FAIMS Operator's Manual Revision B

FAIMS Operator's Manual Revision B
FAIMS
Operator’s Manual
70111-97134 Revision B
June 2007
For Research Use Only
Not for use in Diagnostic Procedures
© 2007 Thermo Fisher Scientific Inc. All rights reserved.
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Printing History: Revision A printed in July 2006. Revision B printed in June 2007.
Software Version: Xcalibur 2.0 SR2, Quantum 1.4, LTQ 2.4
Thermo Fisher Scientific San Jose performs complete testing and evaluation of its products to ensure full
compliance with applicable domestic and international regulations. When the system is delivered to you, it
meets all pertinent electromagnetic compatibility (EMC) and safety standards as described below.
EMC Directive 89/336/EEC, 92/31/EEC, 93/68/EEC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
EN 61326-1
(1997)
EN 61000-4-6
(1996, 2001)
EN 55011
(1998)
EN 61000-4-11
(1994, 2001)
EN 61326
(1998)
EN 61000-3-2
(1995)
EN 61000-4-2
(1998)
EN 61000-3-3
(1995)
EN 61000-4-3
(2002)
CFR 47 - Part 15 - Subpart B: 2005 - Class A
EN 61000-4-4
(1995, 2001)
CFR 47 - Part 18: 2005
EN 61000-4-5
(1995, 2001)
Low Voltage Safety Compliance
This device complies with Low Voltage Directive EN 61010-1:2001.
Changes that you make to your system may void compliance with one or more of these EMC and safety
standards. Changes to your system include replacing a part or adding components, options, or peripherals
not specifically authorized and qualified by Thermo Fisher Scientific. To ensure continued compliance with
EMC and safety standards, replacement parts and additional components, options, and peripherals must be
ordered from Thermo Fisher Scientific or one of its authorized representatives.
FCC Compliance Statement
THIS DEVICE COMPLIES WITH 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.
CAUTION: Read and understand the various precautionary notes, signs, and symbols
contained inside this manual pertaining to the safe use and operation of this product before
using the device.
Notice on Lifting and Handling of
Thermo Fisher Scientific San Jose Instruments
For your safety, and in compliance with international regulations, the physical handling of this
Thermo Fisher Scientific San Jose instrument requires a team effort for lifting and/or moving the instrument.
This instrument is too heavy and/or bulky for one person alone to handle safely.
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Thermo Fisher Scientific San Jose Instruments
In compliance with international regulations: If this instrument is used in a manner not specified by
Thermo Fisher Scientific San Jose, the protection provided by the instrument could be impaired.
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Scientific, über die Verwerter, und weitere Hinweise, die nützlich sind, um die Produkte zu
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WEEERoHS.
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sujettes à la directive RoHS sont disponibles sur www.thermo.com/WEEERoHS.
C
Contents
Thermo Scientific
Chapter 1
FAIMS Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
FAIMS Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Components of the FAIMS System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Chapter 2
FAIMS Control Software: TSQ Quantum Series. . . . . . . . . . . . . . . . . . . . . . . . . . . .17
FAIMS Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Saving the Settings in a Tune File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Copying the Optimized CVs to Instrument Setup and LCquan . . . . . . . . . . . . 22
Putting the FAIMS System in Standby . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Chapter 3
FAIMS Control Software: LTQ Series . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
Configuring FAIMS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Setting FAIMS Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Optimizing the Compensation Voltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Saving the Settings in a Tune File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Putting the FAIMS System in Standby . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Chapter 4
Getting Started Using FAIMS on TSQ Quantum Series Mass Spectrometers . .31
Setting Up the Syringe Pump to Infuse Sample . . . . . . . . . . . . . . . . . . . . . . . . . 31
Setting Up the Mass Spectrometer and FAIMS System . . . . . . . . . . . . . . . . . . . 33
Configuring the Syringe Pump and Infusing the Polytyrosine . . . . . . . . . . . . . . 36
Running CV Scans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Verifying a Stable Ion Beam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Testing the FAIMS Selectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Further Optimization of FAIMS Parameters for Selectivity . . . . . . . . . . . . . . . . 47
Saving the Settings in a Tune File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Copying the Optimized CVs to Instrument Setup or LCquan. . . . . . . . . . . . . . 48
Flushing the System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Chapter 5
Getting Started Using FAIMS on LTQ Series MS Detectors . . . . . . . . . . . . . . . . .51
Setting Up the Syringe Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Setting Up the MS Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Configuring the Syringe Pump and Infusing the Calibration Solution . . . . . . . 55
Running CV Scans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Verifying a Stable Ion Beam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Testing the FAIMS Selectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
FAIMS Operator’s Manual
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Contents
Further Optimization of FAIMS Parameters for Selectivity . . . . . . . . . . . . . . . . 63
Saving the Settings in a Tune File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Flushing the Sample Transfer Line, Sample Tube, and H-ESI Probe. . . . . . . . . 64
Chapter 6
Advanced Optimization of FAIMS Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .65
Optimizing the selectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Optimizing the Sensitivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Chapter 7
Getting Connected. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69
Chapter 8
Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .77
Safety, Instrument, and Performance Considerations . . . . . . . . . . . . . . . . . . . . 77
Cleaning the FAIMS Electrodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Replacing Gas Purification Cartridges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Replacing AC Fuses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Chapter 9
Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103
Chapter 10
Site Preparation and System Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . .109
Installation Guidelines. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Dimensions and Weight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Electrical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Gases and Regulators. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Data System Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Installation Equipment and Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Installation Checklist. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Appendix A FAIMS Optimization Flowchart. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .119
Chapter A
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FAIMS Operator’s Manual
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .123
Thermo Scientific
P
Preface
About This Manual
This manual describes the information required to use the Thermo Scientific high-Field
Asymmetric waveform Ion Mobility Sprectrometry (FAIMS) system on TSQ Quantum series
and LTQ series mass spectrometers. This guide also describes maintenance and
troubleshooting information.
This manual assumes that the FAIMS system has been installed by Thermo Fisher Scientific’s
authorized representative and is ready for use. Information in this manual about setting up the
FAIMS system on your instrument is provided only in the event you must remove or
reassemble parts.
Related Documentation
In addition to this Operator’s Manual, Thermo Fisher Scientific provides the following
documents for the TSQ Quantum series and LTQ series mass spectrometers:
• Preinstallation Requirements Guide
• Getting Connected
• Getting Started
• Hardware Manual
Safety and Special Notices
Make sure you follow the precautionary statements presented in this guide. The safety and
other special notices appear in boxes.
Safety and special notices include the following:
CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION
notice is accompanied by an appropriate CAUTION symbol.
Thermo Scientific
FAIMS Operator’s Manual
iii
Preface
Hazard Symbols
IMPORTANT Highlights information necessary to prevent damage to software, loss of
data, or invalid test results; or may contain information that is critical for optimal
performance of the system.
Note Highlights information of general interest.
Tip Helpful information that can make a task easier.
Hazard Symbols
Hazard symbols identify important information to protect the user from personal injury and
to prevent damage to the FAIMS system. Failure to comply with these precautions violates
the safety standards of the design and intended use of the equipment.
The following symbols are used on the FAIMS system and in this documentation to indicate
safety cautions that indicate risks for people. Disregard for these cautions may cause personal
harm.
Indicates the presence or use of compressed gas.
Indicates danger from high voltages.
Indicates potential harm due to hot surfaces.
Indicates danger from toxic substances.
Indicates danger from corrosive substances.
Indicates danger from flammable substances.
Indicates the presence of alternating current (AC) power.
Indicates the system protective earth location.
Indicates a general caution for additional care to be taken.
iv
FAIMS Operator’s Manual
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Preface
General Safety and Instrument Considerations
General Safety and Instrument Considerations
Observe the following:
CAUTION When working with the FAIMS system, always follow these general safety and
instrument considerations, as well as others described throughout this manual. Disregard
for these cautions may cause harm to the user or the FAIMS system.
• The FAIMS system (referring to both its waveform generator and temperature control
modules) must be connected to the mass spectrometer for normal operation. Do not
operate the temperature control module without connecting it to the mass spectrometer
or the waveform generator.
• Do not attempt to open the waveform generator or the temperature controle module. All
servicing must be performed by a Thermo Fisher Scientific authorized representative.
• The FAIMS waveform generator applies high voltages. Power down the FAIMS system
before performing any procedures that cause exposure to these voltages.
• Use the FAIMS system and mass spectrometer only in the manner specified by Thermo
Fisher Scientific Corporation. Any other use may impair the protection provided by the
equipment.
• During operation, components of the mass spectrometer and the FAIMS system may
become very hot. Ensure that components are cool before attempting to handle them.
• Observe good laboratory practices when working with chemicals (for example, when
cleaning the FAIMS electrodes). Use a fume hood and wear appropriate personal
protective equipment.
• To prevent overheating of the FAIMS system, do not block its top ventilation holes.
• Inspect all components and connections on a regular basis to ensure they remain in
proper working condition.
• Replace the AC fuse only with the appropriate fuse, as described in “Replacing AC Fuses”
on page 101.
The following symbols are used on the FAIMS system to indicate whether power is being
supplied to the FAIMS waveform generator or temperature control modules:
Indicates the position of the power switch to apply power to the FAIMS
waveform generator and temperature control modules.
Indicates the position of the power switch when power is not being
applied to the FAIMS waveform generator or temperature control
modules.
Identifies the location of the fuse. The fuse value appears beside this
symbol.
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FAIMS Operator’s Manual
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Preface
Environmental Considerations
Environmental Considerations
The following table describes the environmental considerations for the FAIMS system. Unless
specified otherwise, values apply to both the waveform generator and the temperature control
module.
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FAIMS Operator’s Manual
Requirement
Description
Input voltage range
120 to 240 V at 50 to 60 Hz AC
Maximum current
(waveform generator)
• 2.5 A at 120 VAC
Maximum current
(temperature control
module)
• 5 A at 120 VAC
• 1.3 A at 240 VAC
• 2.5 A at 240 VAC
Installation environment
Installation category II, Pollution degree 2
Operating temperature
15º C to 30º C
Operating humidity
5% to 95% RH non-condensing
Operating altitude
0 to 2000 meters above sea level
Storage temperature
-40 ºC to 70 ºC
Storage humidity
5% to 95% RH non-condensing
Input air pressure
(temperature control
module)
Minimum: 40 psi
Maximum: 60 psi
Thermo Scientific
Preface
Performance Considerations
Performance Considerations
When working with the FAIMS system, the following can affect FAIMS system performance:
• When handling stainless steel components such as the FAIMS electrodes, ensure that the
surfaces are not scratched.
• The high voltage lead includes a wire of a fixed length and rings at either end of the lead
that can easily be damaged if not handled properly. Damage to the high voltage lead
caused by stretching or bending the lead is not covered by warranty.
Contacting Us
There are several ways to contact Thermo Fisher Scientific.
Assistance
For new product updates, technical support, and ordering information, contact us in one of
the following ways:
Visit Thermo Scientific on the Web
www.thermo.com/finnigan
Contact Technical Support
Phone:
Fax:
E-mail:
Knowledge base:
1-800-685-9535
1-561-688-8736
[email protected]
http://www.thermokb.com
Find software updates and utilities to download at http://mssupport.thermo.com.
Contact Customer Service
For ordering information in the U.S. and Canada:
Phone:
1-800-532-4752
Fax:
1-561-688-8731
Web site:
www.thermo.com/finnigan
Changes to the Manual and Online Help
To suggest changes to this guide or to the Help, use one of the following:
• Fill out a reader survey online at www.thermo.com/lcms-techpubs.
• Send an e-mail message to the Technical Publications Editor at
[email protected]
Thermo Scientific
FAIMS Operator’s Manual
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1
FAIMS Overview
This chapter provides an overview of the high-Field Asymmetric waveform Ion Mobility
Spectrometry (FAIMS) system. This chapter also describes the components of the FAIMS
system and the general system operation. The FAIMS system with the TSQ Quantum Ultra
and LTQ XL are shown below.
Figure 1.
Thermo Scientific
FAIMS system and TSQ Quantum Ultra
FAIMS Operator’s Manual
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FAIMS Overview
FAIMS Operation
Figure 2.
FAIMS system and LTQ XL
FAIMS Operation
FAIMS adds another dimension of selectivity to LC/MS/MS experiments, providing the
additional selectivity that is often required in challenging LC/MS/MS assays.
Using FAIMS, only selected ions pass from the ion source to the mass spectrometer. The
result is increased selectivity, improved detection limits, and increased throughput.
Selection of Ions
FAIMS continuously selects and focuses ions at atmospheric pressure using changes that occur
in ion behavior when exposed to high electric fields.
At low field strengths, the ion mobility is independent of the applied electric field. However,
at high electric fields (for example, greater than 2.5 KV/cm) the mobility of an ion changes
with electric field strength. These compound-dependent changes in the mobility of an ion at
high field relative to low field provide ion selectivity within the FAIMS interface.
In the FAIMS system, alternating high and low electric fields are applied to a set of
concentrically cylindrical electrodes. Alternating electric fields are supplied via a waveform
generator that produces an asymmetric waveform. This asymmetric waveform applies a high
electric field, called the dispersion voltage (DV), between the electrodes for a short period of
time and then applies a lower electric field for a longer time.
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FAIMS Overview
FAIMS Operation
When the FAIMS electrodes are installed on the mass spectrometer, desolvated ions are
introduced into the annular region between the two cylindrical electrodes and are carried
toward the mass spectrometer by a flow of gas, called the carrier gas. The ions move radially
between the electrodes as the result of the applied asymmetric waveform. Because the mobility
of the ion during the application of the DV is different than during the low voltage portion of
the waveform, ions begin to drift towards one of the two electrodes. This is illustrated in
Figure 3. If an ion reaches an electrode surface, it is discharged and neutralized.
Figure 3. Illustration of the FAIMS effect (parallel plate example), showing ion drift
To prevent an ion from being discharged, a small dc potential, called the compensation
voltage (CV), is applied to the inner electrode. The CV compensates for the drift that an ion
experiences as the result of the application of the asymmetric waveform. This is illustrated in
Figure 4.
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FAIMS Overview
FAIMS Operation
Figure 4. Illustration of the FAIMS effect (parallel plate example), with compensation voltage (CV),
showing ion transmission
The CV needed to compensate for drift is ion dependent. Therefore, the CV is a selection
parameter for transmitting a subset of ions to the mass spectrometer.
Figure 5 shows plots of the ion signal intensity versus CV for a drug and its metabolite. The
drug can be selected because the metabolite does not contribute signal at the monitored CV of
the drug.
Figure 5. FAIMS-MS/MS selection of drug and metabolite
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FAIMS Overview
FAIMS Operation
Summary of FAIMS Parameters
The setable parameters for FAIMS are:
• Dispersion voltage (DV)
• Compensation voltage (CV)
• Electrode temperatures
• Carrier gas composition
• Carrier gas flow rate
Dispersion Voltage
The dispersion voltage (DV) is the peak potential of the asymmetric waveform. As the DV
increases, the CV tends to increases as does the ion intensity. The DV is most often set to its
maximum value of ±5000 V. The polarity is set to negative for positive ions and positive for
negative ions.
Compensation Voltage
The compensation voltage (CV) is the dc potential offset that is applied to the inner electrode
to transmit selected subsets of ions through the electrodes. The CV is typically negative for
positive ions and positive for negative ions. The CV is tuned for a specific ion, as was shown
in Figure 5.
Electrode Temperatures
Temperature can affect ion selection by changing the gas density within the electrodes.
Temperature control enables stable conditions to be reached quickly and maintained
indefinitely. The electrodes need to be temperature controlled, otherwise the CV changes
during system equilibration. The inner and outer electrode temperatures are adjusted
independently. They are controlled by air flowing past the electrodes. Differences between the
temperatures of the inner and outer electrodes can be used to enhance selectivity. Standard
temperature settings are 70 ºC for the inner electrode and 90 ºC for the outer electrode.
Figure 6 shows how the CV peak width changes for minoxidil as the temperature difference
between the inner and outer electrodes increases.
Note Generally, intensity decreases as the difference in temperature between electrodes
increases, if the inner electrode temperature is lower than the outer electrode
temperature. Intensity tends to increase as the difference in temperature between the
electrodes increases, if the inner electrode temperature is higher than the outer electrode
temperature.
