MAN - MFG006 - RevF - Expression CMS User's Manual

CMS Product Family User’s
Manual
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. CMS Internal Component and Voltage Schematic .......................................................... 22
1.4.3. expression CMS Source Housing ..................................................................................... 23
MAN_MFG006_RevF Original Instructions Page 2

CMS User’s Manual
1.4.4. Electrospray Ionization (ESI) ........................................................................................... 23

1.4.5. Electrospray Ionization (ESI) Source Housing ................................................................. 24
1.4.6. Atmospheric Pressure Chemical Ionization (APCI).......................................................... 24
1.4.7. Atmospheric Pressure Chemical Ionization (APCI) Source Housing ............................... 25
1.4.8. Atmospheric Pressure Interface (API) ............................................................................. 25
1.5. Vacuum System ................................................................................................................... 30
1.5.1. Vacuum System Stages ................................................................................................... 30
1.5.2. Roughing Pump (External) .............................................................................................. 31
1.6. Calibrant System ................................................................................................................. 31
1.7. Human Machine Interface (HMI) ........................................................................................ 32
1.8. Physical Interfaces............................................................................................................... 33
1.8.1. Interfacing with Flash and LC .......................................................................................... 33
1.8.2. Integrated Auto-sampler................................................................................................. 34
1.8.3. Rheodyne MRA100-000TM Splitter .................................................................................. 35
1.8.4. SSI Series 1+ Pump .......................................................................................................... 36
2. Instrument Specifications ................................................................................................... 37
2.1. Performance Specifications ................................................................................................ 37
2.2. Hardware Specifications ..................................................................................................... 38
2.2.1. Electrical Specification .................................................................................................... 38
2.2.2. Input/Output ................................................................................................................... 38
2.2.3. Internal Components of System ..................................................................................... 40
3. Software System ................................................................................................................. 42
3.1. Mass Express™ .................................................................................................................... 42
3.2. Data Express™ ..................................................................................................................... 43
4. Practical CMS Guidelines .................................................................................................... 44
4.1. Electrospray Mass Spectrometry Guidelines ...................................................................... 44
4.2. Sample Concentration Guidelines....................................................................................... 45
4.3. Typical ESI Parameters ........................................................................................................ 46
4.4. Typical APCI Parameters ..................................................................................................... 47
4.5. Sample Preparation Guidelines........................................................................................... 48
5. Maintenance ....................................................................................................................... 49
5.1. Troubleshooting .................................................................................................................. 49

CMS User’s Manual
5.2. Replacing CMS Components ............................................................................................... 50

5.2.1. Removing the Ion Source Housing .................................................................................. 50
5.2.2. Reinstalling the Ion Source Housing ............................................................................... 51
5.2.3. Cleaning the Capillary ..................................................................................................... 51
6. Appendix ............................................................................................................................. 53

CMS User’s Manual
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.
61 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: info@advion.com
Technical Support Email: support@advion.com
Order Management Email: orderentry@advion.com

CMS User’s Manual
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: info@advion.com
Technical Support Email: esupport@advion.com
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.

CMS User’s Manual
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.
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 Autosampler is a registered trademark of CETAC Technologies.
Mass Rate Attenuator MRA® 100-000 Splitter is a registered trademark of Rheodyne.
SSI Series 1+ Pump® is a registered trademark of Scientific Systems, Inc.

CMS User’s Manual
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.

CMS User’s Manual
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.

CMS User’s Manual
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.

CMS User’s Manual
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.

CMS User’s Manual
1.2.5. Environmental and European Union (EU) Standards

Compliance
RoHS Compliance
The European Parliament and the Council of the European Union authorized Directive
2011/65/EU on the restriction of the use of certain hazardous substances in electrical
and electronic equipment. This new directive, also referred to as RoHS ("ro-has")
requires that manufactures reduce usage of six hazardous substances to minimum
acceptable levels.
The six substances affected are:
 Lead (Pb)
 Hexavalent chromium (Cr +6)
 Mercury (Hg)
 Polybrominated biphenyl (PBB)
 Cadmium (Cd)
 Polybrominated diphenyl ether (PBDE)
Advion has designed the system described in this document using only RoHS compliant
components as specified by their respective manufacturers.
WEEE Compliance
The Waste Electrical and Electronic Equipment (WEEE) Directive (2012/19/EU), adopted
by EU Commission on 13 August 2012, is introducing producer responsibility on all
Electric and Electronic appliances.
NOTE: This product complies with the WEEE Directive

(2012/19/EU) marking requirements. The affixed label
indicates that you must not discard this
electrical/electronic product in domestic household
waste.
To return unwanted products, contact your local Advion
office.

