presence of an
acid such as formic or acetic acid (typically 0.1% concentration) allows the protonation of the
molecular ion to occur and produce the [M+H]+ ion; in negative ionization mode the presence of
a base such as ammonium hydroxide (typically 0.1% concentration) allows the deprotonation of
the molecular ion to occur to produce the [M-H]- ion.
A heated coaxial gas (also nitrogen) can be used to assist in the evaporation of the solvent and
improve sensitivity. This is referred to as “heated desolvation gas” and will be described in later
sections of the manual.
Electrospray is a relatively soft ionization technique with little to no fragmentation of the
molecular ion. Fragmentation of the molecular ion can be induced by increasing the
electrostatic field gradient in the ion source. Setting ion source parameters to induce or
minimize fragmentation in the expression CMS will be discussed in later sections.
Shown below is an ESI source housing, front and back.

1.4.3. Atmospheric Pressure Chemical Ionization (APCI)
During APCI, constant current at high voltage is applied to the corona discharge pin causing a
glowing spark which can be visible when in operation. The nebulized sample plume which is
heated up to a maximum temperature of 400 °C degrees passes over the corona discharge pin in
the source chamber. Chemical ionization occurs at the point at which the corona discharge
provides a charge transfer between the solvent and analyte molecules. This results in charged
analyte molecules that can now be focused by electrostatic fields.
APCI is based on gas-phase chemistry and occurs largely through proton transfer. Neutral
molecules can be ionized by APCI.
Positive Ion Production

H3O+ + M (vapor) → MH+ + H2O
Negative Ion Production
B- + MH (vapor) → M- + BH
Corona discharge APCI is an efficient ionization process that operates in both positive ion (best
'sensitivity' for compounds with high gas-phase proton affinity) and negative ion (best
'sensitivity' for compounds with high gas-phase acidity) modes. APCI can be used for volatile
molecules with a molecular mass below 1,000 Da (both polar and relatively non-polar
molecules). It can provide molecular weight information with little or no fragmentation
(protonated molecule).
Shown below is an APCI source housing. The corona discharge pin is pre-installed in the source
block. Carefully adjust the position of the pin to center its tip over the cone-shaped capillary
inlet, 2-4 mm above.
2-4mm
Corona discharge pin

1.4.4. Atmospheric Solids Analysis Probe (ASAP)
Direct analysis using the ASAP combined with the APCI ion source offers a minimally invasive
method allowing for a rapid and direct sampling without any sample preparation prior to
analysis. This technique allows for the rapid investigation (<30 sec) of targeted materials. Shown
below is an APCI source housing block modified with the ASAP probe at front.
To use the ASAP for analysis, follow the steps:

1. Obtain the brass insertion rod and one glass capillary from the kit provided.
2. Insert the open end of the glass capillary into the hole in the end of the brass insertion rod.
Once the glass capillary is fully seated, tighten the handle of the brass insertion rod. The
capillaries are the correct length so that when seated in the probe they extend the correct
distance.
(NOTE: the act of tightening the rod should hold the glass capillary from falling out. The handle
will need to be loosened and retightened for each glass capillary used.)
Open end of the Capillary seated

glass capillary
3. Before analyzing samples, the glass should be pre-cleaned of fingerprint residue by inserting
through the probe guide into the stream of hot N2 coming from the APCI probe.
4. The APCI Probe should be pointed directly at the rounded end on the glass capillary and 1cm
above it when the probe rod is fully inserted into the guide. Adjustment of the APCI Probe
position will be required if this is not the case.

5. To analyze samples, remove the brass rod from the source and touch the closed end of the
glass melting point capillary to the sample powder or solution.
5a. For dry powders, the sample should be wiped using a Kim-Wipe® from the capillary
before being inserted into the source.
5b. For concentrated or dilute solutions, the sample should be allowed to dry on the
capillary before being inserted into the source.
6. A sample TIC should appear in the real-time view window in Mass Express within 5 sec.
7. The glass melting point capillary may be reused several times, as long as it is cleaned
between analyses and no carry over is observed (compound dependent).
1.4.5. Volatile APCI (vAPCI)
The vAPCI source allows users to sample volatile compounds. It is integrated in Mass Express
v3.1 or later. The source uses the Venturi effect to draw in sample gas through a heated sample
line, preventing condensation. A liquid may be added through the nebulizer to help ionize the
sample. The vAPCI may also be operated as a standard APCI source.
The vAPCI source housing has a black shielding on top that protects users from the high
temperature surface. The dongle key is to be plugged in to the CMS. Once the software
identifies its source type as vAPCI, the ion source is ready to use. The 1-meter long, flexible silver
tube at the left is the sampling tube.
Dongle
key
Sampling tube

Follow the steps to use the vAPCI ion source for analysis:
1) Ensure the APCI probe and corona discharge pin are correctly positioned.
(NOTE: The corona discharge pin should be 2-3 mm above the center of the inlet cone)
2) The CMS system should be tuned for APCI operation prior to starting vAPCI.
3) Set Transfer tube temperature to 100°C. Wait for temperature equilibration.
(NOTE: 100-105°C is recommended)
The tubing may be warm when operation temperature reached.
4) To apply external solvent flow into the ion source (which may assist ionization), connect the
PEEK tubing directly from the calibrant vial to the top of vAPCI probe.
5) To run samples without any solvent flow, install the stainless steel APCI plug into the union
on the top of the vAPCI Probe.
6) To analyze samples, take the tubing and stick into any container that has volatile samples.
NOTE: DO NOT touch the sample with the tubing. Otherwise, any liquid sample will be suck
into the CMS and the high concentration may contaminate the chamber. Any solid sample
that stuck in the tubing may cause clogging.
7) For best results,

a. Warm up the sample to 50-60 °C to enhance the diffusion.
b. Cover the top of your container and open it right before sampling.
8) A sample TIC should appear in the real-time view window in Mass Express within 5 sec.

