Thermo Fisher Scientific FAIMS Pro System User guide

FAIMS Pro System

User Guide

High-Field Asymmetric Waveform Ion Mobility

Spectrometry System

98100-97000 Revision A January 2019

EASY-Spray NG, FAIMS Pro, Nanospray Flex NG, and TSQ are trademarks; Unity is a registered service

mark; and Orbitrap, Pierce, Thermo Scientific, and Tribrid are registered trademarks of Thermo Fisher

Scientific Inc. in the United States.

The following are registered trademarks in the United States and other countries: Liquinox is a registered

trademark of Alconox, Inc. Microsoft and Windows are registered trademarks of Microsoft Corporation.

The following are registered trademarks in the United States and possibly other countries: Tygon is a registered

trademark of Saint-Gobain Performance Plastics Company. Viton is a registered trademark of DuPont

Performance Elastomers LLC.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the

product operation. This document is copyright protected and any reproduction of the whole or any part of this

document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this

document is for reference purposes only. System configurations and specifications in this document supersede

all previous information received by the purchaser.

This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This

document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of

Sale shall govern all conflicting information between the two documents.

Release history: Rev A, January 2019

Software version: (Thermo) Foundation 3.1 SP5 and later, Xcalibur 4.2 and later, Tune 3.1 and later

For Research Use Only. Not for use in diagnostic procedures.

Regulatory Compliance

Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with

applicable North American and European regulations. Your system meets the applicable requirements in the

electromagnetic compatibility (EMC) and product safety standards described in this section.

Unauthorized changes that you make to your system will void regulatory compliance and may defeat the built-in

protections for your instrument. Some examples of unauthorized changes include using replacement parts or adding

components, options, or peripherals that Thermo Fisher Scientific has not qualified and authorized. Unauthorized

changes can also result in bodily injury and/or damage to your system and laboratory.

Ensure continued compliance with regulatory standards:

• Follow all installation instructions provided in the documentation that comes with your system.

• Order replacement parts (as specified in the instrument manual) and additional components, options, and periph-

erals directly from Thermo Fisher Scientific or an authorized representative.

FCC Compliance Statement

Low Voltage Directive 2014/35/EU

This device complies with Low Voltage Directive 2014/35/EU and the safety standards EN 61010-1:2010, UL

61010–1:2012, CAN/CSA 22.2 61010-1-12; EN 61010-2-010:2014, UL 61010-010:2015, CAN/CSA 22.2 61010-

2-010:2015.

EMC Directive 2014/30/EU

This device was tested by TÜV Rheinland of North America and complies with the following EMC standards:

47 CFR 15, Subpart B, Class A: 2015 EN 55011:2009 + A1 EN 61000-4-4: 2012

CISPR11: 2009 + A1 IEC/EN 61326-1: 2013 EN 61000-4-5: 2014

ICES-003 Issue 6: 2016 IEC 61000-3-2: 2014 EN 61000-4-6: 2014

AS/NZS CISPR22: 2009 IEC/EN 61000-3-3: 2013 IEC/EN 61000-4-11: 2004 /

ISH1:2010

AS/NZS CISPR32: 2015 IEC/EN 61000-4-2

VCCI CISPR 32: 2015 IEC 61000-4-3: 2006 + A2

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.

Notice on Lifting and Handling of

Thermo Scientific Instruments

For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific

instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or bulky for one

person alone to handle safely.

Notice on the Proper Use of

Thermo Scientific Instruments

In compliance with international regulations: This instrument must be used in the manner specified by Thermo Fisher

Scientific to ensure protections provided by the instrument are not impaired. Deviations from specified instructions on

the proper use of the instrument include changes to the system and part replacement. Accordingly, order replacement

parts from Thermo Fisher Scientific or one of its authorized representatives.

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.

WEEE Directive

2012/19/EU

Thermo Fisher Scientific is registered with B2B Compliance (B2Bcompliance.org.uk) in the UK and with the

European Recycling Platform (ERP-recycling.org) in all other countries of the European Union and in Norway.