CMS User’s Manual
Declaration of Conformity
We Advion, Inc. of 61 Brown Road, Ithaca, New York 14850 USA declare that the product as originally
delivered:
Equipment: Mass Spectrometer
Model names: expression CMS, expressionS CMS, expressionL CMS
comply with the essential requirements of the following applicable European Directives and carries the CE mark
accordingly:
2014/35/EU The Low Voltage Directive

2014/30/EU The Electromagnetic Compatibility Directive
2012/19/EU Waste Electrical and Electronic Equipment Directive
2011/65/EU Restriction of the use of certain hazardous substances (RoHS)
and conforms with the following product standards:
Category Standard Classification
Safety EN61010-1:2010 Equipment Class I, Installation Category II

EN 61010-2-061:2015 Pollution Degree 2
EMC EN 55011:2009 + A1:2010 Class A

EN 61326-1:2013 Class A
Australia: AS/NZS CISPR 11:2004 Class A

Canada: ICES-001, Issue 4: 2006 Class A
USA: FCC Part 15 Class A
Year Mark First Applied: 2012
I hereby declare that the equipment named above has been designed to comply with the relevant sections of the
above referenced Directives and Standards.
03-Aug-2018
Jamey Jones Date
Senior Vice President, Operations and Technology

CMS User’s Manual
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.

CMS User’s Manual
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.

CMS User’s Manual
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.

CMS User’s Manual
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)

CMS User’s Manual
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:

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).

CMS User’s Manual
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.

CMS User’s Manual
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.

CMS User’s Manual
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.

CMS User’s Manual
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 expression CMS can either be configured in electrospray ionization (ESI) or 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.
Refer to "Replacing CMS Components" for instructions of how to switch between the ESI and
APCI modes.
1.4.2. CMS Internal Component and Voltage Schematic

CMS User’s Manual
1.4.3. expression CMS Source Housing
Source
Housin
1.4.4. Electrospray Ionization (ESI)
Electrospray ionization (ESI) involves the nebulization of the sample 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.

CMS User’s Manual
1.4.5. Electrospray Ionization (ESI) Source Housing
Front and Rear
1.4.6. 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).

CMS User’s Manual
1.4.7. Atmospheric Pressure Chemical Ionization (APCI) Source

Housing
Corona discharge pin
1.4.8. 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).

CMS User’s Manual
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 (b) in the API source block (a) and enter the hexapole (ion transfer) region.
Extraction electrode voltage ranges from 0 – 10V.

CMS User’s Manual
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.

CMS User’s Manual
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.)

CMS User’s Manual
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.

CMS User’s Manual
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).

CMS User’s Manual
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. The calibrant delivery system is controlled through Mass Express software
which can switch on or off pneumatic valves in the instrument (refer to the Mass Express and
Data Express manuals). 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 calibrant vial can be removed by pulling the lever out (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.

CMS User’s Manual
The following diagram shows the placement of the calibrant vial on the expression CMS:
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.

CMS User’s Manual
Procedure:
 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).
 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
Blue - System in operate and scanning
1.8. Physical Interfaces

Peripheral control outputs all coupling the expression CMS to normal or reversed phase
chromatography systems or other devices. The expression CMS accepts a contact closure (digital
input) signal from external devices, such as liquid chromatographs and flash purification systems
for acquisition triggering.
In addition to the expression CMS, 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 LC
The expression CMS accepts a contact closure (digital input) signal from external devices, such
as liquid chromatographs and flash purification systems for acquisition triggering.