1.4.6. Atmospheric Pressure Interface (API)
The atmospheric pressure interface (API) is at a pressure of approximately 2 mbar to provide a

pressure differential between the ionization region (i.e., ESI and APCI occur at atmospheric
pressure). Ions are sampled through the inlet capillary in the source chamber (based on gas
dynamics and electrostatic fields) and experience supersonic expansion at the exit of the
capillary in the API.
Ions are then electrostatically focused into an extraction lens in the API and enter the hexapole
(ion transfer) region which is differentially pumped to a pressure of 5 x 10-3 mbar. The pressure
in the hexapole region is critical to facilitate collisional cooling of the ions (slowing the ions) to
enable the ion trajectories to collapse onto the central axis and enter the quadrupole region.
The key is to indiscriminately focus all ions from the hexapole region (regardless of m/z) and into
the quadrupole region to optimize the sensitivity of the expression CMS (this will be discussed in
more detail in future sections).
Heated Capillary Inlet (refer to diagram below): Ions are sampled through the heated inlet
capillary (a) in the source chamber (based on gas dynamics and electrostatic fields). Voltage
ranges from 0 - 180V and temperature ranges from 20 - 300°C. The ions experience supersonic
expansion at the exit of the capillary in the API source block (b).
API Source Block (refer to diagram below): The pressure in the API source block (b) is at a
pressure of approximately 2 mbar. Ions exiting the heated inlet capillary (a) experience
supersonic expansion. Source voltage ranges from 0 – 115V (dynamic).
Extraction Electrode (refer to diagram below): Ions are electrostatically focused into the
extraction lens in the API source block (b) and enter the hexapole (ion transfer) region.
Extraction electrode voltage ranges from 0 – 10V.

Hexapole (refer to diagram below): Ions enter the hexapole region from the extraction lens
electrode (1a). The hexapole (ion transfer) region (1b) is differentially pumped to a pressure of 5
x 10-3mbar. The higher pressure in the hexapole region facilitates collisional cooling of the ions
(slowing the ions) to enable the ion trajectories to collapse onto the central axis (2) and enter
the quadrupole region (3). The hexapole RF voltage scans between 0 -500V (dynamic) with a DC
voltage bias of +/-10V.

Note: The pressure in the expression CMS is measured in the hexapole region using a vacuum
sensor (1.0 x 10-5mbar to atmosphere). The vacuum sensor is an ultra-compact wide range
vacuum transducer based on thermal conductivity MEMS (Micro-Electron Mechanical Systems)
sensor technology. Mass Express uses the pressure measurement to protect the expression
CMS from significant pressure spikes that could damage internal components (such as the
detector). During pump down, the software will not allow the instrument to be placed into the
“Operate” mode until 30 minutes has lapsed.
Quadrupole Mass Analyzer (refer to diagram below): The quadrupole mass analyzer in the
expression CMS consists of four parallel rods (c) that have DC and RF potentials applied to them.
The ions entering from the hexapole region (b) are focused and traverse along the center axis of
the quadrupole's. Ions of a particular m/z will have a stable trajectory depending on the RF and
dynamic electrostatic fields in the quadrupole and will consequently pass through to the
detector.
Detector (refer to diagram below): Ions exiting the quadrupole region (1a) pass through into
the detector (1b). The detector in the expression CMS consists of an electron multiplier (3a)
with a voltage/gain range of 0 – 2000V and a high energy conversion dynode (2a) with a
switchable voltage of +/- 10kV depending on ion detection mode.
A positive ion entering the detector impacts the conversion dynode (which is set to -10kV) and
generates secondary electrons that are focused into the electron multiplier and are amplified
(i.e., each electron impact event on the surface of the electron multiplier produces multiple
electrons, resulting in a cascading/amplification effect). A negative ion entering the detector

impacts the conversion dynode (which is set to +10kV) and generates secondary, positively
charged ions that are focused into the electron multiplier and generates an electrons that are
amplified (through the same cascading effect described above).
The amplified electron current is measured at a collection plate, converted from an analogue-to-
digital signal and displayed as a mass spectrum in the software. (Refer to the Mass Express and
Data Express manuals.)
Note: Operating at excessively high pressures and/or electron multiplier voltages can
permanently degrade the detector.
Mass Express will not allow the instrument to be placed into “Operate” mode if the Pirani
pressure (hexapole region) exceeds 1.0 x 10-2 mbar which correlates to a pressure of > 1.0 x 10-5
mbar in the analyzer region.
Increasing the detector voltage increases the amplification/gain of the signal as well as
background noise. This may provide more intense peaks, however the life of the detector can be
significantly degraded (voltages of 1000 – 1400V are typically used). If the detector voltage
approaches 2000V and no significant signal gain is observed, it could indicate the need to
replace the detector.

1.5. Vacuum System
1.5.1. Vacuum System Stages

The expression CMS is differentially pumped with 3 main regions/stages on the turbo-molecular
pump:
1) Boost Stage: The boost stage evacuates the API source block to a pressure of about 2 mbar
and pumps away the majority of the neutral molecules and particles while allowing ions to
be electrostatically focused into the hexapole region. This is critical as neutrals entering the
mass analyzer can degrade the signal-to-noise and overall sensitivity of the instrument.
2) Drag Stage: The drag stage evacuates the hexapole region to a pressure of about 5 x 10-
3
mbar. This pressure is critical as it facilitates collisional cooling of the ions (slowing the ions
down) to enable the ion trajectories to collapse onto the central axis and enter the
quadrupole region. This “ion transfer” stage indiscriminately focuses all ions (regardless of
m/z) into the quadrupole region.
3) Turbo-molecular Pump Stage: The turbo-molecular pump stage evacuates the quadrupole
analyzer region to a pressure of about 5 x 10-6 mbar. This vacuum is necessary to provide the
optimum operating conditions for the quadrupole analyzer. It is also critical to maintain low
pressures in this region as high voltages are applied (to prevent electrical discharges which
can damage internal components such as the quadrupole and detector).