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FAIMS Overview
FAIMS Operation
Figure 6. Effect of the temperature difference of the electrodes on the intensity and compensation
voltage for minoxidil, with the outer electrode temperature higher than the inner electrode
temperature
Carrier Gas Composition
The carrier gas transports ions through the electrode assembly. The interaction of the carrier
gas with the ion affects selectivity and sensitivity. See Figure 7. For most analyses, a carrier gas
composition of 50:50 N2:He is optimal.
Note For the analysis of some environmental and low molecular weight compounds,
using100% nitrogen and a positive DV for positive ions or a negative DV for negative ions
may result in improved sensitivity.
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1
Figure 7.
FAIMS Overview
FAIMS Operation
Effect of %He on the intensity and resolution for atrazine
Carrier Gas Flow Rate
The optimal carrier gas flow rate is between 2.5 and 4 L/min. If the carrier gas flow rate is set
too low, the arriving ions are not well desolvated. In such cases, one of several observations
may be made:
• There are several peaks in the CV spectrum for a particular m/z value. These may arise
from variously solvated species.
• The transmission CV differs from a previously observed value for a particular ion.
• The ion signal intensity is lower.
• The CV required for the transmission of solvated species will be different than for
desolvated ions.
A carrier gas flow rate set too high may cause turbulence in front of the entrance plate. The
ion intensities will decrease from the optimal value, but the CV of transmission will remain
unchanged.
The effect of the carrier gas flow rate on the intensity and CV is illustrated in Figure 8. A
good starting point is a combined flow rate of 3.5 L/min of He + N2.
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FAIMS Overview
Components of the FAIMS System
Figure 8.
Effect of carrier gas flow rate on the intensity and compensation voltage for
terephthalic acid
Components of the FAIMS System
The major components of the FAIMS system include:
• FAIMS Waveform Generator
• FAIMS Temperature Control Module
• FAIMS High Voltage Lead
• FAIMS Interface Assembly
• FAIMS Electrode Assembly
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1 FAIMS Overview
Components of the FAIMS System
FAIMS Waveform Generator
Figure 9 shows the front of the FAIMS waveform generator.
High voltage
lead flange
Connection panel
Figure 9.
FAIMS waveform generator (front)
The FAIMS waveform generator includes:
• Function generator that produces the asymmetric waveform and dc voltages required to
operate the FAIMS
• Gas flow system
• Connection panel for the power supplies required to operate the electrodes and other
types of interfaces
• High-voltage lead flange for connecting the high voltage lead
• Safety interlocks
The gasses, power, and communications inputs and outputs of the waveform generator are
shown in Figure 10.
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Components of the FAIMS System
Figure 10. Gases, voltages, and communication of the waveform generator
Function Generator
The function generator performs the following operations:
• Produces the asymmetric waveform supplied to the electrodes. The asymmetric waveform
provides a maximum dispersion voltage (DV) of ± 5000 V and operates at a frequency of
750 kHz.
• Produces the outer bias and compensation voltages that are applied to the FAIMS
electrodes.
Gas Flow System
The FAIMS electrodes require a supply of clean, dry carrier gas. The carrier gas assists in
desolvation and transport of ions through the electrodes. The standard mixture is 50:50
He:N2.
During FAIMS operation, gases from external sources are provided to the gas flow system
located in the waveform generator. Each gas passes through its own purification cartridge.
The gas purification cartridges, located in the rear compartment of the waveform generator,
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Components of the FAIMS System
can last several months depending on the purity of gases and the frequency of use. For
information about replacement cartridges, see “Replacing Gas Purification Cartridges” on
page 100.
After leaving the gas purification cartridge, each gas enters a mass flow controller, calibrated
specifically for that gas. The gasses are mixed in a tee union and the gas is then delivered to the
region of the FAIMS electrodes located between the entrance plate and the outer electrode.
The gas is delivered using Teflon® tubing to the region of the FAIMS electrodes located
between the entrance plate and the outer electrode.
CAUTION A continuous gas flow through the electrodes is essential for optimal
performance of the FAIMS interface. Never use the ion source without a gas flow.
Connection Panel
The connection panel provides access to the electronics, communications, and gases. This
panel is located at the front of the waveform generator, as Figure 11 shows.
Receptacle for main
power cord and on/off
switch
Carrier gas
outlet port
Power indicator
Inlet gas ports
(He, N2, CO2)
Connector for entrance
plate voltage cable
Communication port to the
TSQ Quantum ro LTQ
Ion Max interlock port
Figure 11. Connection panel on the FAIMS waveform generator
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High Voltage Lead Flange
The high voltage lead flange allows quick connection of the high voltage lead to the waveform
generator. This flange also makes up part of the FAIMS safety interlock system. A brass
contact located in the middle of the flange transfers the specialized waveform from the
waveform generator to the high voltage lead. For high-voltage to be applied to the contact, the
high-voltage lead must be in place and connected to the FAIMS interface assembly.
FAIMS Temperature Control Module
The temperature control module monitors and controls the temperature of the FAIMS
electrodes. See Figure 12.
Figure 12. FAIMS temperature control module.
The temperature control module does the following:
• Monitors the temperatures of the inner and outer heaters in the heater assembly
• Supplies a readback to the software from thermocouple measurements taken in the
exhaust lines
• Adjusts the output of the heaters to ensure that the desired temperature is maintained
within ±1 ºC
Connections for the external gas supply, electrodes, and communications are available from
the connection panel, located at the rear of the temperature control module. The gas and
control inputs and outputs of the temperature control module are shown in Figure 13.
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Components of the FAIMS System
Figure 13. Gas and control inputs and outputs of the temperature control module
FAIMS High Voltage Lead
The high-voltage lead is a stainless steel tube through which the wire carrying the asymmetric
waveform and the inner bias voltage is passed, as Figure 14 shows. The high-voltage lead
connects to the high-voltage flange on the waveform generator and to the high-voltage lead
adapter on the interface assembly. The lead is slightly flexible for easier installation.
The high-voltage lead is part of the FAIMS interface safety interlock system. If the
high-voltage lead is not connected to both the high voltage lead flange on the waveform
generator and the high-voltage lead adapter on the interface assembly, voltages are not be
supplied.
During installation of the FAIMS interface, the authorized Thermo Fisher Scientific
representative adjusts the high voltage lead to fit the mass spectrometer. Changes, such as
bending or stretching this lead after initial installation may affect the unit’s performance.
Damages due to these types of changes made without the assistance of an authorized
representative are not covered by warranty.
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Figure 14. FAIMS high voltage lead (TSQ Quantum)
FAIMS Interface Assembly
The FAIMS interface assembly adapts the mass spectrometer's ion source so that it can
accommodate the FAIMS electrodes. Through the interface assembly, voltages, carrier gas,
and heated air are applied to the electrodes. All interlock conditions must be satisfied before
the FAIMS interface becomes operational.
The Figure 15 shows the interface assembly, including the electrodes.
High-voltage
lead adapter
Heater box
Electrode assembly
and entrance plate
Gas exhaust ports
Figure 15. FAIMS interface assembly and electrodes
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Components of the FAIMS System
API probe port
Ion Max housing
Outer electrode
Inner electrode
Entrance plate
Ion transfer tube
(ion source interface)
Figure 16. FAIMS components inside the Ion Max source housing
FAIMS Electrode Assembly
The electrodes are central to the FAIMS system. Positioned between the ion source and the
mass spectrometer’s ion transfer tube, the electrodes selectively transmit subsets of ions to the
mass spectrometer. There is a 2.5 mm separation between the inner and outer electrodes. The
inner and outer electrodes are secured between two endcaps, as Figure 17 shows.
Carrier gas and the electrode heating gasses enter the electrode assembly through ports in the
left endcap. Also, the outer electrode bias voltage and the entrance plate voltage are supplied
via the left endcap. The FAIMS interface supplies the dispersion and compensation voltages
to the inner electrode by a push pin contact.
The carrier gas exits the outer electrode and gets redirected by the entrance plate (not shown)
to the ion entrance. At the ion entrance, the carrier gas enters the electrode assembly and
transports the ions through the electrode assembly.
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Components of the FAIMS System
Right endcap
Carrier gas
exit
Ion entrance
Outer electrode
Left endcap
Figure 17. FAIMS electrode assembly (front)
Safety Interlocks
In addition to the standard TSQ Quantum and LTQ safety interlocks, the following
conditions must be satisfied before the FAIMS system applies voltage to the electrodes:
• H-ESI or APCI probe must be installed
• High-voltage lead must be connected
• Bias voltage cable must be connected
• Communication between the waveform generator and the TSQ Quantum or LTQ must
be functional
CAUTION Safety interlocks protect you. Do not tamper with these interlocks.
Xcalibur displays a popup error message and places the system in standby if one or more of
the above conditions is not met. In addition, Xcalibur displays a popup error message and
places the system in standby if a thermal fault occurs or if the maximum allowable number of
discharge events is reached.
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FAIMS Control Software: TSQ Quantum Series
During an experiment, Xcalibur’s FAIMS control software manages the voltages, gas
composition, gas flow rate, and temperature settings used for FAIMS separations. These
parameters can be constant for the duration of an experiment or they may be changed at
predefined intervals over the course of the experiment.
Note When the TSQ Quantum is turned on, Quantum firmware will check for FAIMS
attachment by sending commands to the FAIMS waveform generator. If the Quantum
receives valid responses to these commands, the firmware will assume that FAIMS is
currently attached to the mass spectrometer. When you open the Quantum Tune or
Instrument Setup, Xcalibur enables you to create instrument methods or tune methods
specific to FAIMS.
This chapter provides an overview of the FAIMS control software in the following sections:
• FAIMS Settings
• Saving the Settings in a Tune File
• Copying the Optimized CVs to Instrument Setup and LCquan
• Putting the FAIMS System in Standby
For a tutorial on performing a FAIMS analysis using a polytyrosine calibration solution, see
“Getting Started Using FAIMS on TSQ Quantum Series Mass Spectrometers” on page 31.
FAIMS Settings
The following FAIMS parameters can be controlled by Xcalibur:
• Compensation voltage
• Outer bias voltage
• Dispersion voltage
• Gas composition and flow rate
• Electrode temperatures
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FAIMS Settings
There are two places where you can set FAIMS parameters:
• FAIMS Control view
• Tune Table view
FAIMS Control View
Y To set FAIMS parameters by using the FAIMS Control view
1. Choose Start > Programs > Xcalibur > Quantum Tune to open the Quantum
Tune window.
2. Click the FAIMS button on the toolbar to display the FAIMS Control view. See
Figure 18.
3. Enter the values of the FAIMS settings in the appropriate boxes and click Apply. (You
can also use the up and down arrows to change the settings.) Begin with the standard
operating values listed in Table 1 or Table 2.
4. Obtain a CV spectrum (that is, ion intensity versus CV) by performing a CV ramp. To
perform a CV ramp, type the starting and ending CV voltages in the Start (V) and Stop
(V) boxes and click Start. To find the optimum CV value, select Optimization first.
Note If the range between the start and stop values is 10 V or less. Xcalibur uses
a CV increment of 0.1 V instead of 0.3 V. Thus, the FAIMS Control view
enables a fine CV optimization if the peak’s resolution is sharp and you want to
find the most optimum CV.
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FAIMS Settings
Figure 18. FAIMS Control view
Table 1. Standard operating values for positive ions
Thermo Scientific
FAIMS Parameter
Value
Compensation voltage
Scan -30 to +10 V
Outer bias voltage
Same as the heated capillary
Dispersion voltage
-5000 V
Gas percentage
50% He
Gas flow
3.5 L/min
Inner electrode temperature
70 °C
Outer electrode temperature
90 °C
API probe position
Probe depth: C
Micrometer: 1
Lateral position: center
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FAIMS Settings
Table 2. Standard operating values for negative ions
FAIMS Parameter
Value
Compensation voltage
Scan -10 to +30 V
Outer bias voltage
Same as the heated capillary
Dispersion voltage
+5000 V
Gas percentage
50% He
Gas flow
3.5 L/min
Inner electrode temperature
70 °C
Outer electrode temperature
90 °C
API probe position
Probe depth: C
Micrometer: 1
Lateral position: center
Tune Table View
You can also set FAIMS parameters individually in the Tune Table view.
Y To set FAIMS parameters using the Tune Table View
1. Click on the Full Instrument Control button on the toolbar in Quantum Tune to open
the Device view, as Figure 19 shows.
Figure 19. Device view showing the FAIMS devices
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Saving the Settings in a Tune File
2. Click on a FAIMS parameter listed under FAIMS Devices to display the Tune Table for
that parameter, as Figure 20 shows.
Figure 20. Tune table for the compensation voltage
Note If you optimize the CV from the Tune Table view, the optimization
procedure ramps the CV for each ion from +10 to -30 V (-10 to +30 V for
negative ions) in increments of 0.3 V.
You can automatically optimize only the compensation voltage and the outer bias
voltage.
Saving the Settings in a Tune File
In Instrument Setup, the acquisition time is divide into segments. Each segment can use a
different tune method with different mass spectrometer and FAIMS settings. Tune methods
are saved in tune files with extension .TSQTune.
To save the mass spectrometer and FAIMS settings in a tune file
1. Choose File > Save Tune As to open the Save As dialog box.
2. Browse to the destination folder of the tune file.
3. Enter a name for the new tune file and click Save to save the settings in the tune file.
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Copying the Optimized CVs to Instrument Setup and LCquan
Copying the Optimized CVs to Instrument Setup and LCquan
You can export the selected ion monitoring (SIM) or selected reaction monitoring (SRM)
settings, including the optimized CVs, to Instrument Setup and LCquan. These settings can
then be saved in an Instrument Method or an LCquan Method.
Y To copy the optimized CVs to Instrument Setup or LCquan
1. In Quantum Tune, click the Define Scan button on the Control / Scan Mode toolbar to
display the Define Scan view.
2. Right-click anywhere in the Define Scan view and select Copy Scan Event from the menu
that appears.
3. Click on the TSQ Quantum icon in Instrument Setup to display the MS Detector page,
or choose Start > Programs > Xcalibur > LCquan to display the Scan Editor page of
LCquan.
4. Select a scan event on the Scan Event bar.
Note You can change CVs between scan events, but not the other FAIMS settings.
5. Right-click anywhere and select Paste Scan Event from the menu that appears. Xcalibur
pastes the SIM or SRM masses, tube lens voltages, and CVs from Quantum Tune into the
SIM or SRM table, as Figure 21 shows.
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Putting the FAIMS System in Standby
Figure 21. LCquan, showing the imported CVs
Putting the FAIMS System in Standby
When FAIMS is not being used, put it in standby rather than powering it down. When
FAIMS is put in standby:
• All voltages are turned off. Voltages are reinstated to their pre-standby values when
FAIMS is put back into operation.
Note Voltages can also be turned off by manually setting them to “0”. Standby is
a faster way to do this and provides the benefit of quickly reinstating the voltage
values.
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Putting the FAIMS System in Standby
• N2 gas flow to the electrodes continues at a flow rate of 1.5 L/min, which keeps the
electrodes clean.
Y To put the FAIMS in standby
In Quantum Tune, click the On button.
Y To resume operation
In Quantum Tune, click the Standby button.
All user-definable settings in the control software are enabled.
Although all voltages are turned off when FAIMS is put on standby or powered down,
standby is the preferred option.
N2 gas flow to the electrodes continues in standby. Because powering down the FAIMS stops
the gas flow, the electrodes may require cleaning before the system is used again. For this
reason, powering down the FAIMS is recommended only under one or both of these
circumstances:
• The electrodes are being removed for cleaning.
• The system will not be used for an extended period of time.
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3
FAIMS Control Software: LTQ Series
During an experiment, Xcalibur’s FAIMS control software manages the voltages, gas
composition, gas flow rate, and temperature settings used for FAIMS separations. These
parameters can be constant for the duration of an experiment or they may be changed at
predefined intervals over the course of the experiment.