If this product is located in Europe and you want to participate in the Thermo Fisher Scientific Business-to-Business

(B2B) Recycling Program, send an email request to weee.recycle@thermofisher.com with the following information:

• WEEE product class

• Name of the manufacturer or distributor (where you purchased the product)

• Number of product pieces, and the estimated total weight and volume

• Pick-up address and contact person (include contact information)

• Appropriate pick-up time

• Declaration of decontamination, stating that all hazardous fluids or material have been removed from the product

For additional information about the Restriction on Hazardous Substances (RoHS) Directive for the European Union,

search for RoHS on the Thermo Fisher Scientific European language websites.

IMPORTANT This recycling program is not for biological hazard products or for products that have been medically

contaminated. You must treat these types of products as biohazard waste and dispose of them in accordance with

your local regulations.

Thermo Scientific FAIMS Pro System User Guide vii

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Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

Accessing Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

Viewing the Product Manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv

Accessing the Help Menu Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv

Viewing Online User Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv

Providing Documentation Feedback. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv

Compatible Mass Spectrometers and API Sources. . . . . . . . . . . . . . . . . . . . . . . xv

Special Notices, Symbols, and Cautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi

Safety Precautions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii

Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xix

Chapter 1 FAIMS Theory. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

What is FAIMS Technology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

FAIMS Value Points . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Supported FAIMS Platforms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Standard-Resolution and High-Resolution Modes . . . . . . . . . . . . . . . . . . . . . . . 3

Standard Resolution Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

High Resolution Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Additional Available Modes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Chapter 2 FAIMS Operation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7

Selection of Ions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

FAIMS Pro Instrument-Control Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Dispersion Voltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Compensation Voltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Electrode Temperatures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Carrier Gas Flow Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Readback Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Configuring the System Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Calibration Solutions and Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

FAIMS Component On/Off Status Under Varying Power Conditions . . . . . . . 15

Chapter 3 Functional Description. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17

Main Controller Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Housing Adapter and RF Transformer Box. . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Contents

viii FAIMS Pro System User Guide Thermo Scientific

Electrode Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Electrode Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Gas Delivery to the FAIMS Electrodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Chapter 4 Installing the FAIMS Pro System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25

Removing the MS Ion Sweep Cone. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Installing the Electrode Assembly to the Housing Adapter . . . . . . . . . . . . . . . . 27

Connecting the Nitrogen Gas and Electrical Cables to the MCB . . . . . . . . . . . 28

Installing the FAIMS Pro System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Installing the EASY-Spray NG Ion Source on the FAIMS Pro System . . . . . . . 30

Installing the Nanospray Flex NG Ion Source on the FAIMS Pro System . . . . . 31

Chapter 5 Generating a FAIMS Diagnostics Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33

Running the FAIMS User Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Diagnostics Results of the Tune DV RF Process . . . . . . . . . . . . . . . . . . . . . . . . 37

Diagnostics Results of Check DV RF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Example Diagnostics Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Chapter 6 Identifying Optimal CV Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53

Configuring the CV Scan Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Defining the Scan Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Saving the Optimal CV Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Chapter 7 Conducting an Example FAIMS Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57

Using Tune to Acquire Sample Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Using Method Editor Templates to Acquire Sample Data. . . . . . . . . . . . . . . . . 62

Using FreeStyle to View Previously Acquired Sample Data . . . . . . . . . . . . . . . . 63

Chapter 8 Maintaining the FAIMS Pro System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .65

Maintenance Schedule. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Tools and Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Shutting Down the LC/MS/FAIMS Pro System . . . . . . . . . . . . . . . . . . . . . . . . 68

Flushing the Inlet Components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Removing Components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Removing the Ion Source from the FAIMS Pro System. . . . . . . . . . . . . . . . . 70

Removing the Electrode Assembly from the Housing Adapter. . . . . . . . . . . . 70

Removing the Electrode Set from the Entrance Plate. . . . . . . . . . . . . . . . . . . 71

Removing the FAIMS Pro System from the MS . . . . . . . . . . . . . . . . . . . . . . 72

Cleaning Components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

Cleaning the Entrance Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

Cleaning the Electrodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Cleaning the RF Transformer Box’s Air Filter . . . . . . . . . . . . . . . . . . . . . . . . 75