1.5.2. Roughing Pump (External)
The expression CMS uses an Edwards RV12 rotary vane pump. The rotary vane pump is used to
back the turbo-molecular pump and to evacuate the gas/sample throughput from the system to
the house exhaust. The RV pump is a two-stage, oil-sealed, sliding-vane vacuum pump. When
the pump is switched off, an inlet-valve seals the inlet and prevents the suck-back of air and oil
into the vacuum system. The oil level and condition can be inspected in the oil-box through a
sight-glass.
Alternatively the backing pumping may be provided by an Edwards XDS15i dry scroll pump,
which has similar pumping performance to the RV12 but is completely oil free and requires no
mist filter or other special exhaust considerations.

1.6. Calibrant System
The expression CMS uses a pressurized calibrant delivery system via the use of a regulated
nitrogen supply. In some early CMS models there are two (2) calibrant vials installed, and in new
models there are only one (1). The number of calibrant vials are configurable within Mass
Express Software (refer to the Mass Express software manuals). The calibrant delivery system is
controlled through the software which can switch on or off pneumatic valves in the instrument.
When the pneumatic valve is switched on, the calibrant vial is pressurized and in turn “pushes”
the calibrant through the PEEK tubing and into the MS stream.
The following diagram shows the placement of the calibrant vial on the expression CMS:
The calibrant vial can be removed by pulling the lever out along the dash lines below.
(Note: ensure vial is not pressurized when attempting to remove the calibrant vial).
The pressure supplied to each pneumatic valve is factory preset and can only be changed by a
Field Service Engineer.

1.7. Human Machine Interface (HMI)
Display: The expression CMS has been developed to operate on a laptop computer with at least
a 15.4" view screen and 1280 x 800 resolution.
USB: The expression CMS requires USB 2.0.
Keyboard: The expression CMS requires a standard 104-key keyboard (USB wired interface
preferred).
Mouse: The expression CMS is designed for a USB wired interface optical mouse.
Network: The expression CMS does not require a network connection for standard control.
Power On/Off: The expression CMS power On/Off switch is located on the rear top right corner
of the instrument. The PEM (Power Entry Module) used to power the expression CMS is a dual
purpose module which provides the physical On/Off switch but also the voltage configuration
(120V / 220V).
Power Reset: The expression CMS does NOT have an independent power reset switch. It is
possible to reset the electronics without pumping down the turbo pump simply by removing the
USB cable waiting until the blue LED on the front of the expression CMS flashes once and then
reconnect the USB. The system has been designed to keep the turbo pump on after the power
is turned off (or interrupted) for a short period to allow for electronic resets.
Flow Injection Analysis (FIA): The expression CMS has an integrated Rheodyne injection valve
that allows the user to directly introduce a sample to the MS stream. The expression CMS can
be coupled to a LC system or an isocratic pump to provide a constant eluent flow rate (refer to
Additional System Options). This feature is particularly useful when an analytical column
(chromatographic separation) is not required where samples are relatively pure and free from
salts and non-volatile buffers.
1. Rotate the valve to the "Load" position. Using a 100uL syringe, flush the Rheodyne valve
with at least 5 loop-volumes using the sample of interest (default loop volume on the
expression CMS is 5µL).
2. Rotate the valve to the "Inject" position to divert the eluent flow to introduce the
sample into the MS stream.
Status indicator:
Green – System is powered on, standby mode
Blue – System is in operate mode
Blue (blinking) – System is acquiring

1.8. Physical Interfaces
Peripheral control outputs all coupling the expression CMS to normal or reversed phase
chromatography systems or other devices. Advion recommends and offers the following system
options that can enhance the efficiency, performance and results of the expression CMS in your
laboratory:
1.8.1. Interfacing with Flash and Liquid Chromatography (LC)
The expression CMS accepts a contact closure (digital input) signal from external devices, such
as flash purification systems and LC systems and for acquisition triggering. Advion provides full
integration (control, data acquisition, and analysis) packages with Agilent Technologies’ LC
systems allows users a streamlined approach for their LC – CMS methods.
1.8.2. Plate Express™
Plate Express™ is a device that provides a simple, automated means of obtaining mass spectra
directly from thin-layer chromatography (TLC) plates, combined with the expression CMS
creating a technique known as TLC – CMS. Using this technique chemists can quickly and
confidently identify products even in complex mixtures without additional sample preparation.
 Identify spots in <1 minute
 Avoid the risk of overloading the mass spectrometer – TLC spots contain the ideal
amount of sample for mass spectrometry
 Software controlled – spectra obtained within a few mouse clicks
 Simplify the process of obtaining spectra – ideal for multi-user labs

1.8.3. Rheodyne MRA100-000TM Splitter
The MRA100-000™ (Mass Rate Attenuator valve) is an active flow splitting device (6-position, 4-
port) that delivers a small aliquot of a high flow stream into a Mass Spec stream. It is used in
conjunction with the expression CMS to perform dilution of concentrated samples from high
flow streams such as normal phase flash chromatography, prep-scale LC and flow reactors..
The MRA100-000™ allows users to select from among fifty-nine discreet split ratios ranging from
100:1 to 100,000:1. The ability to select from a wide range of split ratios adds convenience,
productivity and time savings to your analytical applications and laboratory procedures. Unlike
ordinary passive splitters, the MRA100-000™ provides flexibility of use for different applications
and allows methods to be changed or adjusted without changing to a different splitter or
adjusting tubing. The MRA100-000™ split ratios remain accurate and consistent over time since
its split ratios will remain unaffected by mobile phase viscosity, tubing length, and temperature
changes. The device can be used in analytical scale to prep scale flow rate applications with little
or no observable post-column analyte band broadening.
The Rheodyne has the following device specifications:

 Temperature Range: 0° - 40°C, non-condensing.
 Storage and Shipment Temperature: -40° to 75°C.
 Maximum Relative Humidity: 80% up to 31°C decreasing to 50% at 40°C.
 Maximum Operating Pressure: 6.9 MPa (69 bar, 1000 psi).
 Wetted Surfaces: Stainless steel and RPC-8™.
 Connections: Accepts 10-32 male threaded fittings.
 Weight: 2.1 kg (4.6 lb).
 Dimensions: 19.1 cm (7.5 in) x 14.1 cm (5.6 in) x 7.8 cm (3.1 in).
 CE Mark represents compliance with EN61326-1.