This chapter provides an overview of the FAIMS control software in the following sections:
• Configuring FAIMS
• Setting FAIMS Parameters
• Optimizing the Compensation Voltage
• Saving the Settings in a Tune File
• Putting the FAIMS System in Standby
For a tutorial on performing a FAIMS analysis using the LTQ’s tuning and calibration
solution, see “Getting Started Using FAIMS on LTQ Series MS Detectors” on page 49.
Configuring FAIMS
You use Xcalibur Instrument Configuration to specify that a FAIMS system is installed on
your LTQ series MS detector.
Y To configure the FAIMS system
Choose Start > All Programs > Xcalibur > Instrument Configuration to open Xcalibur
Instrument Configuration.
1. Click on the LTQ icon in the Configured Devices window.
2. Click Configure to display the LTQ Configuration dialog box.
3. Select FAIMS to display the FAIMS page.
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Setting FAIMS Parameters
Figure 22. Instrument Configuration - FAIMS page
4. Select
FAIMS Configured.
CAUTION Do not change the CV dwell time or maximum number of DV discharges
unless you are instructed to by Thermo Fisher Scientific Technical Support or Field
Service.
5. Click OK and restart the PC to apply the configuration settings.
Setting FAIMS Parameters
You can set the following FAIMS parameters from Xcalibur:
• Compensation voltage
• Outer bias voltage
• Dispersion voltage
• Gas composition and flow rate
• Electrode temperatures
You set FAIMS parameters in the FAIMS Control dialog box.
Y To set FAIMS parameters
1. Choose Start > All Programs > Xcalibur > LTQ Tune to open the Tune Plus window.
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Setting FAIMS Parameters
2. Click the FAIMS Control button on the toolbar (or choose Setup > FAIMS Control) to
display the FAIMS Control dialog box.
Figure 23. FAIMS Control dialog box
Enter the values of the FAIMS settings in the appropriate boxes and click Apply. Begin with
the standard operating values listed in Table 3 or Table 4.
.
Table 3. Standard operating values for positive ions
Thermo Scientific
Scan Parameter
Value
FAIMS Parameter
Value
Compensation voltage
Scan -30 to +10 V
Outer bias voltage
Same as the heated capillary
Dispersion voltage
-5000 V
Gas percentage
50% He
Gas flow
3.5 L/min
Inner electrode temperature
70 °C
Outer electrode temperature
90 °C
API probe position
Probe depth: C
Micrometer: 1
Lateral position: center
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Optimizing the Compensation Voltage
.
Table 4. Standard operating values for negative ions
Scan Parameter
Value
FAIMS Parameter
Value
Compensation voltage
Scan -10 to +30 V
Outer bias voltage
Same as the heated
capillary
Dispersion voltage
+5000 V
Gas percentage
50% He
Gas flow
3.5 L/min
Inner electrode temperature
70 °C
Outer electrode temperature
90 °C
API probe position
Probe depth: C
Micrometer: 1
Lateral position: center
Optimizing the Compensation Voltage
You optimize the compensation voltage (CV) by performing a CV scan. Refer to “Running
CV Scans” on page 53 for an example of running CV scans using the LTQ tuning and
calibration solution.
Y To optimize the compensation voltage
1. Choose Start > All Programs > Xcalibur > LTQ Tune to open the Tune Plus window.
2. Click on the Tune button (or choose Control > Tune) and then the FAIMS tab to display
the FAIMS page.
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Optimizing the Compensation Voltage
Figure 24. FAIMS page of the Tune dialog box
3. Select Base Peak or Masses to specify optimizing the CV for the base peak or up to four
selected masses.
4. If you selected Masses, enter up to four masses in the mass table.
5. Specify the starting and ending voltages for the CV scan.
• For positive ions, scan from -50 to +10 V.
• For negative ions, scan from -10 to 50 V.
Note If the range between the start and stop values is 10 V or less. Xcalibur uses a CV
increment of 0.1 V instead of 0.3 V. Thus, the FAIMS page enables a fine CV
optimization if the peak’s resolution is sharp and you want to find the most optimum CV.
6. Click the Display Graph button on the Tune Plus toolbar to display the CV plot.
7. Click Start to begin the CV scans.
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Saving the Settings in a Tune File
LTQ plots the ion intensities versus CV for the base peak or the masses you specified.
LTQ enters the optimum CV for each mass in the CV column of the FAIMS page.
Saving the Settings in a Tune File
In Instrument Method, the acquisition time is divide into segments. Each segment can use a
different tune method with different MS detector and FAIMS settings. Tune methods are
saved in tune files with extension .LTQTune.
To save the MS detector and FAIMS settings in a tune file
1. Choose File > Save As to open the Save As dialog box.
2. Browse to the destination folder of the tune file.
3. Enter a name for the new tune file and click Save to save the settings in the tune file.
Putting the FAIMS System in Standby
When FAIMS is not being used, put it in standby rather than powering it down. When
FAIMS is put in standby:
• All voltages are turned off. Voltages are reinstated to their pre-standby values when
FAIMS is put back into operation.
• N2 gas flow to the electrodes continues at a flow rate of 1.5 L/min, which keeps the
electrodes clean.
Y To put the FAIMS in standby
In Tune Plus, click the On button.
Y To resume operation
In Tune Plus, click the Standby button.
All user-definable settings in the control software are enabled.
Although all voltages are turned off when FAIMS is put in standby or powered down, standby
is the preferred option.
N2 gas flow to the electrodes continues in standby. The N2 gas flow cools the electrodes and
keeps them clean. Because powering down the FAIMS stops the gas flow, the electrodes may
require cleaning before the system is used again. For this reason, powering down the FAIMS is
recommended only under one or both of these circumstances:
• The electrodes are being removed for cleaning.
• The system will not be used for an extended period of time.
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Getting Started Using FAIMS on TSQ Quantum
Series Mass Spectrometers
This chapter describes a procedure for running a FAIMS experiment on a TSQ Quantum
series mass spectrometer. The procedure uses a polytyrosine – 1, 3, 6 tuning and calibration
solution, but you can use your own analyte.
Note Before using the FAIMS system, your mass spectrometer needs to be properly
tuned and calibrated, without the FAIMS interface, in the H-ESI/MS mode. Refer to
TSQ Quantum Getting Started.
Y To perform the FAIMS experiment
1. Set up the syringe pump to infuse sample.
2. Set up the mass spectrometer and FAIMS system.
3. Infuse a low concentration tuning and calibration solution containing
polytyrosine – 1, 3, 6 directly into the H-ESI source by using the syringe pump.
4. Run CV scans.
5. Test the efficiency and stability of the spray of the polytyrosine solution into the mass
spectrometer.
6. Test selectivity.
7. Further optimize the FAIMS parameters.
8. Save the settings in a Tune file.
9. Copy the optimized CVs to Instrument Setup or LCquan.
Setting Up the Syringe Pump to Infuse Sample
Use a syringe pump as the sample introduction device. The syringe pump enables you to
infuse the polytyrosine tuning and calibration solution directly into the H-ESI source for
extended periods.
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Setting Up the Syringe Pump to Infuse Sample
The syringe and the syringe pump are located on the front panel of your TSQ Quantum mass
spectrometer. The plumbing connections for H-ESI/MS sample introduction from the
syringe pump are shown in Figure 25 and Figure 26.
Y To set up the syringe pump for infusion
1. Place the mass spectrometer and FAIMS system in standby.
a. Choose Start > Programs > Xcalibur > Quantum Tune to open the Quantum Tune
window.
b. From the Quantum Tune window, choose
Control > Standby (or click the On/Standby button).
2. Connect a 4 cm (1.5 in.) segment of Teflon® tube with a fingertight fitting and a ferrule
to an LC union.
The LC union has coned-bottom, 10-32 receiving ports. Figure 25 shows the suggested
fittings for connecting the syringe to the LC union.
LC union
(P/N 00101-18202)
Fingertight fitting
(P/N 00101-18081)
Ferrule
(P/N 00101-18196)
Teflon tube
(P/N 00301-22803)
Figure 25. Plumbing connections for the syringe.
Note To minimize the possibility of cross-contamination, use a different syringe and
a different sample transfer line for your tuning and calibration solution than you do
for your samples and compound optimization solution.
3. Load a clean syringe with the polytyrosine – 1, 3, 6 tuning and calibration solution.
(Refer to “Appendix A: Solution Formulations” of TSQ Quantum Getting Started for the
procedure for preparing the tuning and calibration solution.)
4. Insert the syringe needle into the segment of Teflon tube.
5. Place the syringe into the syringe holder of the syringe pump.
6. While squeezing the blue release button on the syringe pump handle, push the handle
forward until it just contacts the syringe plunger.
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Setting Up the Mass Spectrometer and FAIMS System
7. Using fingertight fittings and ferrules, connect an infusion line of PEEK tubing
(0.005-in. ID × 1/16-in OD) between the LC union and the grounding union that is
held by the grounding union holder on the H-ESI probe.
Figure 26 shows the suggested fittings and ferrules for connecting the LC union to the
grounding union. Both the LC union and the grounding union have 10-32, coned-bottom
receiving ports.
Grounding union holder on the
H-ESI probe
Grounding union, 10-32 internal ports, 0.010-in. thru-hole
(P/N 00101-18081)
Ferrule
(P/N 00101-18196)
Fingertight fitting
(P/N 00101-18081)
PEEK
tubing
Figure 26. Plumbing connections for the infusion line between the LC union and the grounding union
Setting Up the Mass Spectrometer and FAIMS System
Y To set up the mass spectrometer and FAIMS system for the FAIMS/polytyrosine
experiment
1. Position the H-ESI probe as follows:
• Lateral position: center
• Front to back position: micrometer 1.5 back
• Probe depth: B
2. Choose Start > Programs > Xcalibur > Quantum Tune to open the Quantum Tune
window.
On
Off
Thermo Scientific
Standby
3. Click on the On/Standby button on the toolbar to turn on the mass spectrometer. (The
three different states of the On/Standby button are shown at the left.)
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Setting Up the Mass Spectrometer and FAIMS System
4. Ensure that the mass spectrometer is in the positive ion polarity mode. You can determine
the ion polarity mode of the mass spectrometer by observing the state of the Polarity
button (as shown at the left).
5. Click the FAIMS button on the toolbar to display the FAIMS Control view.
6. In the FAIMS Control view, input the FAIMS settings that are listed in Table 5.
.
Table 5. FAIMS settings for polytyrosine - 1,3,6
FAIMS Parameter
Value
Outer bias voltage (V)
35
Dispersion voltage (V)
-5000
Total gas flow (L/min)
4
% He
50
Inner electrode temperature (ºC)
70
Outer electrode temperature (ºC)
90
7. Click Apply to apply the FAIMS settings.
8. Observe the readbacks in FAIMS Control view. Verify that the readbacks match the
setpoints.
9. Click on the Define Scan button on the toolbar to display the Define Scan view.
10. Click on SIM and Q1MS.
11. In the Define Scan view, input the instrument settings that are listed in Table 6.
.
Table 6. Instrument settings for polytyrosine
Parameter
Value
Scan width (m/z)
10
Scan time (sec.)
0.2
Q1 peak width (m/z)
0.7
Aux valve flow (units)
5
Capillary temperature (ºC)
270
Capillary offset (V)
35
12. Clear (
) the Use Tube Lens Value option.
13. In the SIMS table, input the SIMS settings that are listed in Table 7.
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Setting Up the Mass Spectrometer and FAIMS System
.
Table 7. SIMS settings for polytyrosine
Mass (m/z)
Tube Lens (V)
CV (V)
182.0
50
-10
508.0
75
-10
997.0
125
-10
14. Click Apply to apply the settings.
15. Click the Full Instrument Control button to display the Device view and Tune Table
view, as Figure 27 shows.
16. Click each H-ESI parameter in the Device view to display that parameter’s setting in the
Tune Table view.
Figure 27. Spray voltage selected in the Device view and displayed in the Tune Table view
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Configuring the Syringe Pump and Infusing the Polytyrosine
17. In the Tune Table view, set each H-ESI parameter to the value that is listed in Table 8.
Table 8. H-ESI parameters for polytyrosine
H-ESI Parameter
Value
Spray voltage (V)
4000
Vaporizer temperature (ºC)
30
Sheath gas pressure (psi)
5
Aux valve flow (units)
5
Capillary temperature (ºC)
270
Capillary offset (V)
35
18. Click Apply to apply the settings.
19. Click Ion Source H-ESI in the device view to display the readbacks for the H-ESI
parameters. Verify that the readbacks match the setpoints.
Configuring the Syringe Pump and Infusing the Polytyrosine
Y To configure the syringe pump and infuse the polytyrosine – 1, 3, 6 tuning and
calibration solution
1. Choose Setup > Syringe Pump & Sample Loop to display the Syringe Pump and Sample
Loop view in the top right corner of the workspace, as Figure 28 shows.
Figure 28. Syringe Pump and Sample Loop view
2. In the Syringe Flow Control box, select On to activate the Flow Rate spin box.
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Running CV Scans
3. Enter 5.00 in the Flow Rate spin box to set a flow rate of 5.00 µL/min. (The flow rate
can be adjusted within the range of 1.00 to 15.00 µL/min to achieve the best ion beam
intensity and stability.)
4. In the Syringe Type box, specify the syringe type.
5. In the Syringe Size box, specify the syringe size.
6. Click Apply to apply these settings and to start the syringe pump. The
polytyrosine – 1, 3, 6 tuning and calibration solution should now flow into the ion
source.
Running CV Scans
Y To run a CV scan for each SIM ion
1. Click the Full Instrument Control button on the toolbar in Quantum Tune to display
the Device view.
Figure 29. Device view showing the FAIMS devices
2. Click Compensation Voltage to display the Tune view for the compensation voltage, as
Figure 30 shows.
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Running CV Scans
Figure 30. Tune view for the compensation voltage
3. Click Optimize to begin the optimization of the CVs. The optimization procedure ramps
the CV for each SIM ion from -30 to +10 V (-10 to +30 V for negative ions).
The ion intensity versus CV plots are shown in Figure 31.
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Verifying a Stable Ion Beam
Figure 31. Optimization CV scans of polytyrosine - 1, 3, 6
Verifying a Stable Ion Beam
If your initial ion signal was weak or unstable, you need to establish a stable ion beam and
optimize the CV again. The intensity and stability of the ion beam largely depends on the
performance of the ion source. You can adjust the ion source settings to optimize the ion
beam intensity and stability.
Y To observe the intensity and stability of the ion beam
1. Set the FAIMS parameters corresponding to polytyrosine - 3 (m/z 508).
a. Click the FAIMS button on the toolbar to display the FAIMS Control view.
b. In the FAIMS Control view, input the FAIMS settings that are listed in Table 9.
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Verifying a Stable Ion Beam
.
Table 9. FAIMS settings for polytyrosine - 3
FAIMS Parameter
Value
Compensation voltage (V)
-16.98
Outer bias voltage (V)
35
Dispersion voltage (V)
-5000
Total gas flow (L/min)
4
% He
50
Inner electrode temperature (ºC)
70
Outer electrode temperature (ºC)
90
c. Click Apply to apply the FAIMS settings.
2. Set the scan parameters.
a. On the toolbar, click on the Instrument Method Development Workspace button.
The Instrument Method Development workspace appears.
b. Click on Full Scan and Q1MS to display the Full Scan parameters and to select the
Q1MS scan mode.
c. In the Scan Range box, select Entry Mode: Center Mass to display the Center Mass
and Scan Width spin boxes.
d. In the Center Mass box, enter 508.2 to set the center of the scan range to m/z 508.2.
e. In the Scan Width box, enter 10.000 to set the scan width to m/z 10.000.
f.
In the Scan Time spin box, enter 0.20 to set the scan time to 0.20 s.
g. Confirm that the Source CID, Data Processing, and Q2 CID Gas check boxes are
not selected to ensure that these options are off.
h. Click on Apply to apply these scan parameters.
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Verifying a Stable Ion Beam
Figure 32. Define Scan view, showing typical settings for establishing a stable ion current
Display TIC
Profile
Centroid
3. On the toolbar, click the Display TIC button to begin an ion current trace in the Graph
view in the bottom right corner of the workspace.
4. Ensure that the Profile/Centroid button is in the profile state to display profile type data.
If the button is in the centroid state (as shown at the left), click it to toggle the data type
to profile.