Cleaning the Housing Adapter’s Drain Adapter. . . . . . . . . . . . . . . . . . . . . . . 75

Fixing a Gas Leak Between the MS and the Electrodes . . . . . . . . . . . . . . . . . . . 77

Contents

Thermo Scientific FAIMS Pro System User Guide ix

Reassemble Components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Chapter 9 Replaceable Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83

Additional Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

Consumable Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

Power Cord. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

Chapter 10 Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87

Contents

xFAIMS Pro System User Guide Thermo Scientific

Thermo Scientific FAIMS Pro System User Guide xi

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Figure 1. FAIMS Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Figure 2. FAIMS Pro and Obritrap Lumos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Figure 3. Standard Resolution Mode Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Figure 4. High Resolution Mode Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Figure 5. Animation: FAIMS effect showing ion drift (parallel plate example) . . . . . . . . . . 8

Figure 6. Animation: FAIMS effect with CV showing ion transmission (parallel plate

example) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Figure 7. FAIMS-MS/MS selection of drug and metabolite . . . . . . . . . . . . . . . . . . . . . . . . 9

Figure 8. Gas flow with ions in the cylindrical electrodes . . . . . . . . . . . . . . . . . . . . . . . . . 10

Figure 9. Example ideal FAIMS waveform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Figure 10. LEDs on the MCB front . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Figure 11. Interconnect on the MCB rear . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Figure 12. Adapter housing and RF transformer box (front and back with partial cable) . . . 20

Figure 13. Electrode assembly with unlocked levers (front and right side) . . . . . . . . . . . . . . 21

Figure 14. Entrance plate with and without the electrode assembly (back) . . . . . . . . . . . . . 21

Figure 15. Electrode assembly with unlocked levers (back and bottom) . . . . . . . . . . . . . . . 21

Figure 16. Electrode set removed from the entrance plate . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Figure 17. Partial exploded view of the electrode set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Figure 18. Heater endcap with heater, bushing assembly, and outer electrode . . . . . . . . . . 23

Figure 19. Schematic of the gas delivery to the FAIMS system and MS . . . . . . . . . . . . . . . 23

Figure 20. FAIMS Diagnostics pane - Tune DV RF in progress . . . . . . . . . . . . . . . . . . . . . 34

Figure 21. FAIMS Diagnostics pane - Tune DV RF complete . . . . . . . . . . . . . . . . . . . . . . 35

Figure 22. FAIMS Diagnostics pane - Check DV RF in progress . . . . . . . . . . . . . . . . . . . . 36

Figure 23. FAIMS Diagnostics pane - Check DV RF completed . . . . . . . . . . . . . . . . . . . . 37

Figure 24. High field RF coarse tuning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Figure 25. High field RF fine tuning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Figure 26. Low field RF coarse tuning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Figure 27. Low field RF fine tuning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Figure 28. Wait DV modulation DC to settle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Figure 29. HF & LF modulation DAC adjust . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Figure 30. DV RF ramp check HF amplitude . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Figure 31. DV ramp check of LF Amplitude . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Figure 32. Wait DV modulation DC to settle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Figure 33. Check DV RF Diagnostic Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Figure 33. Check DV RF Diagnostic Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Figure 34. Tune DV RF Diagnostic Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Figure 34. Tune DV RF Diagnostic Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Figures

xii FAIMS Pro System User Guide Thermo Scientific

Figure 34. Tune DV RF Diagnostic Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Figure 34. Tune DV RF Diagnostic Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Figure 35. Results of FAIMS CV Scan in Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Figure 36. Ion Source pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Figure 37. Select FAIMS mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Figure 38. Setup Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Figure 39. Activate FAIMS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Figure 40. Setup CV Scan Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

Figure 41. Report Generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

Figure 42. CV Scan Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Figure 43. CV Scan Results Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Figure 44. Entrance plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

Figure 45. Separate the inner electrode and the outer electrode from electrode set assembly 74

Figure 46. Air filter on the bottom of the RF transformer box . . . . . . . . . . . . . . . . . . . . . . 75

Figure 47. Drain adapter on the housing adapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

Figure 48. O-ring seals for electrode bushing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Figure 49. O-ring seals for the entrance plate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Figure 50. Assembled electrode set. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Figure 51. Electrode set inserted into entrance plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Figure 52. FAIMS assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

Figure 53. FAIMS assembly attached to MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

Thermo Scientific FAIMS Pro System User Guide xiii

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Preface

The FAIMS Pro System User Guide contains the installation instructions, descriptions of the

primary components, and maintenance procedures for the Thermo Scientific™ FAIMS Pro™

system, which is a high-field asymmetric waveform ion mobility spectrometry (FAIMS)

system. To ensure a compatible setup, see Compatible Mass Spectrometers and API Sources.