1.8.4. SSI LS Class binary Pump
The SSI (Scientific Systems Inc.) binary gradient pump has been customized for Advion and is
integrated in Mass Express v3.1 or later. This advanced pumping system is designed for two
solvent high-pressure gradient applications. The system is equipped with two single-head
positive displacement piston pumps integrated into a functional enclosure.
The SSI binary pump operates from 0.01 – 10.00 mL/min at pressure ratings of up to 6000 psi; or
from 0.10 – 40.00 mL/min at up to 1600 psi; allowing both analytical and small-scale preparative
applications.
The SSI binary gradient pump has the following device specifications:
 Flow Rates: 5mL/min, 10mL/min, and 40mL/min (each pump)
 Pressure: Up to 6000 psi for 10 mL/min
 Fluid path: Stainless Steel, PEEK, or Titanium
 Flow Accuracy: ±2% for a flow rate of 0.20 mL/min above, 80:20 Water/IPA at 1000psi
 Flow Precision: 0.2% RSD

1.8.5. SSI Series I+ isocratic pump
The SSI (Scientific Systems Inc.) Series I+ isocratic pump is specifically designed for use with
single quad mass spectrometers for cone wash, infusion pump and sample injection. It is
integrated to be used with the expression CMS to provide a constant, adjustable eluent flow
rate during an experiment.
The SSI Series I+ isocratic pump operates from 0.01 – 10 mL/min at pressure ratings up to 3,000
psi (PEEK) or 5,000 psi (Stainless Steel) allowing both analytical and small-scale preparative
applications. The choice of stainless steel or PEEK fluid paths make the pump ideal for pumping
solutions as diverse as distilled water, organic solvents, or radioactive slurries.
The SSI Series I+ isocratic pump has the following device specifications:
 Flow Rates: 0.01 - 10 mL/min
 Pressure: 0 to 5,000 psi for 10 mL/min Stainless Steel
0 to 3,000 psi for 10 mL/min PEEK
 Flow Accuracy: ±2% for a flow rate of 0.2 mL/min above, 80:20 Water/IPA at 1000 psi
 Flow Precision: 0.5% RSD

1.8.6. Vici valve
The Vici valve (Valco Instruments Co. Inc.) is integrated in Mass Express v3.1 or later. The
standard interface allows simple positioning commands – step and Home for selectors, A and B
for two position – via direct input signals from switch closures, relay contacts, or TTL-compatible
interfaces. Actuators include universal 24 volt DC power supply and a manual remote.
The Vici valves and selectors has a wide range of turning torques, covering three actuator
versions: high speed, medium speed/medium torque, and high torque.
Features of the Vici valve:

 One actuator works with two position valves and selectors
 Simplified, universal communication protocol
 Variety of interfaces
 Three versions for various valve torque requirements
 Autosensing universal power supply, 110/230 VAC to 24 VDC

2. Instrument Specifications
2.1. Performance Specifications
The expression CMS has the following performance specifications:
 Footprint - Width: 27 cm (10.6 in); Depth: 54.9 cm (21.6 in)

 Ion Source: ESI (constant voltage 0 – 5kV) or APCI (constant current 0 – 15 μA) option
(easily interchangeable)
 Flow rate range:
o expression CMS
 10 μL/min to 0.5 mL/min for ESI
 10 μL/min to 1.0 mL/min for APCI
o expression S and expression L CMS
 10 μL/min to 1 mL/min for ESI
 10 μL/min to 2 mL/min for APCI
 Nebulization gas: 0.5 L/min
 Heated desolvation/APCI gas: 1 to 10 L/min
 House vacuum is required to exhaust source chamber for optimal performance and for
operation with high temperature desolvation gas
 Mass accuracy and resolution is adequate to provide accurate (A+1) and (A+2) isotope
peaks.
 The abundance of naturally occurring isotopes is accurately produced from the full-scan
mass spectra.
 Mass calibration stability of ±0.1 Da over the defined mass range (10 – 1200 for S
systems and 10-2000 for L systems) over 12 hours
 Scan rate:
o expression CMS: 5,000 AMU s-1 (compatible with UPLC)
o expression S and expression L CMS: 10,000 AMU s-1 (compatible with UPLC)
 Linear dynamic range of 5 x 103
 Polarity Switching:
o expression CMS: Sequential Analysis
o expression S and expression L CMS: Single Analysis (50ms switching same
analysis)
 Inlet capillary cleaning or replacement:
o expression CMS: Vent mass spectrometer to remove
o expression S and expression L CMS: Remove under vacuum conditions

2.2. Hardware Specifications
2.2.1. Electrical Specification
The expression CMS system has the following electrical specifications:

 Voltage: 100 - 240 VAC
 Frequency: 50 -60 Hz
 CMS Fuse: 6 Amps
 Max Power Consumption: 600 VA
The main supply voltage fluctuations must not exceed ±10% of the nominal voltage. Other
transient over-voltages must be in accordance with an Installation Category II (Over-voltage)
requirement.
The quality of line power is critical for the longevity and performance of your expression CMS.
To ensure the highest level of performance, reliability and confidence it is recommended that
one or more of the following conditioning devices be used:
 Line conditioner
 Noise suppression transformer
 Uninterrupted Power Supply (UPS) – highly recommended (1000 VA)
2.2.2. Input/output
Contact closures
 4 outputs (DO 1-4)
 4 TTL/contact inputs (DI 1-4)
Analog Inputs (AI 1-4)

 Four channels
 16 bit
 Software selectable ranges to 10V
Analog Outputs (AO 1-4)