5. Ensure that the mass spectrometer is in the positive ion polarity mode. You can
determine this by observing the state of the Polarity button (as shown at the left).
Positive Polarity
Negative Polarity
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Verifying a Stable Ion Beam
6. Determine if you have a stable ion beam.
a. In the Spectrum view in the bottom left corner of the workspace, observe the mass
spectrum. You should see signal at the polytyrosine – 3 mass.
b. Click anywhere in the Spectrum view to enable the Display buttons on the File /
Display toolbar.
c. Click on the Creep toolbar button to invoke the creep Y-axis normalization mode.
This enables you to observe changes in the intensities of the ions. The profile mass
spectrum at m/z 508 is shown in Figure 33.
Figure 33. Instrument Method Development workspace, showing stable ion beam
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Testing the FAIMS Selectivity
Note Adjust the sheath gas pressure to establish a stable ion beam. Too low a sheath
gas pressure can cause a loss of signal stability, whereas too high a pressure can cause
a loss of peak intensity.
7. Observe the signal of the polytyrosine – 3 ion.
• If the tops of the peaks are steady, you have a stable ion beam and you do not need to
adjust the H-ESI source settings. The peak height should not vary by more than
about 30% from scan to scan.
•
If the top of the peak is unsteady, you need adjust the H-ESI source settings. Start by
adjusting the pressure of the sheath gas.
Note The TIC can be observed in the Graph view in the bottom right corner of the
workspace. Large fluctuations in the TIC may indicate an unstable ion beam.
8. If you changed the ion source settings to obtain a stable beam, repeat the CV scan as
described in “Running CV Scans” on page 37.
Testing the FAIMS Selectivity
Use the CV scans in Figure 31 on page 39 to develop a strategy for FAIMS selectivity. Ideally
you want to choose a CV at which the intensity of the ion of interest is high and the
intensities of the unwanted ions are low.
Y To test the FAIMS selectivity
1. Set the scan parameters.
a. On the toolbar, click the Instrument Method Development Workspace button. The
Instrument Method Development workspace appears.
b. Click Full Scan and Q1MS to display the Full Scan parameters and to select the
Q1MS scan mode.
c. Set the scan parameters as shown in Figure 34.
d. Click on Apply to apply these scan parameters.
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Testing the FAIMS Selectivity
Figure 34. Define Scan view, showing settings for a full scan mass spectrum of polytyrosine - 1, 3, 6
Profile
Centroid
2. Ensure that the Profile/Centroid button is in the centroid state to display centroid type
data. If the button is in the profile state (as shown at the left), click it to toggle the data
type to centroid.
3. Set the CV to select the polytyrosine - 3 ion.
a. Click on the FAIMS button on the toolbar to display the FAIMS Control view.
b. Enter -16.98 in the Compensation Voltage box and click Apply. Figure 35 shows the
mass spectrum with FAIMS selection of the polytyrosine - 3 ion.
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Testing the FAIMS Selectivity
Figure 35. Mass spectrum with FAIMS selection of polytyrosine - 3
4. Enter -0.60 in the Compensation Voltage box and click Apply to select the
polytyrosine - 1 ion. Figure 36 shows the mass spectrum with FAIMS selection of the
polytyrosine - 1 ion.
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Further Optimization of FAIMS Parameters for Selectivity
Figure 36. Mass spectrum with FAIMS selection of polytyrosine - 1
The selection of polytyrosine - 1 is superior to that of polytyrosine - 3 because its CV
spectrum does not overlap those of polytyrosine - 3 or 6 at -0.60 V.
Further Optimization of FAIMS Parameters for Selectivity
To optimize the FAIMS settings other than the CV, see Chapter 6, “Advanced Optimization
of FAIMS Settings.” on page 65.
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Saving the Settings in a Tune File
Saving the Settings in a Tune File
An acquisition is divided into time segments. Each segment can use a different tune method
with different mass spectrometer and FAIMS settings. Tune methods are saved in tune files
with extension .TSQTune.
To save the mass spectrometer and FAIMS settings in a tune file, see “Saving the Settings in a
Tune File” on page 21.
Copying the Optimized CVs to Instrument Setup or LCquan
You can export the SIM or SRM settings, including the optimized CVs, to Instrument Setup
or LCquan. These settings can then be saved in an instrument method or LCquan method.
To copy the optimized CVs to Instrument Setup or LCquan, see “Copying the Optimized
CVs to Instrument Setup and LCquan” on page 22.
Flushing the System
This topic describes how to clean your mass spectrometer after performing this polytyrosine
example. It is recommended that you clean the mass spectrometer before acquiring data on
your analyte of interest.
Y To clean the mass spectrometer
1. Turn 0ff the flow of liquid from the syringe pump.
a. Choose Setup > Syringe Pump & Sample Loop to display the Syringe Pump and
Sample Loop view in the top right corner of the workspace. See Figure 28
on page 36.
b. In the Syringe Flow Control group box, select Off and then click Apply to stop the
syringe pump.
2. Click the On/Standby button on the toolbar to place the mass spectrometer in standby.
On
Standby
3. Remove the syringe from the syringe pump holder.
a. Lift the handle off the syringe while depressing the black release button on the
syringe pump handle.
b. Remove the syringe.
c. Remove the tip of the syringe needle from the end of the Teflon tube on the syringe
adapter assembly.
4. Clean the syringe thoroughly with a solution of 50:50 methanol – water.
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Flushing the System
5. Flush the sample transfer line, sample tube, and H-ESI probe.
a. Fill the cleaned syringe with a solution of 50:50 methanol–water (or with another
appropriate solvent).
b. While holding the plunger of the syringe in place, carefully insert the needle of the
syringe into the end of the Teflon tube on the syringe adapter.
c. Flush the sample transfer line, sample tube, and H-ESI probe with the solution by
slowly depressing the syringe plunger. Visually check that the solution is exiting the
tip of the H-ESI probe on the inside of the probe assembly.
d. Remove the needle of the syringe from the syringe adapter.
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Detectors
This chapter describes a procedure for running a FAIMS experiment on an LTQ series MS
detector. The procedure uses the LTQ’s caffeine, MRFA, and Ultramark 1621 tuning and
calibration solution, but you can use your own analyte.
Note Before using the FAIMS system, your MS detector needs to be properly tuned and
calibrated, without the FAIMS interface, in the H-ESI/MS mode. Refer to LTQ Getting
Started.
Y To perform the FAIMS experiment
1. Set up the syringe pump to infuse the tuning and calibration solution containing caffeine,
MRFA, and Ultramark 1621 directly into the H-ESI source by syringe pump infusion.
2. Set up the MS detector.
3. Configure the syringe pump and start infusion.
4. Run CV scans.
5. Verify that there is a stable ion beam.
6. Test selectivity.
7. Save the settings in a Tune file.
8. Flush the sample line, sample tube, and H-ESI probe.
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Setting Up the Syringe Pump
Setting Up the Syringe Pump
The syringe pump allows you to infuse a sample solution for extended periods of time. You
use the syringe pump to introduce tuning and calibration solution into the H-ESI source.
Note To minimize the possibility of cross-contamination, use a different syringe and
length of PEEK tubing for the tuning and calibration solution than you would for your
sample solution.
Y To set up the syringe pump for infusion
1. Fill a clean syringe with the caffeine, MRFA, and Ultramark 1621 tuning and calibration
solution. For instructions on preparing the tuning and calibration solution, refer to the
Getting Started manual.
2. Connect a 4 cm (1.5 in.) segment of Teflon® tube with a fingertight fitting and a ferrule
to an LC union.
The LC union has coned-bottom, 10-32 receiving ports. Figure 37 shows the suggested
fittings for connecting the syringe to the LC union.
3. Insert the syringe needle into the segment of Teflon tube.
LC union
(P/N 00101-18202)
Fingertight fitting
(P/N 00101-18081)
Ferrule
(P/N 00101-18196)
Teflon tube
(P/N 00301-22803)
Figure 37. Plumbing connections for the syringe.
4. Place the syringe into the syringe holder of the syringe pump.
5. While squeezing the release button on the syringe pump handle, push the handle forward
until it just contacts the syringe plunger.
6. Using fingertight fittings and ferrules, connect an infusion line of PEEK tubing
(0.005-in. ID × 1/16-in OD) between the LC union and the grounding union on the
H-ESI probe.
Figure 38 shows the suggested fittings and ferrules for connecting the LC union to the
grounding union. Both the LC union and the grounding union have 10-32, coned-bottom
receiving ports.
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Setting Up the MS Detector
Grounding union holder on the
H-ESI probe
Grounding union, 10-32 internal ports, 0.010-in. thru-hole
(P/N 00101-18081)
Ferrule
(P/N 00101-18196)
Fingertight fitting
(P/N 00101-18081)
PEEK
tubing
Figure 38. Plumbing connections for the infusion line between the LC union and the grounding union
Setting Up the MS Detector
Y To set up the LTQ series MS detector for the FAIMS experiment
1. Position the H-ESI probe as follows:
• Lateral position: center
• Front to back position: micrometer 1.5 back
• Probe depth: B
2. Click on the On/Standby button on the toolbar to turn on the mass spectrometer. (The
three different states of the On/Standby button are shown at the left.)
On
Off
Positive Negative
Standby
3. Ensure that the LTQ is in the positive ion polarity mode. You can determine the ion
polarity mode of the LTQ by observing the state of the Polarity button (as shown at the
left).
4. Set the H-ESI source parameters.
a. Click the H-ESI icon on the toolbar (or choose Setup > Heated ESI Source) to
display the Heated ESI Source dialog box.
b. In the Heated ESI Source dialog box, input the H-ESI settings that are listed
in Table 10.
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Setting Up the MS Detector
.
Table 10. H-ESI settings for the LTQ tuning and calibration solution experiment
H-ESI Parameter
Value
Heater temperature (ºC)
20
Sheath gas flow rate
12
Aux gas flow rate
5
Sweep gas flow rate
0
Spray voltage (kV)
5.5
Capillary temperature (ºC)
270
Capillary voltage (V)
25
Tube lens voltage (V)
100
c. Click Apply to apply the H-ESI settings.
d. Observe the readbacks in Heated ESI Source dialog box. Verify that the readbacks
match the setpoints.
Figure 39. H-ESI source setpoints and readbacks
5. Set the scan parameters.
a. Click the Define Scan button to display the Define Scan dialog box.
b. In the Define Scan dialog box, input the scan settings that are listed in following
table.
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Configuring the Syringe Pump and Infusing the Calibration Solution
.
Table 11. Scan settings
Scan Parameter
Value
Mass range
Normal
Scan rate
Normal
Scan type
Full
Microscans
1
Maximum injection time (ms)
10
Source fragmentation
Off
First mass (m/z)
150
Last mass (m/z)
2000
c. Click Apply to apply the scan settings.
Configuring the Syringe Pump and Infusing the Calibration Solution
You use the Syringe Pump dialog box to configure and start the syringe pump.
Y To configure and start the syringe pump
1. Click on the syringe pump icon on the toolbar (or choose Setup > Syringe Pump) to
display the Syringe Pump dialog box.
2. In the Syringe Flow Control box, select On.
3. Enter 3.00 in the Flow Rate box to set a flow rate of 3.00 µL/min. (The flow rate can be
adjusted to achieve the best ion beam intensity and stability.)
4. In the Syringe Type box, select the syringe type.
5. In the volume box, select the syringe volume.
6. Click Apply to apply these settings and to start the syringe pump. The tuning and
calibration solution should now flow into the ion source.
Running CV Scans
You determine the optimum compensation voltage for an ion by performing a CV scan.
Y To perform CV scans for caffeine, MRFA, and Ultramark (m/z 1522) ions
1. Click the FAIMS Control icon on the toolbar (or choose Setup > FAIMS Control) to
display the FAIMS Control dialog box.
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Running CV Scans
2. In the FAIMS Control dialog box, input the following FAIMS settings.
Table 12. FAIMS settings for the LTQ tuning and calibration solution
FAIMS Parameter
Value
Compensation voltage (V)
-24
Outer bias voltage (V)
same as capillary
voltage (here 25 V)
Dispersion voltage (V)
-5000
Total gas flow (L/min)
3.75
% He
50
Inner electrode temperature (ºC)
70
Outer electrode temperature (ºC)
90
3. Click Apply to apply the FAIMS settings.
4. Observe the readbacks in FAIMS Control view. Verify that the readbacks match the
setpoints.
Figure 40. FAIMS setpoints and readbacks
5. Click on the Tune button and then the FAIMS tab to display the FAIMS page of the
Tune dialog box.
6. In the FAIMS page, input the following FAIMS settings.
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Running CV Scans
.
Table 13. FAIMS tune settings for the LTQ tuning and calibration solution
FAIMS Parameter
Value
What to Optimize On
Masses
Mass 1
195
Mass 2
524
Mass 3
1522
Start (V)
-40
Stop (V)
0
Figure 41. FAIMS page of the Tune dialog box, before the CV scans
7. Click the Display Graph button in the Tune Plus toolbar to display the graph window.
8. Click Start to begin the CV scans.
The optimization procedure ramps the CV for each ion from -40 to 0 V. Tune Plus plots
the intensity versus CV for each ion and determines the optimum CV. Tune Plus lists the
optimum CVs in the CV column of the FAIMS page.
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Running CV Scans
Figure 42. CV scans for caffeine, MRFA, and Ultramark (m/z 1522 ion)
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Verifying a Stable Ion Beam
Figure 43. FAIMS page of the Tune dialog box, showing the optimum CVs
Verifying a Stable Ion Beam
If your initial ion signal was weak or unstable, you need to establish a stable ion beam and
optimize the CVs again. The intensity and stability of the ion beam largely depends on the
performance of the ion source. You can adjust the ion source settings to optimize the ion
beam intensity and stability.
Y To check the stability of the ion beam
1. Set the scan parameters.
a. Click the Define Scan button to display the Define Scan dialog box.
b. In the Define Scan dialog box, input the scan settings for m/z 195 that are listed in
the following table.
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Verifying a Stable Ion Beam
.
Table 14.Scan settings for observing the caffeine ion signal
Scan Parameter
Value
Mass range
Normal
Scan rate
Normal
Scan type
SIM
Microscans
1
Maximum injection time (ms)
50
Source fragmentation
Off
FAIMS CV (V)
-10.2
Input
Center/Width
Mass 1 (m/z)
195
Width 1 (m/z)
10
c. Click the Apply to apply the settings.
2. On the toolbar, click the Display Spectrum View button.
The Spectrum view appears.
3. On the toolbar, click the Profile/Centroid button to display the peaks as
profile
.
4. Observe the peak as calibration solution infuses. Consider the following questions about
the ion current signal:
• Is the signal present?
• Is the signal stable, varying by less than about 15% from scan to scan?
If you answered “yes” to the questions in step 4, then your MS detector is operating
properly.
If you answered “no” to either of these questions, try the following troubleshooting
measures:
• Ensure that the fused-silica sample tube does not extend beyond the tip of the ESI
needle. For instructions on inserting the fused-silica sample tube, refer to the Ion Max
and Ion Max-S API Source Hardware Manual.
• Ensure that the entrance to the ion transfer capillary is open and clean.
• Ensure that the solution entering the probe is free of air bubbles and that the tubing
and connectors are free of leaks.
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Testing the FAIMS Selectivity
• Ensure that the flow rate of the sheath gas is set to a minimum value of 8 units.
If you modify the H-ESI source parameters, rerun the CV scans as described in “Running CV
Scans” on page 53.
Testing the FAIMS Selectivity
Use the CV scans in Figure 42 on page 56 to develop a strategy for FAIMS selectivity. Ideally
you want to choose a CV at which the intensity of the ion of interest is high and the
intensities of the unwanted ions are low. In this example we use the CVs listed in Figure 43.
Y To test the FAIMS selectivity
1. Set the scan parameters.
a. Click the Define Scan button to display the Define Scan dialog box.
b. In the Define Scan dialog box, input the scan settings that are listed in Table 11
on page 53.
2. Select the caffeine ion (m/z 195).
a. Enter -10.2 in the FAIMS: CV box.
b. Click Apply to apply the FAIMS settings.
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Testing the FAIMS Selectivity
Figure 44. Mass spectrum with FAIMS selection, showing the selected caffeine ion at m/z 195.