Also, because this guide uses drawings of various connections and component parts to help

illustrate procedures, be sure to start from , no matter where it appears.

Contents

• Accessing Documentation

• Providing Documentation Feedback

• Compatible Mass Spectrometers and API Sources

• Special Notices, Symbols, and Cautions

• Safety Precautions

•Contacting Us

Accessing Documentation

The FAIMS Pro system includes complete documentation.

•Viewing the Product Manuals

•Accessing the Help Menu Options

•Viewing Online User Documentation

For mass spectrometer (MS) requirements, refer to the release notes on the software DVD.

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xiv FAIMS Pro System User Guide Thermo Scientific

Viewing the Product Manuals

The Thermo Fisher Scientific™ service engineer installs the instrument control applications

and the instrument manuals on the data system computer.

To view the product manuals

From the Microsoft™ Windows™ taskbar, choose Start > All Apps (Windows 10) or

All Programs (Windows 7) > Thermo Instruments > model x.x, and then open the

applicable PDF file.

Accessing the Help Menu Options

Follow this procedure to view the Help systems for the instrument-control applications.

To view the Help

Do the following as applicable:

• Thermo Tune instrument-control application: Click the Options icon, , and

choose Tu n e H e l p.

• Thermo Xcalibur™ Method Editor application: Choose an option from the Help

menu (or press the F1 key).

Viewing Online User Documentation

Visit the Thermo Fisher Scientific website for product manuals and more.

To view user documentation from the Thermo Fisher Scientific website

1. Go to thermofisher.com.

2. Point to Services & Support, and click Manuals on the left.

3. In the Refine Your Search box, search by the product name.

4. From the results list, click the title to open the document in your web browser, save it, or

print it.

To return to the document list, click the browser Back button.

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Thermo Scientific FAIMS Pro System User Guide xv

Providing Documentation Feedback

To suggest changes to the documentation or to the Help

Complete a brief survey about this document by clicking the button below.

Thank you in advance for your help.

Compatible Mass Spectrometers and API Sources

Use the FAIMS Pro system with the appropriate Thermo Scientific MS and ion source for

nanoelectrospray (commonly referred to as nanoES or nanospray™) analysis. Table 1 lists

several compatible MSs. For information about your specific system, refer to the product

manuals.

CAUTION If you connect the FAIMS Pro system to another type of MS, you might

impair the safety protection provided by the equipment.

Table 1. Compatible Thermo Scientific ion sources and mass spectrometers

Ion source models Mass spectrometer models

•EASY-SprayNG™

• Nanospray Flex NG™

• Orbitrap™ Tribrid™ Seriesa

•TSQ™SeriesII

aIn 2019, the name “Orbitrap Fusion™ Series” changed to “Orbitrap Tribrid Series.”

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xvi FAIMS Pro System User Guide Thermo Scientific

Special Notices, Symbols, and Cautions

Make sure you understand the special notices, symbols, and caution labels in this guide. Most

of the special notices and cautions appear in boxes; those pertaining to safety also have

corresponding symbols. Some symbols are also marked on the instrument itself and can

appear in color or in black and white. For complete definitions, see Table 2.

Table 2. Notices, symbols, labels, and their meanings (Sheet 1 of 2)

Notice, symbol, or label Meaning

IMPORTANT Highlights information necessary to prevent damage to

software, loss of data, or invalid test results; or might contain

information that is critical for optimal performance of the

product.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Caution: Read the cautionary information associated with this

task.