 Four channels
 16 bit
 Unsigned
 Software selectable ranges to 10V

Power entry
On/Off switch
110V or 220V
<BACK>
N2 Gas Inlet
60 psi
Rear I/O panel
<FRONT>
USB connection
to computer
Front I/O panel

To Edwards
To House exhaust
pump
To Waste

2.2.3. Internal Components of System
Schematic
The following is a schematic of the basic internal components of the expression CMS:
CAD Overhead View
The following is a computer-aided drawing (CAD) of an overhead view of the basic internal
components of the expression CMS:

CAD CMS Right Side (internals)
Following is a computer-aided drawing (CAD) of the right side of the basic internal components
of the expression CMS:
Low Voltage
(LV) Power
Supplies
FIA Valve (manual
injection)
Source HV Power
Supply Head Amp Board
Detector HV
Backplane
Power Supply
Board
CAD CMS Left Side (internals)
Following is a computer-aided drawing (CAD) of the left side of the basic internal components of
the expression CMS:
RF
chamb
er
Pirani
Vacuum (vacuum)
Chamber gauge
Voltage
transformer Turbo
pump
Digital board
Calibration vial
Quadrupole regulator (~15 PSI)
board
Source gas
regulator
(60PSI)
3. Software System
3.1. Mass Express™
Advion Mass Express is a software application included with the installation of the Advion
expression CMS. It is used to control the operation of the expression CMS and to launch the
Data Express, the post-data processing software used to analyze the MS data acquired from the
expression CMS. Mass Express can be launched from Window's start menu as well the shortcut
that installs on your desktop. Data Express is also available with a desktop installation license,
independent from the expression CMS and Mass Express.
Mass Express allows you to choose the operation mode for the expression CMS to perform
Manual Run, Auto Run and Sample List experiments and control the location of the data. You
may also optimize the scanning method and performance of ion sources (electrospray ionization
[ESI] and atmospheric-pressure chemical ionization [APCI] to run an experiment. Mass Express
also provides access to instrument-level information allowing you to control and monitor the
status of the expression CMS at all times.
Refer to the Advion Mass Express user manual and software help application for further details.

3.2. Data Express™
Advion Data Express is a post-data processing software application used to analyze mass
spectrometer (MS) data acquired from the Advion expression CMS or other MS system. Data
Express can read and analyze data files acquired from the Advion expression CMS in DatX
format, (with file extension *.datx) as well as standard MS data in Net CDF format (*.cdf)
exported or converted by other MS systems.
Data Express is part of the expression CMS control software, Advion Mass Express. It is also
available with a desktop installation license, independent from the expression CMS and Mass
Express. As part of the Mass Express installation, Data Express can be launched from Window's
start menu as well the shortcut button at the lower right corner of the Mass Express. If launched
from Mass Express, Data Express will automatically display the latest MS data file (either the file
currently being acquired or the last acquired if the acquisition has already completed).
Following are some key features of Data Express:

 It is a stand-alone desktop data analysis application, but accessible with one click from
Mass Express.
 Data Express creates one single data file (*.datx) which includes all the spectra,
chromatograms, method, and instrument setting (ion source tune/calibration)
information to be reviewed in Data Express. No special set-up or database is needed.
 Multiple data can be opened for comparison.
 TIC, XICs, Base Peak chromatograms and all spectra can be displayed stacked or
overlaid.
 You can import/export from/to Net.CDF (industrial standard).
 You can export to CSV, PDF, JPEG.
Refer to the Advion Data Express user manual and software help application for further details.

4. Practical CMS Guidelines
4.1. Electrospray Mass Spectrometry Guidelines
The following electrospray mass spectrometry guidelines for samples, solvents, and buffers have
demonstrated proven results, and we recommend that you follow them whenever possible for
successful experimentation using the expression CMS:
Samples:
 Work the best if they contain an ionizable functional group (-NH2, CO2H, SO3H, Ph-OH).
 May also ionize if they form adducts with ammonium acetate, ammonium formate,
sodium or potassium, and analyte masses might show at the respective mass additions
of xx, yy, zz and aa.
 Must be free of non-volatile additives such as EDTA, phosphate buffers, SDS, Triton X-
100, and DMSO.
 Sample concentrations above 20 µg/mL increase the formation of cluster ions and may
cause intensity ratios to be unreliable.
Compatibility:
 Solvents compatible with aqueous electrospray ionization (ESI) conditions include

methanol, acetonitrile and isopropanol.
 Non-aqueous solvents include chloroform and methylene chloride.
 Buffers compatible with ESI include acetic acid, ammonium acetate, ammonium
formate, formic acid and trifluoroacetic acid.

4.2. Sample Concentration Guidelines
The following sample concentration guidelines have demonstrated proven results, and we
recommend that you follow them whenever possible for successful experimentation using the
expression CMS:
 Electrospray full scan MS typically requires sample concentration from 1 – 20 µg/mL (5

to 100 pMol/µL or 10 – 200 ng per 10 µL injection).
 Electrospray ionization (ESI) response becomes non-linear at high sample concentration.
 Increasing sample concentration >20 µg/mL does not improve results.
 Concentrated samples increase the formation of dimer and cluster ions.
 If a molecule doesn’t ionize in ESI mode, change the sample pH or ionization mode
(polarity, APCI) rather than increasing the sample concentration.
 Poor mass spectral quality may not be immediately obvious.
 Problem caused by high sample concentration:
o Incorrect isotope ratios due to saturation of data system
o Unreliable abundance ratios caused by saturation of main peak or non-linearity
of response
o Sample carryover due to contamination in injection port and valve and MS
capillary.
o Plugging of HPLC tubing/sprayer capillary due to poor solubility.