3. Select the MRFA ion (m/z 524).
a. Enter -27.73 in the FAIMS: CV box.
b. Click Apply to apply the FAIMS settings.
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Testing the FAIMS Selectivity
Figure 45. Mass spectrum with FAIMS selection, showing the selected MRFA ion at m/z 524.
4. Select the Ultramark ion (m/z 1522).
a. Enter -14.54 in the FAIMS: CV box.
b. Click Apply to apply the FAIMS settings.
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Further Optimization of FAIMS Parameters for Selectivity
Figure 46. Mass spectrum with FAIMS selection, showing the selected Ultramark ions.
Note The Ultramark ions are chemically similar, so they have similar optimum CVs.
Further Optimization of FAIMS Parameters for Selectivity
To further optimize the FAIMS settings for selectivity, change the settings in Table 12
according to the suggestions in Chapter 5. Rerun the CV scans as described in “Running CV
Scans” on page 53. Observe the mass spectra with the newly optimized CVs.
Saving the Settings in a Tune File
The acquisition time is divided into segments. Each segment can use a different Tune Method
with different mass spectrometer and FAIMS settings. Tune Methods are saved in Tune files
with extension .LTQTune.
To save the mass spectrometer and FAIMS settings in a Tune file, see “Saving the Settings in
a Tune File” on page 30.
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Flushing the Sample Transfer Line, Sample Tube, and H-ESI Probe
Flushing the Sample Transfer Line, Sample Tube, and H-ESI Probe
Y To flush the sample transfer line, sample tube, and H-ESI probe
1. Turn off the flow of liquid from the syringe pump.
a. Click on the syringe pump icon on the toolbar (or choose Setup > Syringe Pump) to
display the Syringe Pump dialog box.
b. Select Off and then click Apply to stop the syringe pump.
2. Click the On/Standby button on the toolbar to place the LTQ in standby.
On
Standby
3. Fill a clean syringe with a solution 5% formic acid in water or an appropriate solvent.
The solvent you use to flush the sample transfer line, sample tube, and H-ESI probe
assembly depends on the sample matrix. For example, if you are using a buffered solution
of a high concentration, an acidic solution is appropriate.
4. While holding the plunger of the syringe in place, carefully insert the needle of the
syringe into the free end of the Teflon tube.
5. Slowly depress the syringe plunger to flow the solution through the sample transfer line,
sample tube, and H-ESI probe.
6. Remove the needle of the syringe from the Teflon tube.
7. Repeat step 3 through step 6 with a solution of 50:50 methanol / water.
8. Repeat step 3 through step 6 with acetone.
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Advanced Optimization of FAIMS Settings
Standard operating parameters for FAIMS are provided in Table 15. When standard
operating parameters do not provide the necessary selectivity, first follow the flowchart in
Appendix A, “FAIMS Optimization Flowchart.”
Table 15. Standard FAIMS operating parameters
FAIMS Parameter
Positive Ions
Negative Ions
Allowed Range
Compensation voltage (CV)
ramp -30 to +10 V
ramp -10 to +30 V
-200 to +200 V
Dispersion voltage (DV)
-5000 V
+5000 V
-5000 to -2000 V, 0 V,
+2000 to +5000 V
Outer bias voltage
set same as capillary
offset
set same as capillary
offset
-200 to +200 V
Inner electrode
temperature
70 ºC
70 ºC
30 to 120 ºC
Outer electrode
temperature
90 ºC
90 ºC
30 to 120 ºC
%He
50% He
50% He
0 to 50% He
Carrier gas flow
3.5 L/min
3.5 L/min
0 to 5 L/min per gas
This chapter describes advanced optimization of FAIMS parameters for higher selectivity and
sensitivity.
Optimizing the selectivity
In addition to the CV, the following FAIMS parameters can also be optimized:
• Dispersion voltage
• Gas composition
• Inner and outer electrode temperatures
• Outer bias voltage
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Optimizing the selectivity
Optimization of these parameters will change the CV values needed to transmit specific
analytes. Therefore, when optimizing these parameters, use CV ramps to examine the effect of
various values on the transmission of the analyte through the FAIMS electrodes.
To minimize solution switchover time when using single-analyte reference solutions, perform
several steps with one reference solution before switching to another reference solution.
When decreasing the helium content of the carrier gas or the electrode temperatures, ramp the
CV over a wider range, for example from +10 to -40 V (-10 to +40 for negative ions).
Thermo Fisher Scientific recommends that you follow these procedures in the order
described.
Y To vary dispersion voltage to optimize selectivity
1. Collect a CV ramp at -5000 V (positive ions) or +5000 V (negative ions).
2. Examine the CV traces.
3. Decrease the DV by 500 V (magnitude) and ramp the CV.
4. Examine the CV traces.
5. Repeat step 3.
Y To vary gas composition to optimize selectivity
1. Set the DV to the optimal value determined in the previous procedure or set the DV to
±5000 V if the optimal value is unknown.
2. Decrease helium to 25% and ramp the CV.
3. Examine the CV traces and do one of the following:
• If selectivity has noticeably improved, investigate the effect of increasing and
decreasing the DV.
• If selectivity did not noticeably improve, decrease helium to 0%, increase DV to
±5000, and ramp the CV. Examine the CV traces.
Y To vary the electrode temperatures to optimize selectivity when there is partial
separation between the CV peaks for the analytes
1. Set the DV and gas composition to the optimal values determined in the previous
procedures.
2. From an initial temperature of 90 °C on the outer electrode and 70 °C on the inner
electrode, decrease the temperature on the inner electrode in 10 °C increments. Ramp the
CV and examine selectivity and signal intensity.
Note For a temperature of 90 °C on the outer electrode, the inner electrode is
limited to a low temperature of approximately 45 °C.
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Advanced Optimization of FAIMS Settings
Optimizing the Sensitivity
3. If the signal intensity increases, the temperature values may be too high for the analyte. In
this case, proceed to the next procedure for analytes with little or no CV peak separation.
Note Generally, intensity decreases as the difference in temperature between
electrodes becomes larger, if the inner electrode temperature is lower than the outer
electrode temperature. Intensity tends to increase as the difference in temperature
between the electrodes becomes larger, if the inner electrode temperature is higher
than the outer electrode temperature.
Y To vary the electrode temperatures to optimize selectivity when there is little or no
separation between the CV peaks for the analytes
1. Decrease the outer electrode temperature to 70 °C and the inner electrode temperature to
50 °C.
2. Repeat the procedures for varying the DV and gas composition to optimize selectivity, as
necessary.
3. If more selectivity is required, decrease the outer electrode temperature to 50 °C and the
inner electrode temperature to 40 °C. Repeat the procedures for varying the DV and gas
composition to optimize selectivity, if necessary.
Y To vary outer bias voltage to optimize selectivity
1. Using the optimal conditions determined for the dispersion voltage, gas composition, and
temperature, set the outer bias voltage to 5, 20, and 35 V (-5, -20, and -35 V for negative
ions) and ramp the CV at each voltage.
2. Examine the traces to determine if selectivity is sufficient. Some signal intensity may be
lost in the optimization of the outer bias voltage.
Optimizing the Sensitivity
Optimization of sensitivity, by varying the FAIMS settings, should be secondary to achieving
the required selectivity. Try adjusting the H-ESI or APCI probe settings and position to
optimize sensitivity.
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Getting Connected
The initial installation of the FAIMS system is performed by a Thermo Fisher Scientific Field
Service Engineer. If the FAIMS interface must be removed and then re-installed on the mass
spectrometer at a later time, this chapter describes how to connect cables and gas lines to the
FAIMS system and between modules of the FAIMS system.
Figure 47 shows a block diagram of the communication connections of the TSQ Quantum or
LTQ, FAIMS temperature control module (TCM), and FAIMS waveform generator (WG).
The TSQ Quantum or LTQ communicate with the FAIMS waveform generator via an
RS 232 connection. The TSQ Quantum or LTQ communicate with the FAIMS temperature
control module through the Ethernet hub via an Ethernet connection.
Figure 47. Waveform generator (WG), temperature control module (TCM), and TSQ Quantum or
LTQ communication
Figure 48 shows a block diagram of the gasses, power, and communication inputs and
outputs of the waveform generator.
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Figure 48. Block diagram showing the gasses, power, and communication inputs and outputs of
the waveform generator
Figure 49 shows a block diagram of the gasses, power, and communication inputs and
outputs of the temperature control module.
Figure 49. Gases, voltages, and communication of the temperature control module (TCM)
Figure 50 shows the power panel of the TSQ Quantum, and Figure 51 shows the power
panel of the LTQ.
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Carrier gasses are supplied to the FAIMS system through three quick-disconnect fittings on
the connection panel of the waveform generator. These inlet gas ports are labeled He, N2, and
CO2. Figure 52 shows the connection panel of the FAIMS waveform generator.
Operating Mode
On
Communication
(to temperature
control module via
the
ethernet hub)
System Reset
Forepumps On
Vent Valve Closed
Ethernet Link OK
Ethernet
100 Base T
Service Mode
Electronics
Off
Main Power
Forepump 1
Power In
Forepump 2
Qualified Service
Personnel Only
Comm
Communication
(to waveform
generator)
Figure 50. Power panel of the TSQ Quantum
Peripheral Control
Start Ready Start
In Out Out
+ -
Communication (to
temperature control
module via the
ethernet hub)
Ethernet
100 Base T
Main Power
On
Reset
Mech. Pumps
A 5.5 MAX
Power In
V 230 V
Hz 50/60
10A
Electronic Normal
Analog Input
Service Mode
Off
Figure 51. Power panel of the LTQ
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Communication (to waveform
generator)
Figure 52. 15-pin connector on LTQ
Receptacle for main
power cord and on/off
switch
Carrier gas
outlet port
AC power
indicator
Inlet gas ports
(He, N2, CO2)
Connector for entrance
plate voltage cable
Communication port to the
TSQ Quantum’s power panel
or LTQ’s front panel
Ion Max interlock port
Figure 53. Connection panel on the FAIMS waveform generator
The procedures to connect the gas sources to the waveform generator depend on the
laboratory environment. A Thermo Fisher Scientific Field Service engineer will help to
connect the gas sources during the initial installation.
Note For the gas cartridges to be sealed from the environment when these gas lines are
removed, the quick disconnect functionality must be used. Removing the lines using the
Swagelock nut causes the gas cartridges to be left open to absorb water from the air.
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Y To connect the gas line to the temperature control module
1. Attach a length of ¼ in. gas line tubing to the compressed gas line.
2. Insert the other end of the gas line tubing into the quick disconnect fitting on the IN port
on the temperature control module.
Figure 53 shows the connection panel of the FAIMS temperature control module.
Main power inlet and
On/Off switch
Communication with FAIMS
interface heaters
AC power indicator
Unheated inner electrode
temperature control gas (to
FAIMS interface heaters)
Unheated outer electrode
temperature control gas (to
FAIMS interface heaters)
Electrode temperature
control gas inlet
Communication (to TSQ
Quantum or LTQ via
Ethernet hub)
Figure 53. Connection panel on the temperature control module
Figure 54 shows the connection panel on the heater box of the FAIMS interface.
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Curtain voltage from
waveform generator
carrier gas from
waveform generator
Outer electrode gas
from TCM
Inner electrode gas
from TCM
Communication
with TCM
Figure 54. Connection panel on the FAIMS interface heater box
Y To connect the gas lines to the temperature control module and FAIMS interface
heater box panel
1. Attach a length of ¼ in. gas line tubing to the compressed gas line.
2. Insert the other end of the gas line tubing into the quick disconnect fitting on the IN port
on the temperature control module , as Figure 53 shows.
3. Using ¼ in. OD tubing, connect the O-ELEC ports on the temperature control module
and FAIMS interface heater box, as Figure 54 shows.
4. Using ¼ in.OD tubing, connect the I-ELEC ports on the temperature control module
and the FAIMS interface heater box.
Y To make the electrical connections
1. Connect one end of the Fischer cable to the BIAS/CURTAIN VOLTAGE connector on
the connection panel of the FAIMS waveform generator (Figure 52) and the other end to
the WFG connector on the FAIMS interface heater box, as Figure 54 shows.
2. Connect the heater cable between the HEATER connector on the temperature control
module, as Figure 53 shows, and the TCM connector on the FAIMS interface heater box,
as Figure 54 shows.
3. Connect the interlock cable between the MS CONTROL connector on the waveform
generator, as Figure 52 shows, and the connector on the Ion Max housing.
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Table 16 lists FAIMS cables and Table 17 lists carrier gas lines.
Table 16. FAIMS cables list
From
Label
To
Quantum or LTQ
Ethernet 100
Base T
Ethernet hub
Ethernet hub
Label
TCM
COMM
Quantum
Comm
WG
COMM
LTQ
(15-pin connector
on front)
WG
COMM
WG
MS CONTROL
FAIMS interface
heater box
WFG
FAIMS interface
heater box
TCM
To
Label
Electrode
temperature control
gas source
TCM
IN
N2 source
WG
N2
He source
WG
He
Ion Max interlock
WG
BIAS/CURTAIN
VOLTAGE
TCM
HEATER
Table 17. gas lines list
From
Thermo Scientific
Label
WG
GAS OUT
FAIMS interface
heater box
FAIMS
TCM
I-ELEC
FAIMS interface
heater box
I-ELEC
TCM
O-ELEC
FAIMS interface
heater box
O-ELEC
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8
Maintenance
This chapter provides information about how to maintain the FAIMS system and contains
the following:
• Safety cautions when performing any maintenance procedures and performance
considerations
• Procedure for cleaning the FAIMS electrodes, including the equipment required and the
frequency of cleaning
• Procedure for inspecting and replacing the O-rings in the electrode assembly
• Procedure for replacing the gas purification cartridges
• Procedure for replacing the AC fuses
Safety, Instrument, and Performance Considerations
CAUTION Do not attempt to open the waveform generator or the temperature control
module. All servicing of the waveform generator or the temperature control module must
be performed by a Thermo Fisher Scientific Field Service Engineer.
CAUTION When working with the FAIMS interface, always follow the general safety and
instrument considerations described in “General Safety and Instrument Considerations”
on page v, as well as others described throughout this manual. Disregard for these
cautions may cause harm to you or the FAIMS interface.
CAUTION The FAIMS interface applies high voltages and failing to power down the
FAIMS interface before performing certain procedures will expose the user to these
voltages.
When working with the FAIMS interface, be aware of the performance considerations, as
described in “General Safety and Instrument Considerations” on page v.
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Maintenance
Cleaning the FAIMS Electrodes
Cleaning the FAIMS Electrodes
The FAIMS electrode set is made of stainless steel. The electrodes are cleaned before
installation on the mass spectrometer to remove any water or contaminants deposited on their
surfaces during shipping and storage.
After initial installation, the frequency of cleaning depends on the cleanliness of samples being
analyzed, continuity of gas flow through the electrodes, condition of the gas purification
cartridges, and the occurrence of discharge events within the electrodes. When a decline in
performance of the electrodes cannot be attributed to another cause, the electrodes should be
cleaned.
Cleaning the electrodes requires approximately one hour.
Cleaning Equipment
Cleaning the FAIMS electrodes requires the following equipment:
• An ultrasonic bath
• An oven that can be set to a minimum of 105 ºC for drying the stainless steel electrodes
after cleaning
• An ovenproof glass dish large enough to hold the electrodes while in the oven
Cleaning Procedures
Because the electrodes have already been installed, they must first be removed from the
FAIMS interface and disassembled. Once the electrodes have been cleaned, they can be
reassembled and reinstalled.
Cleaning the FAIMS electrodes involves the following tasks, which must be performed in the
order listed:
1. Stop the LC flow and place the TSQ Quantum Ultra in Standby.
2. Turn off the waveform generator by using its power switch.
3. Disconnect the LC line from the H-ESI or APCI probe.
4. Remove the FAIMS interface and the Ion Max housing.
5. Remove the FAIMS interface from the Ion Max housing.
6. Remove the electrode assembly from the FAIMS interface.
7. Disassemble the electrodes.
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8. Clean the electrodes in an ultrasonic bath and dry them in an oven.