Chemical hazard: Observe safe laboratory practices and

procedures when handling chemicals. Only work with volatile

chemicals under a fume or exhaust hood. Wear gloves and other

protective equipment, as appropriate, when handling toxic,

carcinogenic, mutagenic, corrosive, or irritant chemicals. Use

approved containers and proper procedures to dispose of waste

oil and when handling wetted parts of the instrument.

Hot surface: Allow any heated components to cool before

touching them.

Risk of electric shock: This instrument uses voltages that can

cause electric shock and personal injury. Before servicing the

instrument, shut it down and disconnect it from line power.

While operating the instrument, keep covers on.

Risk of eye injury: Eye injury can occur from splattered

chemicals, airborne particles, or sharp objects. Wear safety

glasses when handling chemicals or servicing the instrument.

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Thermo Scientific FAIMS Pro System User Guide xvii

Safety Precautions

Read and understand the following cautions that are specific to the shutdown of the MS

system or to the removal of parts for cleaning.

Sharp object: Avoid handling the tip of the syringe needle.

Trip obstacle: Be aware of cords, hoses, or other objects located

on the floor.

Table 2. Notices, symbols, labels, and their meanings (Sheet 2 of 2)

Notice, symbol, or label Meaning

CAUTION If you must turn off the MS in an emergency, turn off the main power switch

located on the right-side power panel. This switch turns off all power to the MS,

including the forepump, without harming components within the system. However, do

not use this method as part of the standard shutdown procedure. Instead, see Shutting

Down the LC/MS/FAIMS Pro System. To turn off the LC, autosampler, and data system

computer in an emergency, use their respective on/off switch or button.

CAUTION To avoid an electrical shock, be sure to follow the instructions in Shutting

Down the LC/MS/FAIMS Pro System.

CAUTION Do not turn the MS on if you suspect that it has incurred any kind of electrical

damage. Instead, disconnect the power cord and contact Thermo Fisher Scientific

technical support for a product evaluation. Do not attempt to use the MS until it has been

evaluated. (Electrical damage might have occurred if the system shows visible signs of

damage, or has been transported under severe stress.)

CAUTION The FAIMS Pro system must connect to a certified Thermo Scientific MS,

which supplies high voltage capable of delivering a maximum of 8 kV and 100 μA. If you

connect the FAIMS Pro system to another type of MS, you might impair the protection

provided by the equipment.

CAUTION Do not place any objects (for example, containers with liquids) on top of the

MS, unless instructed to in the documentation. Leaking liquids might contact the

electronic components and cause an electrical short circuit.

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xviii FAIMS Pro System User Guide Thermo Scientific

CAUTION Do not perform any servicing other than that contained in this manual. To

avoid personal injury or damage to the FAIMS Pro system, do not perform any servicing

other than that contained in this manual or related manuals unless you are qualified to do

so.

CAUTION Do not disconnect the power cords at the MS or MCB while the other ends are

still plugged into the electrical outlet.

Risk of electric shock: The FAIMS Pro system must be properly earthed through a supply

outlet that has an earthing connection. If you are not sure, check with a qualified electrician.

CAUTION Allow heated components to cool to room temperature (approximately

20 minutes) before servicing them.

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Thermo Scientific FAIMS Pro System User Guide xix

Contacting Us

Contact Email Telephone QR Codea

aYou can use your smartphone to scan a QR Code, which opens your email application or browser.

U.S. Technical Support us.techsupport.analyze@thermofisher.com (U.S.) 1 (800) 532-4752

U.S. Customer Service

and Sales

us.customer-support.analyze@thermofisher.com (U.S.) 1 (800) 532-4752

Global Support To find global contact information or customize your request

1. Go to thermofisher.com.

2. Click Contact Us, select the country, and then select the type of support

you need.

3. At the prompt, type the product name.

4. Use the phone number or complete the online form.

To find product support, knowledge bases, and resources

Go to thermofisher.com/us/en/home/technical-resources.

To find product information

Go to thermofisher.com/us/en/home/brands/thermo-scientific.

Note To provide feedback for this document, go to surveymonkey.com/s/PQM6P62 or send an email message to

Technical Publications (techpubs-lcms@thermofisher.com).

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xx FAIMS Pro System User Guide Thermo Scientific

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