4.3. Typical ESI Parameters
Ion Source Settings
CMS, CMS S CMS L

Capillary Temp 250 oC 250 oC
Capillary Voltage 180V 180V
Source Voltage 20V 20V
Offset
Source Voltage Span 20V 45V
ESI Gas Temperature 250 oC 250 oC
+ESI Voltage 3500V 3500V
-ESI Voltage 2000V 2000V
Tune Settings
CMS, CMS S CMS L

Extraction Electrode 9.5V 9.5V
Hexapole Bias 8.5V 8.5V
Hexapole RF Offset 3V 3V
Hexapole RF Span 150V 250V
Ion Energy Offset -1.2 -1.2V
Ion Energy Span -0.4 -0.4V
Resolution Offset 0 0
Resolution Span 0 0
*Detector Gain <1200V <1200V
* New detector gain is typically less than 1200 and increases with usage

4.4. Typical APCI Parameters
Ion Source Settings
CMS, CMS S CMS L

Capillary Temp 250 oC 300 oC
Capillary Voltage 180V 180V
Source Voltage Offset 20V 20V
Source Voltage Span 20V 45V
APCI Gas Temperature 250 oC 250 oC
Corona Discharge 5µA 5µA
Tune Settings
CMS, CMS S CMS L

Extraction Electrode 9.5V 9.5V
Hexapole Bias 8.5V 8.5V
Hexapole RF Offset 3V 3V
Hexapole RF Span 150V 250V
Ion Energy Offset -1.2 -1.2V
Ion Energy Span -0.4 -0.4V
Resolution Offset 0 0
Resolution Span 0 0
*Detector Gain (new) <1200V <1200V
* New detector gain is typically less than 1200 and increases with usage

4.5. Sample Preparation Guidelines
The following sample preparation guidelines have demonstrated proven results, and we
recommend that you follow them whenever possible for successful experimentation using the
expression CMS:
Solid and Oil Samples

 Pre-weigh 0.5 – 1.5 mg of sample into suitable vial.
 Dissolve the sample in 0.5 – 1.5 mL of an appropriate solvent (e.g. methanol,
acetonitrile, or water) to give 1 mg/mL stock solution.
 Dilute the stock solution (10 – 20 µL into 1 mL) to give 10 – 20 µg/mL in the mobile
phase.
Reaction solutions
 Transfer 2 – 3 µL of solution (use a capillary micro-pipette) to a suitable vial and dilute to
1 mL with the appropriate mobile phase.
Flow Injection Analysis

 80/20 Methanol/Water, 0.5 g/L (6.5 mM) ammonium acetate. A guard column is highly
recommended for FIA.
LC/MS Samples
 5 – 100% acetonitrile in water, 0.1% formic acid.

5. Maintenance
The expression CMS requires daily, weekly and monthly maintenance to ensure optimal
operation. Following are recommendations for regular maintenance that you can perform.
Maintenance items not listed below must be performed by an authorized Advion Field Service
Engineer.
5.1. Troubleshooting
Vacuum Systems
Symptoms Cause Suggestions
Base pressure High vacuum pumps Check power to the rotary backing pump
increase off Check to verify the expression CMS has not
Virtual leak been vented
Actual leak Contact Advion or approved service provider
Spectral for additional support
contamination
Sensitivity and Resolution
Loss of Sensitivity Analyzer pressure Check ESI/APCI nebulization/spray and
too high alignment
Source misaligned Review ion source and tune parameters
Electron multiplier Clean inlet capillary
gain down Increase detector gain/voltage by 50V
Ion source is dirty increments
Inlet capillary Contact Advion or approved service provider
clogged for additional support
Excessive Source voltage too Reduce Source Offset and Span in tune
Fragmentation high (inducing in- window by 5V increments
source Reduce ESI Voltage
fragmentation). Reduce APCI Corona Discharge Current
No signal No ion beam Check ESI/APCI nebulization/spray
Review Pirani Pressure (should be >2E10-3
mbar range)
Clean inlet capillary (blocked)
Review ion source and tune parameters
Check detector gain

Resolution low Peak shape shows Adjust Resolution Offset and Span in tune
lift-off window
Peak shape skewed Adjust Ion Energy Offset and Span in tune
window
5.2. Replacing CMS Components
5.2.1. Removing the Ion Source Housing
Perform the following steps to clean inside the source housing and also to change between ESI
and APCI modes.
1. Place the expression CMS into "Standby" mode using Mass Express.
2. Unscrew the ¼-28 PEEK fitting at the top of the source housing.
3. Loosen the two clamps at both sides (enlarged at the right figure).
4. Gently lift and pull out the source housing.

5.2.2. Reinstalling the Ion Source Housing
1. Carefully place the ion source housing on top of the base plate and line up with the rear
electrical connection. Push down until source chamber is seated evenly across the base
plate.
2. Lock down two housing clamps at both sides (as outlined in the figure below).
3. Finger-tighten the ¼-28 PEEK fitting.
5.2.3. Cleaning the Capillary
1. Remove the ion source housing by following the steps above. Wait approximately 15
minutes for the parts to cool down.
Note: This procedure can be carried out without venting the instrument for the –S and –L
models as these have an automatic capillary sealing valve. However, venting is required for
expression CMS base systems.
2. Unscrew the inlet capillary assembly (a) and carefully pull it out of the heater support
(b).

3. Remove the o-ring under the capillary base, then sonicate the capillary in a
methanol:water (50:50) mixture for 30 minutes.
4. If heavily contaminated, sonicate in a methanol:water+0.1% formic acid (50:50) mixture

for 60 minutes.
5. Rinse the capillary thoroughly with acetone, isopropanol, and then.
6. Dry the capillary using compressed nitrogen gas.
7. Check the condition of the o-ring, replace if required. Reinstall the o-ring onto capillary
base.
8. Reinstall the inlet capillary into API block and screw down tight into the heater support.
9. Follow the steps described below to reinstall the ion source housing.