Note When handling the cleaned electrodes, wear powder-free gloves to avoid
contaminating the cleaned electrodes.
9. Inspect the O-rings.
10. Clean the entrance plate.
11. Reassemble the electrode assembly.
12. Reinstall the electrode assembly on the FAIMS interface.
13. Reinstall the FAIMS interface on the Ion Max housing.
14. Reinstall the Ion Max housing on the mass spectrometer.
15. Connect the LC line to the H-ESI or APCI probe.
16. Turn on FAIMS system power.
17. Place the system in the On condition.
Placing the System in Standby Condition
Y To place the TSQ Quantum Ultra system in the standby condition
1. Wait until data acquisition, if any, is complete.
2. Turn off the flow of liquid from the LC (or other sample introduction device) to the API
source.
3. From the Quantum Tune window, choose Control > Standby (or click the
On/Standby button) to put the mass spectrometer and FAIMS system in Standby.
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Note When you choose Control > Standby from Quantum Tune, all voltages to the
FAIMS system are turned off, and N2 at 1.5 L/min is supplied to the electrodes to keep
them clean.
Typically, placing the system in standby is preferred to turning it off. Turning off the
FAIMS system, by using the power switches on the waveform generator and temperature
control model, is recommended only if:
• You are removing the electrodes for cleaning.
• The FAIMS system will not be used for an extended period of time. In this case,
remove and clean the electrodes before they are used again.
4. Leave the mass spectrometer power on.
5. Leave the LC power on.
6. Leave the autosampler power on.
7. Leave the data system power on.
Turning off Power to the waveform generator
Turning off the waveform generator stops gas flows and ensures that voltages to the FAIMS
interface and electrodes are off.
Y To turn off power to the waveform generator
Place the power switch on the waveform generator (see Figure 52 on page 72) in the Off (O)
position.
Disonnecting the LC line From the H-ESI or APCI Probe
Y To disconnect the LC line from the H-ESI or APCI probe
Disconnect the LC line from the grounding union (H-ESI) or probe inlet (APCI) by turning
the fitting counterclockwise until you can pull the fitting and LC line free from the grounding
union or probe inlet.
Removing the FAIMS Interface Assembly and the Ion Max Source Housing
It is best to remove the FAIMS interface and Ion Max housing as a unit.
CAUTION Before removing the FAIMS interface and Ion Max source from the mass
spectrometer, ensure that the waveform generator is turned off.
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Y To remove the FAIMS interface assembly and Ion Max source housing
CAUTION Allow the Ion Max source housing to cool before you remove it.
1. Disconnect the gas lines and cables at the heater box connection pane, as Figure 55
shows.
Figure 55. Gas lines and cable connections to the heater box connection panel
2. Unclip and disconnect the high-voltage lead from the high-voltage adapter on the
interface assembly, as Figure 56 shows.
3. Disconnect the exhaust tube from the heater box, as Figure 56 shows.
4. Disconnect the interlock cable from the Ion Max source.
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High voltage
lead
Interface
assembly
Exhaust tube
Figure 56. FAIMS interface, showing the high voltage lead and exhaust tube
5. Remove the Ion Max housing and FAIMS interface as follows:
a. Remove the drain tube from the Ion Max housing drain.
b. Rotate the two ion source housing locking levers 90 degrees to release the ion source
housing from the ion source mount assembly, as Figure 57 shows.
c. Remove the ion source housing by pulling it straight off of the ion source mount
assembly. Place the housing with the right side down, as Figure 58 shows.
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Ion source
housing
locking levers
Figure 57. Ion Max housing, showing the locking levers
Figure 58. FAIMS interface and Ion Max source housing removed from the mass spectrometer
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Cleaning the FAIMS Electrodes
Removing the FAIMS Interface Assembly from the Ion Max Source Housing
Y To remove the FAIMS interface assembly
CAUTION Allow the FAIMS electrodes and Ion Max housing to cool before you remove
the FAIMS interface from the Ion Max housing.
1. With a 5/32 in. ball driver, loosen and remove the three screws that secure the FAIMS
interface assembly to the Ion Max housing, as Figure 59 shows.
2. Carefully remove the FAIMS interface from the Ion Max housing and set it down with its
entrance plate up, as Figure 60 shows.
Figure 59. FAIMS interface and Ion Max housing, showing the three screws that secure them
together
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Entrance plate
Electrode assembly
mount
Figure 60. FAIMS interface removed from the Ion Max source housing, with the entrance plate up
An exploded diagram of the electrode end of the FAIMS interface is shown in Figure 61.
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Thumbscrews
Entrance plate
Gas and voltage
connector
Electrode assembly
Electrode assembly
mount
Figure 61. Exploded view of the electrode end of the FAIMS interface
Removing the FAIMS Electrode Assembly from the FAIMS Interface
Y To remove the FAIMS electrode assembly
1. Remove the entrance plate.
a. Loosen and remove the three thumbscrews that secure the entrance plate to the
electrode assembly mount, as Figure 61 shows.
b. Lift the entrance plate off the electrode assembly and place it on a clean surface.
2. Carefully disconnect the gas and voltage connector from the electrode assembly, as
Figure 62 shows.
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Figure 62. Disconnecting the gas and voltage connector from the electrode assembly
3. Remove the electrode assembly and mount by pulling them off the two posts, as
Figure 63 shows.
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Figure 63. Removing the electrode assembly and mount
4. Pull the electrode assembly off the mount, as Figure 64 shows.
Tip It may be difficult to remove the electrode assembly if it is hot. Allow it to cool.
If necessary, use methanol as a lubricant.
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Figure 64. Removing the electrode assembly from its mount
Disassembling the FAIMS Electrode Assembly
Figure 65 shows the location of the electrode assembly parts.
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Left endcap
Electrode alignment
bushing
2-012 Viton O-Ring (in inner
electrode internal groove)
Inner electrode
Outer electrode
Electrode alignment
bushing
Right endcap
Sealing screws (2)
(fingertight + 1/4 turn max.)
Figure 65. FAIMS electrode assembly, exploded and assembled views
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Y To dissemble the FAIMS electrode assembly
1. Use a 1/4 in. wrench to loosen the two sealing screws.
2. Remove the right endcap and sealing screws. See Figure 66.
Tip After you loosen the two sealing screws, a good way to separate the endcaps from the
electrodes is to press the sealing screw heads down on the table while holding the outer
electrode.
Figure 66. Removing the right endcap and sealing screws
3. Remove the outer electrode from the inner electrode and left endcap. See Figure 67.
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Figure 67. Inner electrode mounted on the left endcap, and the outer electrode
4. Remove the inner electrode from the left endcap, as Figure 68 shows.
Figure 68. Left endcap and inner electrode
5. Remove the alignment bushings from the inner electrode. See Figure 69.
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Figure 69. Inner electrode and alignment bushings
Cleaning and Drying the FAIMS Electrodes
CAUTION Observe good laboratory practices when working with the chemicals used for
cleaning. Use a fume hood and wear appropriate personal protective equipment.
Y To clean the FAIMS electrodes
1. Place the stainless steel inner and outer electrodes in a solution containing 48:48:4
methanol / distilled water /f ormic acid and place in an ultrasonic bath for approximately
15 min.
2. Carefully remove the electrodes from the cleaning solution.
3. Rinse all surfaces of the electrodes well with distilled water, then methanol, and then
isopropyl alcohol (IPA).
4. Place the electrodes in an ovenproof glass dish and then put the dish in an oven to dry the
electrodes. The oven temperature should be at least 105 ºC. Dry the electrodes for
approximately 20 min.
CAUTION Electrodes being removed from the oven are hot. Insulated gloves should be
worn.
5. When dry, remove the dish containing the electrodes from the oven and allow the
electrodes to cool to room temperature.
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Inspecting the O-rings
The FAIMS electrode assembly includes three O-rings. One O-ring resides inside the inner
electrode, as Figure 70 shows. This O-ring forms a seal with the left endcap.
Figure 70. Inner electrode and O-ring (O-ring resides in a groove inside the electrode)
Note The O-ring inside of the inner electrode is difficult to reinstall. Thermo Fisher
Scientific recommends that you inspect it visually, but do not remove it unless you think it
is damaged. Bad sensitivity due to the bleeding of compressed air inside the FAIMS cell
may indicate a damaged O-ring.
Tip You can use a needle to remove and install the O-ring.
A second O-ring is seated in the outer electrode, and forms a seal between the outer electrode
and the entrance plate, as Figure 71 shows.
Groove for
O-ring
Figure 71. Outer electrode and O-ring
A third O-ring is seated in the electrode assembly mount, and forms a seal between the
electrode assembly and the electrode assembly mount, as Figure 72 shows.
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Groove for
O-ring
Figure 72. Electrode assembly mount and O-ring
Inspect the O-rings for damage and replace them if they are damaged.
Cleaning the Entrance Plate
Y To clean the entrance plate
1. With a lint-free swab, scrub the entrance plate with a solution of detergent and water.
2. Rinse the entrance plate with tap water to remove the detergent.
3. Rinse the entrance plate with distilled water.
4. Place the entrance plate in a tall beaker and immerse it completely in HPLC-grade
methanol. Move the entrance plate up and down in the methanol for 15 s.
5. Remove the entrance plate from the methanol bath, and then rinse it thoroughly with
fresh methanol.
6. Dry the entrance plate with a rapid stream of nitrogen gas.
Reassembling the FAIMS Electrode Assembly
Y To reassemble the electrode assembly
Figure 65 on page 90 shows the locations of the components of the electrode assembly.
Note Wear clean, powder free gloves when handling the clean electrodes.
1. Reinstall the alignment bushings on the inner electrode, as Figure 69 on page 93 shows.
2. Reinstall the inner electrode on the left endcap, as Figure 68 on page 92 shows.
3. Reinstall the outer electrode by inserting the inner electrode and alignment bushings into
the outer electrod, as Figure 67 on page 92 shows.
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4. Reinstall the right endcap and sealing screws, as Figure 66 on page 91 shows.
5. Tighten the two sealing screws until finger tight, and then use a 1/4 in. wrench to tighten
the sealing screws by a maximum of 1/4 turn.
Reassembling the FAIMS Interface
Y To reassemble the FAIMS interface
Figure 61 on page 86 shows the locations of the FAIMS interface components.
1. Seat the electrode assembly on its mount, as Figure 64 on page 89 shows. Orient the
electrode assembly such that the ion entrance in the outer electrode is up, and the left
endcap (with the gas ports) is on the same side as the two holes in the side of the mount.
2. Reinstall the electrode assembly mount on the two posts, as Figure 63 on page 88 shows.
3. Carefully seat the gas and voltage connector onto the left endcap. Make sure that it is
completely seated, as Figure 62 on page 87 shows.
4. Reinstall the entrance plate onto the electrode assembly and secure it with the three
thumbscrews, as Figure 61 on page 86 shows.
Reinstalling the FAIMS Interface on the Ion Max Housing
Y To reinstall the FAIMS interface on the Ion Max housing
1. Orient the Ion Max housing such that the right side is down and the FAIMS entrance is
up.
2. Carefully insert the FAIMS interface into the Ion Max housing such that the entrance
plate is facing the Ion Max window, as Figure 58 on page 83 shows.
3. Insert the three screws that secure the FAIMS interface assembly to the Ion Max housing
and tighten with a 5/32 in. ball driver, as Figure 59 on page 84 shows.
Installing the Ion Sweep Cone
Sweep gas must be used during FAIMS operation. The ion sweep cone must be installed to
use sweep gas.
If the ion sweep cone is already installed, go to Reinstalling the Ion Max Source Housing
Onto the Mass Spectrometer.
Y To install the ion sweep cone
1. Align the gas inlet on the ion sweep cone with the sweep gas supply port on the ion source
mount. Firmly press the ion sweep cone into ion source moun, as Figure 73 and
Figure 74 show.
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2.Reinstall the Ion Max source housing on the mass spectrometer as described in “Reinstalling
the Ion Max Source Housing Onto the Mass Spectrometer” on page 98.
Sweep gas
supply port
Figure 73. Ion source interface, showing the sweep gas supply port in the API cone seal
Gas inlet
Figure 74. Ion sweep cone, showing the gas inlet
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Reinstalling the Ion Max Source Housing Onto the Mass Spectrometer
Y To reinstall the Ion Max ion source housing
1. Carefully align the two guide pin holes on the rear of the ion source housing with the ion
source housing guide pins on the mass spectrometer, and carefully press the ion source
housing onto the ion source mount, as Figure 57 on page 83 and Figure 75 show.
p
Ion source
housing
guide pins
Figure 75. Ion source mount showing ion source housing guide pins
2. Rotate the Ion Max housing locking levers 90 degrees to lock the ion source housing onto
the ion source mount assembly.
3. Reinstall the Ion Max drain tube.
a. Connect the Tygon® tubing to the ion source housing drain fitting.
b. Attach the free end of the hose to a dedicated drain system. Ideally, the drain system
should be vented to a fume exhaust system.
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4. Connect the exhaust tube to the heater box, as Figure 56 on page page 82 shows.
5. Connect the interlock cable to the Ion Max source.
Note Voltages will not be applied to the FAIMS electrodes if the interlock cable is not
properly installed. A popup message in Xcalibur appears to inform you of an interlock
fault.
6. Connect the high voltage lead to the adapter on the FAIMS interface. Secure it with the
two clips.
7. Connect the gas lines and cables to the heater box connection panel, as Figure 76 and
Figure 55 on page 81 show.
O-ELEC
FAIMS
WFG
I-ELEC
TCM
Figure 76. Heater box connection panel
Reconnecting the LC Line to the H-ESI or APCI Probe
Y To connect the LC line from the H-ESI or APCI probe
Insert the LC line, fitting, and ferrule into the grounding union (H-ESI) or probe inlet
(APCI). Turn the fitting clockwise to secure the LC line.
Turning On Power to the FAIMS System
Y To turn on power to the FAIMS system
Place the power switch on the waveform generator in the On (|) position.
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Maintenance
Replacing Gas Purification Cartridges
Placing the System in On Condition
Y To place the mass spectrometer and FAIMS system in the On condition
From the Quantum Tune window or LTQ Tune Plus window, choose Control > On (or
click on the On/Standby button) to turn on the mass spectrometer and FAIMS system.
When you place the system in the On condition, all user-defined settings of the FAIMS
system are activated.
Replacing Gas Purification Cartridges
The carrier gas purification cartridges are located in the back of the waveform generator, as
Figure 77 shows. Gas purification cartridges can last several months when high purity gas is
used. Replace the gas purification cartridges when a change is noted in the compensation
voltage at which an ion is transmitted through the FAIMS interface under known conditions
(such as known DV, carrier gas flow rate, and gas composition).
New purification cartridges or repacking material can be purchased from Chromatographic
Specialties (#C36120), VWR International (#80083-116), or Agilent (#HMT200-2).
Y To replace a gas purification cartridge
1. Close the valve controlling the flow of gas into the FAIMS waveform generator.
2. Loosen the 1/8 in. Swagelock nuts connecting the gas lines to the purification cartridge.
When the lines are disconnected, remove the purification cartridge from the waveform
generator.
3. Attach the gas lines to the replacement cartridge and clip it in place within the waveform
generator.
4. Reopen the valve controlling the gas flow into the FAIMS waveform generator.
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8 Maintenance
Replacing AC Fuses
Figure 77. Gas purification cartridges
Replacing AC Fuses
AC fuses may need to be replaced. For example, if the FAIMS system will not power up,
check whether the fuse is blown.
Replace AC fuses only with the part described in the following table:
Table 18. Waveform generator and temperature control module fuses
Thermo Scientific
FAIMS unit
120 V
240V
Waveform generator
F3A
F3A
Temperature control module
F5A
F5A
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8
Maintenance
Replacing AC Fuses
Figure 78 shows a representation of a fuse compartment and identifies the location of the
replaceable fuse:
Fuse holder
Cover
Figure 78. Fuse compartment.
Y To replace the fuse
1. Place the power switch in the Off (O) position and disconnect the power cord.
2. With the cover hinges forward and down, open the cover using a screwdriver with a small
blade or a similar tool.