CMS User’s Manual
1.8.2. Integrated Auto-sampler
The CETAC ASX-7000 auto-sampler platform is available as an integrated option with the
expression CMS. It is developed with the accuracy and flexibility to operate with different
sample wells and injection ports. The ASX-7000 platform is able to perform difficult operations
such as septum piercing and is highly customizable for a wide range of automation applications,
including LC-MS, fraction collection, titration, liquid handling, and more.
The Advion integrated auto-sampler has the following device specifications:
 Z-Drive Assembly: The Z-Drive assembly moves the sample probe vertically. The
assembly includes a Z-Axis motor assembly as well as the sample probe. The Z-Drive
motor assembly attaches onto the auto-sampler arm.
 Power Indicator Lamp: The power to the auto-sampler is on when the light is active.
 Standards Vials: The number and type of standards vials depends on the application and
the version of the auto-sampler
 Sample Base: The sample base holds the sample and standards vial racks in place.
 Sample Vial Racks: The number and type of sample vial racks depends on the
application and the version of the auto-sampler.
 Sample Vials: The number and type of vials depends on the application and the version
of the auto-sampler.
 Arm: The arm moves the sample prove horizontally.
 Flowing Rinse Station: The rinse station is located at the left end of the stands positions
at the back of the sample base. It comes with tubing used to connect the rinse station to
the rinse source and the waste container.

CMS User’s Manual
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 you 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.

CMS User’s Manual
1.8.4. SSI Series 1+ Pump
The SSI Series 1+ pump uses new manufacturing techniques and proven fluidics to give the
highest performance at an economical cost. It is used with the expression CMS to provide a
constant (adjustable) eluent flow rate during an experiment.
The SSI Series 1+ pump operates from 0.01 – 10.00 mL/min. at pressure ratings of up to 2500
psi; or from 0.10 – 40.00 mL/min. at up to 650 psi; allowing both analytical and small-scale
preparative applications.
The SSI has the following device specifications:
 Flow Rates: 0.01 to 10.00 ml/min

 Pressure: 0 to 5,000 psi for 10 ml Stainless Steel or Bioclean head 0 to 3,000 psi for 10
ml PEEK™ head
 Flow Accuracy: ±3% for a flow rate of 0.20 mL/min above, with 80:20 Water/IPA @
1000psi*
 Flow Precision: 0.5% RSD

CMS User’s Manual
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 10 μL/min to 0.5 mL/min for ESI
o 10 μL/min to 1.0 mL/min for APCI
o expression S and expression L CMS10 μL/min to 1 mL/min for ESI
o 10 μL/min to 2 mL/min for APCI
 Nebulization gas: 0.5 L/mi
 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

CMS User’s Manual
 Polarity Switching:
o expression CMS
 Sequential Analysis (50 ms second switching between analysis for –S
and –L models)
 Single Analysis (50ms switching same analysis)
 Inlet capillary cleaning or replacement:

o expression CMS
 Vent mass spectrometer to remove
 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)

CMS User’s Manual
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

CMS User’s Manual
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:

CMS User’s Manual
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)
CMS User’s Manual
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.

CMS User’s Manual
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.

CMS User’s Manual
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.

CMS User’s Manual
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.

CMS User’s Manual
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

CMS User’s Manual
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

CMS User’s Manual
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.

CMS User’s Manual
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

CMS User’s Manual
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.

CMS User’s Manual
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).

CMS User’s Manual
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.

CMS User’s Manual
6. Appendix
Parts List/Consumables
Part Number Description

CMS-001-ESI expression-S Compact Mass Spectrometer with m/z 1200 mass
range. Single quadrupole analyzer with liquid introduction interface.
Includes electrospray ionization ion source (ESI) and 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).
CMS-001-APCI expression-S Compact Mass Spectrometer with m/z 1200 mass
Includes atmospheric pressure chemical ionization ion source (APCI)
and 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).
expression-L Compact Mass Spectrometer with m/z 2000 mass
Includes electrospray ionization ion source (ESI) and manual flow
CMS-L01-ESI
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).
expression-L Compact Mass Spectrometer with m/z 2000 mass
Includes atmospheric pressure chemical ionization ion source (APCI)
CMS-L01-APCI and 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).

CMS User’s Manual
Part Number Service and Training Options

Installation
SRV302 Installation and basic training for expression Compact Mass Spectrometer
SRV303 12-month warranty upon installation
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)
Training Courses
3-day Training Course at Advion, Ithaca, NY covering the operation and
SRV301 maintenance of the expression CMS, travel and lodging not included. (Two
places are included FOC with CMS purchase)
2-day Training Course at Customer site covering the operation and
SRV401
maintenance of the expression CMS.