6. Appendix
Part Number Description

CMS-B01 expression CMS. Single quadrupole analyzer with liquid introduction
interface. Includes manual flow injection valve. Also includes Mass Express
system control software and Data Express data processing software.
Requires SRV302 installation and basic training and suitable data system
(see below). Includes 2 FOC attendees at Advion Ithaca-based training
course, SRV301 (see below), or customer must purchase an on-site training
course SRV401.
CMS-S01 expression-S CMS with m/z 1200 mass range. Single quadrupole analyzer
with liquid introduction interface. Includes manual flow injection valve.
Also includes Mass Express system control software and Data Express data
processing software. Requires SRV302 installation and basic training and
suitable computer (see below). Includes 2 FOC attendees at Advion Ithaca-
based training course, SRV301 (see below), or customer must purchase an
on-site training course SRV401.
CMS-L01 expression-L Compact Mass Spectrometer with m/z 2000 mass range.
Single quadrupole analyzer with liquid introduction interface. Includes
manual flow injection valve. Also includes Mass Express system control
software and Data Express data processing software. Requires SRV302
installation and basic training and suitable computer (see below). Includes
2 FOC attendees at Advion Ithaca-based training course, SRV301 (see
below), or customer must purchase an on-site training course SRV401.
CMS-E01 expression-E Compact Mass Spectrometer for educational use. Single
quadrupole analyzer with liquid introduction interface. Includes manual
flow injection valve. Minimum performance specifications of: m/z 80 - 800
mass range, 2,000 m/z units per second, sensitivity 100 pg Reserpine at
10:1 S:N in SIM mode. Also includes Mass Express system control software
and Data Express data processing software. Requires SRV302 installation
and basic training and suitable computer (see below). Includes 2 FOC
attendees at Advion Ithaca-based training course, SRV301 (see below), or
customer must purchase an on-site training course SRV401.
Must select at least one Ion Source:
IS-APCI-S01 Atmospheric Pressure Chemical Ionization (APCI) ion source for expression
CMS, for S and L CMS models
IS-ESI-S01 Electrospray Ionization (ESI) ion source for expression CMS, for S and L
CMS models

IS-ASAP-S01 Combined ASAP and Atmospheric Pressure Chemical Ionization (APCI) ion
source for expression CMS, for S and L CMS models
Select One Pumping Option:
PMP101 Edwards RV12 rotary vane pump with oil mist filter and oil return (110 -
240 V a.c.) - included in price of CMS
PMP103 Edwards nXDS15i dry scroll pump (100 - 240 V a.c.) - upgrade to oil-free
backing pump
Part Number Service and Training Options

Installation
SRV106 Installation and training fee for onsite installation of upgrades/options
purchased after initial CMS installation
Service Rates
SRV111 Standard hourly labor rate, Monday through Friday 8 am to 5 pm
SRV107 Overtime/weekend hourly labor rate
SRV108 Round trip hourly travel time charge, capped at a maximum charge
equivalent to 5 hours travel
Service Contracts
SRV304 Extended warranty, 12-month contract. Comprehensive warranty including
all labor and parts (except seals, frits and capillaries), labor and parts for a
planned maintenance visit, and free software upgrades for Mass Express
and Data Express for the warranty period. The warranty does not extend to
peripheral equipment.
SRV305 Planned Maintenance for expression CMS, standard
SRV306 Planned Maintenance for expression CMS, major (every 2nd year)
Part Number Optional Installation Items

ACC305 Roughing pump exhaust kit (5m hose and KF 25 connector to connect to
pump or oil mist filter vent - user will need to provide connection at the
house exhaust side)
ACC306 Vacuum hose extension kit - 2m
ACC310 5m of 1/4" OD PFA tubing for nitrogen supply connection
ACC311 Laptop computer meeting operating specifications for the expression
ACC312 Ion Source exhaust trap
ACC315 Venturi pump ion source exhaust kit (requires ACC312 ion source exhaust
trap)
ACC316 Diaphragm pump ion source exhaust kit (requires ACC312 ion source
exhaust trap)

ACC330 110 VAC Uninterruptable Power Supply and Line Conditioner -15 minute
protection
protection
protection
ACC390 Cart for expression CMS. Mobile, 4-shelf bench with 600 lb maximum total
load. 74" tall, 30" x 24" surfaces. Fabricated from chemical resistant
molded polymer
ACC391 Instrument Cart for expression CMS. 34" High, 42" x 24" surface, 2 shelf.
Heavy duty, vinyl painted steel frame, shock-absorbing pneumatic castors.
1200 lb maximum load.
ACC392 IonBench mobile bench for expression CMS. 34" high, 47" x 35" surface,
970 lb maximum load. Includes integrated noise reduction (-15 db(A))
enclosure with vibration dampening for the backing pump, lockable caster,
and chemical resistant surfaces.
ACC420 Nitrogen Generator - PEAK N118LA - 18 L/min for 230 V operation -
requires ACC422 if operated at 110 V
ACC421 Nitrogen Generator - PEAK NM18L - 18 L/min (requires compressed air
source 8.3 - 10 bar) for 230 V operation - requires ACC422 if operated at
110 V
ACC422 Nitrogen generator transformer - required for 110V operation of ACC420
and ACC421
ACC460 Shock attenuation mounting table for mobile labs.
Part Number Accessories

IS-APCI-001 Atmospheric Pressure Chemical Ionization (APCI) ion source for expression
CMS for original, pre 2014, CMS model.
IS-ESI-001 Electrospray Ionization (ESI) ion source for expression CMS, for original,
pre 2014, model.
IS-ASAP-001 Combined ASAP and Atmospheric Pressure Chemical Ionization (APCI) ion
source for expression CMS, for original, pre 2014, CMS model.
UP-ASAP-001 Atmospheric Solids Analysis Probe (ASAP) ion source upgrade for existing
APCI ion source of expression CMS, for original, pre 2014, CMS models
UP-ASAP-S01 Atmospheric Solids Analysis Probe (ASAP) ion source upgrade for existing
APCI ion source of expression CMS, for S and L CMS models
SWL_LCEXPRESS_ Integrated software for control of Agilent HPLC and UHPLC
AGILENT_1 chromatography equipment
ACC350 Mass Rate Attenuator Valve, IDEX MRA-100-000.