3. Apply slight pressure to pull the fuse holder forward.
4. Replace the fuse and slide the fuse holder back into its compartment.
5. Close the cover.
6. Reconnect the power cord and place the power switch in the On (|) position.
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9
Troubleshooting
This chapter helps you resolve issues that might occur while using the FAIMS interface.
Table 19 describes possible causes for each issue that may occur, along with suggested
solutions or explanations.
CAUTION When working with the FAIMS interface, always follow the general safety and
instrument considerations described in “General Safety and Instrument Considerations”
on page v, as well as others described throughout this manual. Disregard for these
cautions may cause harm to the user or the FAIMS interface.
CAUTION The FAIMS interface applies high voltages and failing to power down the
FAIMS interface before performing certain procedures exposes you to these voltages.
Table 19. Troubleshooting problems and solutions
Problem
Solution
FAIMS will not power up
Power supply not working properly
If the green indicator light on connection panel is off, check the following:
Power source connection. If the power cable is disconnected, reconnect it and verify that
the connection is secure.
AC inlet fuse. If the fuse is blown, replace it. Spare fuses are provided in the Spares kit.
Both neutral and live wires have a fuse. See “Replacing AC Fuses” on page 101.
A Communication Problem has Occurred
The FAIMS is not powered up.
Power up the waveform generator and verify that the green status light on the connection
panel is on.
The IP address of the TSQ Quantum or LTQ
was changed.
The IP address of the FAIMS system must be set to the TSQ Quantum’s or LTQ’s IP address
+1.
Communications cable not connected or
wrong cable is used.
Ensure connection and cable are correct. Cable connections are one-to-one and pin-for-pin
between connectors. The instrument functions as Data Terminal Equipment (DTE). No “null
modem” is required.
Gas Actual Values are Unexpectedly Zero
Gas sources are not connected.
Connect the gas sources.
Gas lines are not connected properly.
Verify that the gas lines are secured properly between controllers, filters and bulk unions.
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Troubleshooting
Problem
Solution
MFC cable is not connected properly.
Ensure the cable is connected properly.
A mass flow controller is not working.
Replace the mass flow controller.
He or N2 tank is empty
Replace He or N2 tank.
Dispersion Voltage Readback is Unexpectedly Near Zero
Power is not being supplied to the FAIMS
waveform generator.
Check that the green light on the waveform generator is on.
Interlocks on the high voltage lead are not
activated.
Check that the high voltage lead is properly installed.
Ion source interlocks are not activated.
Check that the FAIMS interface and mass spectrometer’s ion source are properly installed.
No dispersion voltage specified.
Specify a value for the Dispersion Voltage parameter in the FAIMS control software.
A discharge in the FAIMS electrodes
caused the electronics to shut down.
Check for error messages indicating shutdown due to discharge.
DV Does Not Reach Set Value
Capacitance of system has changed.
Check that the configuration of the high voltage lead has not been altered.
Check all connections to the FAIMS interface assembly.
Mass Spectrometer’s Ion Source Does Not Turn On
FAIMS interface or API probe is not
installed such that the interlocks are
activated.
Check the installation of the FAIMS interface and API probe.
No Ion Signal at All
Power is not being supplied to the FAIMS
waveform generator.
Check that the green light on waveform generator is on.
No communication between the software
host computer and the FAIMS waveform
generator.
Check the serial connection between FAIMS waveform generator and the host computer.
Electrical connections not connected.
Check that the outer bias and high voltage connectors are attached.
Interlocks are not activated.
Check that the interlocks on the high voltage lead and ion source are activated.
No gas being introduced into the FAIMS
electrodes.
Check that the gas lines are installed and a gas supply is available.
Improper voltages specified.
Compare values to the Standard conditions found in Appendix A.
Ion source not working.
Check the ion source.
No sample flow to source.
Check the sample flow.
Check that Gas Flow parameters are specified in the FAIMS control software.
No Signal for Ion of Interest
104
Compensation voltage is incorrect.
Ramp the compensation voltage over a range of +10 to -40 for positive ions, or =10 to +40
for negative ions while monitoring for the m/z of interest to determine the conditions under
which the ion is transmitted.
Dispersion voltage is incorrect.
Check the value of the Dispersion Voltage parameter in the FAIMS control software.
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9
Troubleshooting
Problem
Solution
Carrier gas composition is incorrect.
Check the Gas Flow parameters in the FAIMS control software to verify the carrier gas
composition.
Carrier gas flow rate is too low.
Increase the Total Gas parameter FAIMS control software.
Concentration too low.
Increase the concentration of the analyte and check for a signal.
Solution not being delivered to the ion
source.
Check the delivery lines and connections for leaks.
FAIMS electrodes are dirty.
Remove, disassemble, clean, reassemble, and reinstall the electrodes. See the topic
“Cleaning the FAIMS Electrodes” on page 78.
Gas purification cartridge is wet.
Replace the gas purification cartridge. See the topic “Replacing Gas Purification
Cartridges” on page 100.
Decreased Ion Intensities
Dispersion voltage is incorrect.
Check the value of the Dispersion Voltage parameter in the FAIMS control software.
Compensation voltage is incorrect.
Ramp the compensation voltage while monitoring for the m/z of interest to determine the
conditions under which the ion is transmitted.
Carrier gas flow rate is too high or too low.
Check the Gas Flow parameters in the FAIMS control software to verify the carrier gas
composition. Re-optimize, if necessary.
Different mass spectrometer conditions
used.
Check tune/state file and instrument pressures.
Entrance plate is dirty.
Clean the entrance plate.
FAIMS electrodes are dirty.
Remove, disassemble, clean, reassemble, and reinstall the electrodes.
Gas purification cartridge is wet.
Replace the gas purification cartridge.
Mass spectrometer interface is dirty.
Clean the mass spectrometer interface as described in the documentation provided with
the mass spectrometer.
Position of ion source has changed.
Re-optimize ion source position relative to the FAIMS electrodes.
Compensation Voltage Shifted from Previously Observed Values
Different dispersion voltage.
Check the value of the Dispersion Voltage parameter in the FAIMS control software.
Carrier gas composition is different.
Check the Gas Flow parameters in the FAIMS control software to verify the gas mixture.
Temperatures of the heaters are different.
Check the temperature settings of the electrode heaters and allow equilibrium to be
reached.
Carrier gas flow rate is different.
Check the Total Gas parameter in the FAIMS control software to verify the carrier gas flow
rate.
Solution flow rate is different and
desolvation effects are being observed.
Increase the carrier gas flow rate.
FAIMS electrodes have become
contaminated by a droplet from the ion
source.
Remove, disassemble, clean, reassemble, and reinstall the FAIMS electrodes.
Gas purification cartridges are wet.
Replace the gas purification cartridges.
Gas purification cartridges were wet, but
have been recently replaced.
Previous data was collected under non-ideal conditions.
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Troubleshooting
Problem
Solution
Compensation Voltage Shifts with Gas Flow Rate
Poor desolvation.
If the FAIMS electrodes have been recently cleaned, check for gas leaks after re-assembly.
Increase the gas flow rate until the ion is transmitted at a constant compensation voltage
value.
Gas mixture is changing.
Check the readbacks (which are displayed in the Actual Value box associated with each
parameter) in the FAIMS control software to verify that the carrier gas composition isn’t
changing.
More than One Peak for Ion m/z
Peaks are from different ions.
Confirm ion identities using the mass spectrometer.
Multimeric species are present.
Lower the ion concentration.
Adduct species are present.
Collect the mass spectrum under gentle conditions and look for adduct species. Increasing
the carrier gas flow rate may reduce the presence of adduct species.
Poor desolvation.
Increase the carrier gas flow rate.
Ion can assume more than one
conformation.
The FAIMS is resolving ions of different conformations. This behavior might be observed
with proteins, peptides, and in some cases, small molecules.
Change in Peak Shape
FAIMS electrodes have been reassembled
improperly.
Check the assembly of the electrodes.
Misalignment of FAIMS electrodes on
mass spectrometer.
Check that the entrance plate has not been overtightened.
Incorrect carrier gas flow rate.
Reoptimize the carrier gas flow rate.
Gas purification cartridges are wet.
Replace the gas purification cartridges. If the change in peak shape occurred after
replacing the gas purification cartridges, previous cartridges might have been wet.
High Variability in Signal
API probe position of the ion source is too
close to the inlet of the FAIMS electrodes.
Re-optimize the API probe position.
FAIMS temperatures are too high.
Reduce the temperatures of the inner and outer heaters by 10 °C and collect a CV ramp.
Ion source is not operating properly.
Check that a steady ion beam is being provided.
Carrier gas flow rate too high/too low.
Optimize the carrier gas flow rate.
Gas purification cartridges are wet.
Replace the gas purification cartridges.
Change in Peak Resolution
Gas flow rate or composition has changed.
Check the Gas Flow parameters in the FAIMS control software to verify the gas flow rate
and composition.
Different dispersion voltage.
Check the value of the Dispersion Voltage parameter in the FAIMS control software.
FAIMS electrodes are dirty.
Remove, disassemble, clean, reassemble, and reinstall the electrodes.
Increased Background
Different sample matrix.
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“Dirty” samples may have higher background than “clean” samples.
Thermo Scientific
9
Troubleshooting
Problem
Solution
Dispersion voltage, compensation voltage,
or outer bias voltage changed.
Check the value of the appropriate parameter in the FAIMS control software.
FAIMS electrodes need cleaning.
Remove, disassemble, clean, reassemble, and reinstall the FAIMS electrodes.
Gas purification cartridges are wet.
Replace the gas purification cartridges.
Mass spectrometer conditions changed.
Check the mass spectrometer voltages.
Ion source not working properly.
Check that the ion source is working properly.
Mass spectrometer interface is dirty.
Remove the FAIMS electrodes from the mass spectrometer and check whether background
is higher than normal when the electrodes are not installed.
Optimal Gas Flow Rate Changed
Gas leaks in system.
Check that all gas lines are properly installed.
Check that the FAIMS electrodes are assembled properly.
Solution flow rate has been increased or
decreased.
Desolvation gas requirements change if flow rate is increased or decreased significantly.
Frequent Discharge within the FAIMS Electrodes
Too much helium at the DV and
temperature settings being used.
Reoptimize conditions (DV, temperature and gas composition).
Adduct Species Have Suddenly Appeared
Poor desolvation of ions.
Increase the carrier gas flow rate.
FAIMS electrodes are dirty.
Remove, disassemble, clean, reassemble, and reinstall the electrodes.
Running solution or electrode cleaning
solution is contaminated.
Check if adducts exist after solutions are changed.
Gas lines contaminated.
Bypass gas lines embedded within the FAIMS waveform generator by using new gas lines.
Check if adducts still appear.
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10
Site Preparation and System Specifications
This chapter describes the necessary preparations for the installation of the FAIMS system.
These preparations must be completed before Thermo Fisher Scientific Corporation’s
authorized service personnel arrive at your site.
This chapter discusses the following:
• Installation Guidelines
• Dimensions and Weight
• Configuration
• Environment
• Electrical
• Gases and Regulators
• Data System Computer
• Installation Equipment and Reagents
• Installation Checklist
Installation Guidelines
The FAIMS system must be installed by a Thermo Fisher Scientific Corporation’s authorized
representative. The service representative will then ensure that the instrument is operating
properly.
The person from your organization who will be responsible for the system should be available
during installation to verify the acceptance of the instrument and to receive operation
training.
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10 Site Preparation and System Specifications
Dimensions and Weight
Dimensions and Weight
The FAIMS system includes a waveform generator and a temperature control module. The
dimensions of the waveform generator are:
• Width: 25 cm (10 in.)
• Depth: 38 cm (15 in.)
• Height: 52 cm (20.5 in.)
The dimensions of the temperature control module are:
• Width: 25 cm (10 in.)
• Depth: 38 cm (15 in.)
• Height: 15 cm (6 in.)
The waveform generator and temperature control modules have a combined mass of
approximately 20 kg (45 lb.).
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10
Site Preparation and System Specifications
Configuration
Configuration
The waveform generator must be located next to the TSQ Quantum or LTQ on its left, as
Figure 79 shows.
Figure 79. FAIMS waveform generator, FAIMS interface, and TSQ Quantum
The temperature control module can be placed anywhere as long as the cable and gas lines can
reach the connection panel on the FAIMS interface heater box. Possible locations of the
temperature control module are:
• Next to the waveform generator
• On top of the TSQ Quantum or LTQ
CAUTION Ensure that there is room to access the power switches for the waveform
generator and the temperature control module. The AC power switch of both module
must remain easily accessible. Do not position the modules or other equipment in a way
that hinders access to these switches.
Environment
Locate the FAIMS system in an area that it is kept free from excessive dust.
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Electrical
Operation
Ambient temperature: 15 ºC to 30 ºC
Humidity: 5% to 95% relative humidity, non-condensing
Altitude: 0 to 2000 meters
Storage
Ambient temperature: -40 ºC to 70 ºC
Humidity: 5% to 95% relative humidity, non-condensing
Radio Emissions
Do not place the FAIMS system within an RF field of greater than 5 V/m.
Magnetic Fields
Locate the FAIMS system away from strong magnetic fields.
Electrical
Outlets must be available within reach of the FAIMS system AC power cord. The outlets
must meet the appropriate electrical specifications for your region:
• North America: Single phase 115 VAC, 60 Hz, 2.5 A
• Europe: Single phase 230 VAC 50 Hz, 1.3 A
Gases and Regulators
Gases need to be supplied to the FAIMS system for two separate purposes:
• To desolvate and deliver ions through the electrodes and into the mass spectrometer (the
carrier gas)
• To actively control the electrode temperatures
For the carrier gas, nitrogen and industrial grade helium gases must be available for
installation. Two-stage regulators should be used (delivering gas at a pressure of 40 to 80
p.s.i.) and a connection to a 1/8 in. gas line leading to the FAIMS waveform generator must
be made.
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Site Preparation and System Specifications
Data System Computer
Prior to introduction of the carrier gas to the electrodes, gases are purified using gas
purification cartridges. These cartridges are provided with the system. Typical total gas flow is
2.5 to 4 L/min.
For actively controlling the temperatures of the FAIMS electrodes, compressed air must be
used. When FAIMS is operating, the total gas flow through the electrodes is approximately
3 cubic feet/min (85 L/min). This gas does not come into contact with the solvents from the
ionization source of the mass spectrometer and is typically merged with the exhaust stream of
the TSQ Quantum or LTQ. This gas needs to be delivered at a pressure between 40 and
60 psi with a connection to a 1/4 in. gas line leading to the temperature control module.
To test that the gas supply for temperature control can deliver the necessary flow rate, attach a
30 cm length of 1/4 in. tubing to the gas outlet near the regulator. With the line fully opened,
ensure a pressure of 40 psi can be achieved.
Note All other sinks to the gas supply should be on to represent a normal gas use condition.
For the compressed gas used for controlling the temperatures of the electrodes, Thermo Fisher
Scientific strongly recommends that a desiccant air dryer be used to remove some of the
moisture, oil, and dirt that might be present.
Data System Computer
The Xcalibur FAIMS system control software allows you to control the voltages and the
composition and flow rate of the carrier gas, as well as the temperature of the heating gases
that are applied to the FAIMS electrodes.
The Xcalibur FAIMS system control software communicates with the FAIMS waveform
generator by using a serial connection between the TSQ Quantum or LTQ and the FAIMS
waveform generator.
The control software also communicates with the FAIMS temperature control module via a
dedicated Ethernet port. If an Ethernet port is unavailable, a dedicated USB port can also be
used.
The minimum computer requirements are:
• Microsoft® Windows® 2000 or Microsoft Windows XP
• 1 GHz processor
• 512 MB memory
• Dedicated serial port (RS232)
• Dedicated Ethernet 10baseT, 100baseT, or USB 2.0 port
• 10 MB free hard drive space
• CD-ROM drive
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10 Site Preparation and System Specifications
Installation Equipment and Reagents
Installation Equipment and Reagents
During installation, the service representative cleans the FAIMS electrodes. Cleaning the
FAIMS electrodes requires the following:
• Ultrasonic bath
• Solution of 4% formic acid in 1:1 methanol:water
• Oven that can be set to a minimum of 105 ºC for drying the stainless steel electrodes after
cleaning
• Glass dish large enough to hold the electrodes while in the oven
The following reagents must be available for installation:
• HPLC-grade water or water purified by reverse osmosis
• Formic acid
• Methanol
• Isopropanol
CAUTION Observe good laboratory practices when you work with chemicals (for
example, when making solutions). Use a fume hood and wear appropriate personal
protective equipment.