CMS User’s Manual
Part Number Accessories

Atmospheric Pressure Chemical Ionization (APCI) ion source for expression
IS-APCI-001
CMS for original, pre 2014, CMS model.
Electrospray Ionization (ESI) ion source for expression CMS, for original, pre
IS-ESI-001
2014, model.
Atmospheric Pressure Chemical Ionization (APCI) ion source for expression
IS-APCI-S01
CMS
IS-ESI-S01 Electrospray Ionization (ESI) ion source for expression CMS
Roughing pump exhaust kit (5m hose and KF 25 connector to connect to
ACC305 pump or oil mist filter vent - user will need to provide connection at the
house exhaust side)
ACC306 Vacuum hose extension kit - 2m
5m of 1/4" OD PFA tubing for nitrogen supply connection Active Splitting
ACC310 ACC350
Valve, IDEX MRA-100-000.
Laptop computer meeting operating specifications for the expression CMS,
ACC311 ACC360
Pump for make-up flow, SSI Series 1 Plus HPLC Pump - V10SFT01.
ACC390 ACC400 Cart for expression CMS Auto-sampler, Cetac 130
Nitrogen Generator - PEAK N118LA - 18 L/min Normal Phase Flash
ACC420 ACC370 Chromatography interface accessory kit containing required tubing, fittings,
and cables.
Nitrogen Generator - PEAK NM18L - 18 L/min (requires compressed air
ACC421 ACC371 source 8.3 - 10 bar) Agilent HPLC interface accessory kit containing required
tubing, fittings, and cables.
Shock attenuation mounting table for mobile labs. Laptop computer meeting
ACC460 ACC311
operating specifications for the expression CMS.
SWL_LCEXPRESS_ Integrated software for control of Agilent HPLC and UHPLC chromatography
AGILENT_1 equipment
ACC350 Mass Rate Attenuator Valve, IDEX MRA-100-000.
ACC360 Pump for make-up flow, SSI Series 1 Plus HPLC Pump - V10SFT01.
ACC400 Auto-sampler, Cetac ASX7100
TLC/CMS interface for mass analysis of TLC plates. Oval head, 2 x 4 mm. To
ACC450 interface to CMS requires ACC372 accessory kit and suitable isocratic pump
e.g. ACC360
TLC/CMS interface for mass analysis of TLC plates. Round head, 4 mm. To
e.g. ACC360
TLC/CMS interface for mass analysis of TLC plates. Round head, 5 mm. To
e.g. ACC360

CMS User’s Manual
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. ACC360
UPLC & HPLC interface accessory kit containing required tubing, fittings, and
ACC371
cables.
Direct Injection interface accessory kit containing the required tubing,
ACC372
fittings, and cables. Requires suitable make-up flow pump e.g. ACC360
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. ACC360
TLC interface accessory kit containing the required tubing, fittings, and
ACC374 cables. Requires TLC interface, ACC45x, and suitable make-up flow pump e.g.
ACC360

MAN - MFG006 - RevF - Expression CMS User's Manual

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MAN_MFG006_RevF Original Instructions Page 2

1.4.4. Electrospray Ionization (ESI) ........................................................................................... 23

MAN_MFG006_RevF Original Instructions Page 3

5.2. Replacing CMS Components ............................................................................................... 50

MAN_MFG006_RevF 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_RevF Original Instructions Page 5

Worldwide Advion Distributors

MAN_MFG006_RevF 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 Autosampler is a registered trademark of CETAC Technologies.

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

SSI Series 1+ Pump® is a registered trademark of Scientific Systems, Inc.

MAN_MFG006_RevF 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_RevF 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_RevF 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_RevF 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_RevF Original Instructions Page 11

1.2.5. Environmental and European Union (EU) Standards

NOTE: This product complies with the WEEE Directive

MAN_MFG006_RevF Original Instructions Page 12

Equipment: Mass Spectrometer

Model names: expression CMS, expressionS CMS, expressionL CMS

2014/35/EU The Low Voltage Directive

and conforms with the following product standards:

Category Standard Classification

Safety EN61010-1:2010 Equipment Class I, Installation Category II

EMC EN 55011:2009 + A1:2010 Class A

Australia: AS/NZS CISPR 11:2004 Class A

Year Mark First Applied: 2012

MAN_MFG006_RevF Original Instructions Page 13

1.2.6. General Installation Requirements

1.2.6.1. Lab Environment Requirements

MAN_MFG006_RevF Original Instructions Page 14

System Weight Dimensions

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

MAN_MFG006_RevF Original Instructions Page 15

1.2.6.2. Electrical Requirements and Connections

expression CMS 600VA maximum

1.2.6.3. Electrical Connections