ACC361 Isocratic pump, for direct injection, Plate Express and make up flow
provision. Requires ACC364 if pump is to be mounted underneath Plate
Express
ACC364 Bracket for isocratic pump ACC361 if mounted underneath Plate Express
ACC362 Binary Gradient Pumping system with mixer and method development
software. Flow rate 0.0001 – 5 mL/min at 6,000 psi.
ACC363 Binary Gradient Pumping system with mixer and method development
software. Flow rate 0.0001 – 5 mL/min at 6,000 psi, including degasser
ACC395 UV detector with 4 programmable wavelength channel, 10 mm 20 µl flow

cell
PE-001 Plate Express. CMS interface for analyzing planar surfaces such as TLC
plates, papers and biological tissue samples. Includes 2 x 4 mm oval
extraction head for 250 µm bed depths - other extraction heads may be
purchased separately. Interface to CMS requires ACC374 accessory kit and
suitable isocratic pump e.g. ACC361
PE-A01 Plate Express. Mass spectrometer interface for analyzing planar surfaces
such as TLC plates, papers and biological tissue samples. Includes stand-
alone software control for sealing force, extraction control and automated
purge and back flush. Includes 2 x 4 mm oval extraction head for 250 µm
bed depths - other extraction heads may be purchased separately. Includes
interface kit (ACC374) Mass spectrometer interface requires a suitable
isocratic pump e.g. ACC361.
Part Number Interface Kits

Normal Phase Flash Chromatography interface accessory kit containing
ACC370 required tubing, fittings, and cables. Requires MRA valve, ACC350, and
suitable make-up flow pump e.g. ACC361
UHPLC & HPLC interface accessory kit containing required tubing, fittings,
ACC371
and cables.
Direct Injection interface accessory kit containing the required tubing,
ACC372 fittings, and cables. Includes injection syringe. Requires suitable make-up
flow pump e.g. ACC361
SFC interface accessory kit containing the required tubing, fittings, and
ACC373 cables to split SFC pre-backpressure regulator and add make-up flow.
Requires suitable make-up flow pump e.g. ACC361
TLC interface accessory kit containing the required tubing, fittings, and
ACC374 cables. Requires TLC interface, PE-001, and suitable make-up flow pump
e.g. ACC361

Part Number Consumables

ACC301 Replacement API Heated Capillary
ACC303 Replacement ESI capillary kit for all CMS models (includes capillary,
sleeve, and fitting)
ACC309 Replacement APCI capillary kit (includes capillary, sleeve, and fitting) for S
and L CMS models
1009975 Corona discharge pin for APCI and ASAP ion sources
ACC375 Glass capillaries for ASAP probe (Pk 100)
1011619 HPLC column. Kinetex 2.6 micron XB-C18 100A 50 mm x 2.1mm
ACC470 Replacement head for Plate Express - oval, 2 x 4 mm, for 250 µm bed
depth
depth
depth
ACC322 ESI Calibration/tune standard mix
ACC323 APCI Calibration/tune standard mix

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What are the main components of the expression CMS system?

What are the main components of the expression CMS system?

What are some of the installation requirements for the expression CMS?

What are some of the installation requirements for the expression CMS?

CMS Product Family User’s

MAN_MFG006_RevD Original Instructions Page 2

1.4.4. Atmospheric Solids Analysis Probe (ASAP) ..................................................................... 25

MAN_MFG006_RevD Original Instructions Page 3

5.2. Replacing CMS Components ............................................................................................... 54

MAN_MFG006_RevD Original Instructions Page 4

1. Introduction to expression CMS

1.1. Welcome to the expression CMS Manual

1.1.1. Advion Contact Information

Advion Worldwide Offices

MAN_MFG006_RevD Original Instructions Page 5

Worldwide Advion Distributors

MAN_MFG006_RevD Original Instructions Page 6

1.1.3. Copyright Information

expression™ is a trademark of Advion, Inc.

Microsoft® is a registered trademark of Microsoft Corporation.

ASX-7000® Series Auto-sampler is a registered trademark of CETAC Technologies.

Mass Rate Attenuator MRA® 100-000 Splitter is a registered trademark of Rheodyne.

SSI LC Class Pump® is a registered trademark of Scientific Systems, Inc.

MAN_MFG006_RevD Original Instructions Page 7

1.2. expression CMS Overview

1.2.1. Family of compact mass spectrometers

1.2.2. expression CMS Capabilities

MAN_MFG006_RevD Original Instructions Page 8

1.2.3. Safety Information

READ THIS SECTION CAREFULLY!

Warning A warning indicates an operation that could cause

Caution A caution indicates an operation that could cause

High Voltage A high voltage symbol indicates the danger of electric

Corrosive A corrosive substance is one that will destroy and

Flammable To prevent the ignition of solvent vapors or

MAN_MFG006_RevD Original Instructions Page 9

Electrical Hazards and Precautions

Do not attempt to make adjustments, replacements, or repairs to this instrument except as

Lifting and Handling Hazards

MAN_MFG006_RevD Original Instructions Page 10

Warning Liquids may be under high pressure; wear protective

Caution The expression CMS system is a precision instrument

Warning Two or more people are required to lift the expression

1.2.4. Electrical and Environmental Compliance

MAN_MFG006_RevD Original Instructions Page 11

1.2.5. Environmental and European Union (EU) Standards

MAN_MFG006_RevD Original Instructions Page 12

MAN_MFG006_RevD Original Instructions Page 13

1.2.6. General Installation Requirements

1.2.6.1. Lab Environment Requirements

MAN_MFG006_RevD Original Instructions Page 14

System Weight Dimensions

expression CMS 120 lbs. (54 kg) 26”x 11” x 22”

MAN_MFG006_RevD Original Instructions Page 15

1.2.6.2. Electrical Requirements and Connections

expression CMS 600VA maximum

1.2.6.3. Electrical Connections

Outlet Requirements: (Recommended to have 5 dedicated outlets available.)

MAN_MFG006_RevD Original Instructions Page 16