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Site Preparation and System Specifications
Installation Checklist
Installation Checklist
Part 1: Site Requirements
Table 20. Site requirements check list
Requirement
Satisfied?
Space (page 111)
• Adequate space on the left of the mass spectrometer for the FAIMS waveform
generator
‰
• Adequate space on top of the mass spectrometer or next to the waveform generator
for the FAIMS temperature control module
‰
Environment (page 111)
• Meets requirements for temperature
‰
‰
‰
‰
• Meets requirements for humidity
• Meets requirements for radio emissions
• Meets requirements for magnetic fields
Electrical (page 112)
‰
‰
• Outlets meet the electrical specifications
• Outlets are available within 10 ft. of the location of the FAIMS system
Gases and Regulators (page 112)
• Helium and industrial grade Nitrogen with two-stage regulators (40-80 psi).
• Compressed air supply can achieve a pressure of 40 psi when a 30 cm length of 1/4 in.
tubing is attached to the regulator.
‰
‰
Computer (page 113)
• Meets requirements for the FAIMS system control software
• Dedicated Ethernet port or USB port
• Dedicated serial port
‰
‰
‰
Maintenance Equipment (page 114)
• Ultrasonic bath
‰
• Oven (can operate at 105ºC)
‰
Reagents (page 114)
• Formic acid
• Ammonium acetate
• Methanol and isopropanol
• Reagent grade water or water purified by reverse osmosis
Thermo Scientific
‰
‰
‰
‰
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10 Site Preparation and System Specifications
Installation Checklist
Table 20. Site requirements check list
Requirement
Satisfied?
Solvent Delivery System
‰
‰
‰
• Syringe pump
• HPLC pump
• Autosampler or injection valve
Indicate if any preinstallation actions are required:
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
Part 2: Availability of Personnel
The individual responsible for the daily operation of the FAIMS system in
your lab is:
__________________________________________________________
Will this person will be present for the installation of the FAIMS system and for training in its
operation?
Yes ‰ No‰
The percentage of time that this person will be available during this time is:
_________________________________________ .
Arrangements for the installation of the FAIMS system at your site should be made with:
_________________________________________
who can be contacted at:
E-mail: _________________________________________
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10
Site Preparation and System Specifications
Installation Checklist
Phone: ____________________________________________
Cell Phone: ________________________________________
Lab Address: ________________________________________
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A
FAIMS Optimization Flowchart
The flowchart shown below provides primary and secondary procedures for setting the
FAIMS parameters for positively and negatively charged ions. For positively charged ions, the
two procedures are refered to as mode P1 and mode P2. For negatively charged ions, the two
procedures are refered to as mode N1 and mode N2. Table 21 lists FAIMS parameters for
these modes.
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A
FAIMS Optimization Flowchart
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Figure 80. Flowchart for determining FAIMS parameters for positively charged ions
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A
FAIMS Optimization Flowchart
/FHBUJWF
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Figure 81. Flowchart for determining FAIMS parameters for negatively charged ions
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A
FAIMS Optimization Flowchart
. for the FAIMS flowchart
Table 21.Settings
Starting Parameter
Mode P2
Mode P1
Mode N2
Mode N1
Polarity
Positive ion
Positive ion
Negative ion
Negative ion
Dispersion voltage
-5000 V
+5000 V
+5000 V
-5000 V
Carrier gas
composition
50% He
0% He
50% He
0% He (
Gas flow rate
3.5 L/min
3.5 L/min
3.5 L/min
3.5 L/min
Outer bias voltage
Same as capillary
offset
Same as capillary
offset
Same as capillary
offset
Same as capillary
offset
Narrow CV scan
range
-30 to 10 V
-30 to 10 V
-10 to 30 V
-10 to 30 V
Expanded CV scan
range
-50 to 10 V
-50 to 10 V
-10 to 50 V
-10 to 50 V
High temperature
Inner=70 ºC,
Inner=70 ºC,
Inner=70 ºC,
Inner=70 ºC,
Outer=90 ºC
Outer=90 ºC
Outer=90 ºC
Outer=90 ºC
Inner=50 ºC,
Inner=50 ºC,
Inner=50 ºC,
Inner=50 ºC,
Outer=70 ºC
Outer=70 ºC
Outer=70 ºC
Outer=70 ºC
Low temperature
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Index
A
D
alignment bushings
location (figure) 90
removing (figure) 93
Define Scan view (TSQ Quantum series)
figure 42
opening 34, 41
Device view
displaying 38
figure 38
dispersion voltage (DV)
allowed range 65
discussion 5
optimization 66
C
cables list (table) 75
carrier gas
and waveform generator (figure) 10
composition 6
composition and CV (figure) 6
composition, allowed range 65
effect of flow rate on CV (figure) 8
flow rate 7
flow, allowed range 65
inputs and outputs (figure) 71
optimizing composition 66
CAUTIONS
gas flow and electrodes 11
hot electrodes 93
Ion Max source housing high temperature 80
power down waveform generator 80
tampring with safety interlocks 16
working with chemicals 93
cleaning equipment 78
compensation voltage (CV)
allowed range 65
carrier gas effects (figure) 6
copying to Instrument Setup (TSQ Quantum series) 22
copying to LCquan (TSQ Quantum series) 22
discussion 5
effect of carrier gas flow rate 7
effect of carrier gas flow rate (figure) 8
effect of electrode temperatures on 6
LTQ cal mix scans (figure) 58
polytyrosine 1,3,6 experiment (TSQ Quantum series) 39
polytyrosine 1,3,6 experiment CV scan 38
polytyrosine 1,3,6 experiment CVs (figure) 40
ramp, performing (LTQ series) 29
running CV scans (TSQ Quantum series) 38
scan, performing (TSQ Quantum series) 18, 20
computer requirements 113
Thermo Scientific
E
electrical requirements 111
electrode assembly
cross section (figure) 15
description 15
disassembling 89
endcaps, location (figure) 16
exploded diagram 90
figure 16
O-rings 94
reassembling 95
removing 86, 89
electrode assembly mount
location 85
location (figure) 86, 86
removing 88
electrodes
allowed temperature range 65
cleaning and drying 93
cleaning procedure 78
cross section (figure) 15
gas flow required (CAUTION) 11
location (figure) 90
optimizing temperatures 66
temperature and CV 6
temperature control gas inlet (figure) 73
temperature control gas outlets (figure) 73
termperature 5
entrance plate
cleaning 95
location 85
location (figure) 86, 86
removing 86
FAIMS Operator’s Manual I
Index: F
entrance plate voltage
allowed range 65
equipment and reagents requirements 114
F
FAIMS
carrier gas composition 6
compensation voltage (CV), discusstion 5
control software (LTQ series) 25
control software (TSQ Quantum series) 17
CV ramp, perfoming (LTQ series) 29
CV scan, perfoming (TSQ Quantum series) 18, 20
CV scans (TSQ Quantum series) 39
dispersion voltage (DV), discussion 5
effect (figure) 4
electrode temperatures and CV 6
electrodes and gas flow (CAUTION) 11
electrodes temperatures 5
experiment (LTQ series) 51
flowchart 119
operation 2
overview 1
parameters, discussion 5
polytyrosine 1,3,6 experiment (TSQ Quantum series) 31
process (figure) 3
process, discussion 2
selection of polytyrosine - 1 (figure) 47
selection of polytyrosine - 3 (figure) 46
separation (figure) 4
testing selectivity (LTQ series) 61
testing selectivity (TSQ Quantum series) 44
Xcalibur control (LTQ series)l 25
Xcalibur control (TSQ Quantum series) 17
FAIMS Control dialog box (LTQ series)
figure 27
opening 26
settings 26
FAIMS Control view (TSQ Quantum series)
figure 19
opening 18
settings 18
FAIMS interface
disconnecting gas lines and cables 80
making connections 99
photo of 80
reassembling 95
reinstalling on Ion Max housing 96
removed from Ion Max source housing 85
removing 80, 83
removing from Ion Max 84
FAIMS interface heater box
II
FAIMS Operator’s Manual
connecting gas lines 74
connection panel (figure) 74
FAIMS page - Tune (LTQ series))
figure 29
opening 28
FAIMS settings
advanced optimization 65
flowchart 119
mode N1 119
mode N2 119
mode P1 119
mode P2 119
negative ion mode (table) 20, 28
operating parameters (table) 65, 122
optimizing 65
positive ion mode (table) 19, 27
ranges (table) 65
saving in tune file 30
saving in tune file (TSQ Quantum series) 21
FAIMS system
availability of personnel 116
cables list 75
components 8
computer requirements 113
configuration 111
configuring (LTQ series) 26
connecting modules 69
control software (LTQ series) 25
control software (TSQ Quantum series) 17
dimensions 110
electrical requirements 111
electrode assembly, description 15
environment 111
equipment and reagents requirements 114
gas flow system, discussion 10
gas lines list 75
gas pressure requirements 113
gases and regulators 112
high voltage lead, description 13
high voltage lead, discussion 12
installation checklist 115
interface assembly, description 14
interlocks 16
photo with LTQ 2
photo with TSQ Quantum 1
powering up 99
safety interlocks 16
standby mode (LTQ series) 30
standby mode (TSQ Quantum series) 23
temperature control module, functions 12
troubleshooting (table) 103
waveform generator 8
weight 110
Thermo Scientific
Index: G
Xcalibur control (LTQ series) 25
Xcalibur control (TSQ Quantum series) 17
Xcalibur recognition of (TSQ Quantum series) 17
flowchart 119
fuses
list 101
location 101
replacing 101
G
gas and voltage connector
location (figure) 86, 86
removing 87
gas cartridges
photo of 101
replacing 99
use quick disconnect 72
gas flow system, discusstion 10
gas lines list (table) 75
gas pressure requirements 113
gases and regulators 112
H
H-ESI
flushing 48
polytyrosine 1,3,6 experiment (TSQ Quantum series)
settings 41
polytyrosine 1,3,6 experiment settings (TSQ Quantum series)
34
settings for FAIMS experiment (LTQ series) 54
high voltage lead
description 13
disconnecting 80
discussion 12
figure 13
I
inner electrode
location (figure) 90
installation checklist 115
Instrument 34, 34
interface assembly
description 14
electrode assembly (figure) 14
figure 14
interlocks
description 16
FAIMS Operator’s Manual
Ion Max source housing
high temperature (CAUTION) 80
locking levers, location 83
reinstalling 98
removing 83
removing FAIMS interface 84
ion sweep cone
installing 96
photo of 96, 97
ions
beam stability (LTQ series) 59
beam stability, polytyrosine 1,3,6 experiment
(TSQ Quantum series) 40, 43
drift (figure) 3
selection, polytyrosine - 3 (figure) 46
separation 2
separation (figure) 4
transmission (figure) 4
L
LTQ
FAIMS control software 25
FAIMS experiment 51
photo of 2
LTQ cal mix experiment
caffeine ion selection 61
CV scans (figure) 58
FAIMS settings 56
FAIMS tune page 57
MRFA ion selection 62
optimum CVs 59
scan settings 55
setting up 51
testing selectivity 61
Ultramark ion selection 63
LTQ Configuration dialog box
FAIMS page (figure) 26
FAIMS page, opening 25
M
maintenance procedures
cleaning and drying the electrodes 93
cleaning entrance plate 95
cleaning the electrodes 78
inspecting O-rings 94
overview 77
replacing fuses 101
Thermo Scientific
III
Index: O
O
removing electrode assembly 86, 89
removing electrode assembly mount 88
removing entrance plate 86
removing FAIMS interface 80, 83
removing gas and voltage connector 87
removing Ion Max source housing 83
replacing fuses 101
replacing gas cartridges 99
running a CV scan (LTQ series) 55
running a CV scan (TSQ Quantum series) 36
running CV scans (TSQ Quantum series) 38
running syringe pump (LTQ series) 53
saving FAIMS settings (LTQ series) 63
saving FAIMS settings (TSQ Quantum series) 48
setting up mass spectrometer, FAIMS experiment
(LTQ series) 53
setting up syringe pump 31, 52
testing FAIMS selectivity (TSQ Quantum series) 44
verifying a stable ion beam (LTQ series) 59, 59
verifying a stable ion beam (TSQ Quantum series) 40, 40
O-rings
inspecting 94
locations 94
outer bias voltage
allowed range 65
optimizing 67
outer electrode
location (figure) 90
P
parameters 41, 44
polytyrosine 41
polytyrosine 1,3,6 experiment (TSQ Quantum series)
beam stability 40
CV scan, performing 38
CVs (figure) 40
FAIMS experiment 31
FAIMS settings 34
FAIMS settings, polytyrosine 3 41
H-ESI settings 34, 41
injecting 36
instrument settings 34, 34
selection of polytyrosine - 3 (figure) 46
separation of polytyrosine - 1 (figure) 47
setting up FAIMS system 33
setting up mass spectrometer 33
SIMS settings 34, 35
procedures
advanced optimization of FAIMS parameters 65
cleaning and drying the electrodes 93
cleaning entrance plate 95
cleaning the electrodes 78
connecting FAIMS modules 69
connecting temperature control module gas lines 73
CV scans (TSQ Quantum series) 39
disassembling electrode assembly 89
flushing H-ESI probe 48, 48, 63
installing ion sweep cone 96
making electrical connections to heater box 74
optimizing dispersion voltage 66
optimizing electrode temperatures 66
optimizing outer bias voltage 67
optimizing separation 65
placing FAIMS system in standby 79
powering down the waveform generator 80
powering up FAIMS system 99
reassembling electrode assembly 95
reassembling the FAIMS interface 95
reinstalling FAIMS interface 96
reinstalling Ion Max housing 98
IV
FAIMS Operator’s Manual
R
right endcap
location (figure) 90
S
safety
interlocks 16
safety interlocks
CAUTION 16
description 16
sealing screws
location (figure) 90
selectivity
optimizing 65
polytyrosine 1,3,6 experiment, testing 44
sensitivity
optimizing 67
separation
optimizing 65
separation of ions 2
SIMS 35, 35
standby mode, placing system in
standby (LTQ series) 30
TSQ Quantum series 23
sweep cone 97
syringe
cleaning 48
contamination 32
Thermo Scientific
Index: T
syringe pump
configuring (TSQ Quantum series) 36
installing syringe into 32, 52
running (TSQ Quantum series) 36
setting up for FAIMS experiment 52
gasses, input and output (figure) 10
photo of 8
power down before service (CAUTION) 80
powering down 80
voltages, input (figure) 10
waveform generator cable connector
FAIMS interface heater box, location (figure) 74
T
temperature control gas
inlets, location (figure) 74
temperature control module
COMM port, location (figure) 73, 73
communication with TSQ Quantum 69
connecting gas lines 73
connection panel (figure) 73
control inputs and outputs (figure) 13
description 12
functions 12
gasses (figure) 13
heater cable connector, location (figure) 73
on/off switch, location (figure) 73
photo of 12
temperature control gas (figure) 70
toubleshooting (table) 103
TSQ Quantum
communication with temperature control module 69
communication with waveform generator 69
photo of 1
polytyrosine 1,3,6 FAIMS experiment 31
tune file, saving
LTQ series 30
TSQ Quantum series 21
X
Xcalibur
CV increment 18
CV increment (note) 29
FAIMS control (LTQ series) 25
FAIMS control (TSQ Quantum series) 17
FAIMS Control dialog box (LTQ series), opening 26
FAIMS Control view (TSQ Quantum series), opening 18
FAIMS settings 17
FAIMS settings (LTQ series) 26
recognizing the FAIMS system (TSQ Quantum series) 17
V
voltages
compensation voltage (CV) 5
dispersion voltage (DV) 5
waveform generator (figure) 10
W
waveform generator
communication with TSQ Quantum 69
communications (figure) 10
connection panel (figure) 11
description 8
function generator, discussion 10
functions 8
gas flow system, discussion 10
gas inputs and outputs (figure) 70
FAIMS Operator’s Manual
Thermo Scientific
V
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