Thermo Scientific ISQ EC User manual

ISQ EC and ISQ EM
Mass Spectrometer
Operating Manual
1R120591-0002 Revision E •February 2019

Copyright © 2018 Thermo Fisher Scientific Inc. All rights reserved.
Original Operating Manual
The hardware descriptions in this manual revision refer to the ISQ EC mass spectrometer. For
the manual release history, see page 227.
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without notice, in future revisions.
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purchaser. This document shall in no way govern or modify any Terms and Conditions of Sale.
The Terms and Conditions of Sale shall govern all conflicting information between the two
documents.

ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 3
Contacting Us
There are several ways to contact us:
Ordering Information
For ordering information or sales support for HPLC products, contact
your local Thermo Fisher Scientific sales organization. For contact
information, go to Contact Us on http://www.thermofisher.com.
Technical Assistance
For technical support for HPLC products, contact your local Thermo
Fisher Scientific support organization. For contact information, go to
Contact Us on http://www.thermofisher.com.
Legal Manufacturer Address
Thermo Finnigan LLC, a part of Thermo Fisher Scientific
355 River Oaks Parkway
San Jose, California 95134
United States

Page 4 ISQ EC and ISQ EM Mass Spectrometer Operating Manual

ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 5
Contents
Contacting Us...................................................................................... 3
1 Using this Manual ............................................................................ 9
1.1 About this Manual ................................................................................................10
1.2 Conventions ..........................................................................................................11
1.2.1 Safety Messages.......................................................................................11
1.2.2 Special Notices and Informational Notes.................................................11
1.2.3 Typographical Conventions......................................................................12
1.3 Reference Documentation....................................................................................14
2 Safety............................................................................................. 16
2.1 Safety Symbols and Signal Words.........................................................................17
2.1.1 Safety Symbols and Signal Words in This Manual (Symboles de sécurité
et mentions d’avertissement utilisés dans ce manuel) ........................................17
2.1.2 Observing this Manual .............................................................................19
2.1.3 Safety Symbols on the Instrument...........................................................19
2.2 Intended Use.........................................................................................................22
2.3 Safety Precautions ................................................................................................23
2.3.1 General Safety Information (Consignes Générales de Sécurité) ..............23
2.3.2 Qualification of the Personnel .................................................................24
2.3.3 Personal Protective Equipment ...............................................................26
2.3.4 Electrical Safety Precautions....................................................................28
2.3.5 General Residual Hazards ........................................................................29
2.4 Solvent and Additive Information.........................................................................37
2.5 Compliance Information .......................................................................................38
3 Instrument Overview ..................................................................... 39
3.1 Mass Spectrometer Operating Principle...............................................................40
3.2 Overview of an LC/MS or IC/MS Analysis .............................................................41
3.3 Software Operation ..............................................................................................43
4 Unpacking ...................................................................................... 44
4.1 Unpacking .............................................................................................................45
4.2 Scope of Delivery ..................................................................................................49

Page 6 ISQ EC and ISQ EM Mass Spectrometer Operating Manual
5 Installation......................................................................................50
5.1 Safety Guidelines for Installation......................................................................... 51
5.2 Installing the Mass Spectrometer ........................................................................ 53
5.3 Site Requirements................................................................................................ 55
5.3.1 Workbench.............................................................................................. 55
5.3.2 Power Considerations ............................................................................. 55
5.3.3 Power Cord.............................................................................................. 57
5.3.4 Condensation .......................................................................................... 62
5.3.5 Operating Conditions .............................................................................. 62
5.3.6 Gas Ventilation........................................................................................ 63
5.3.7 Nitrogen Gas Supply................................................................................ 64
5.4 Unpacking the Instrument ................................................................................... 67
5.5 Setting Up the Hardware ..................................................................................... 68
5.5.1 Installing the Foreline Pump ................................................................... 68
5.5.2 Installing the Oil Mist Filter..................................................................... 82
5.5.3 Adding Oil to the Foreline Pump............................................................. 92
5.5.4 Installing the Solvent Trap ...................................................................... 96
5.5.5 Installing the Source Housing Drain Insert and Sweep cone .................. 98
5.5.6 Switching Between HESI and APCI Modes on the ISQ EM Source
Housing .............................................................................................................. 103
5.5.7 Installing the Internal Calibration Solution ........................................... 104
5.5.8 Connecting the IC or LC to the MS Inlet ................................................ 106
5.5.9 Flushing the Calibration Solution .......................................................... 108
5.5.10 Connecting the System to the PC.......................................................... 110
5.6 Summary of Hardware Installation .................................................................... 113
5.7 Powering Up the System.................................................................................... 115
6 Operation .....................................................................................117
6.1 Introduction to this Chapter .............................................................................. 118
6.2 Safety Guidelines for Operation ........................................................................ 119
6.3 MS Instrument Overview ................................................................................... 121
6.4 Configuring the MS in Chromeleon.................................................................... 123
6.5 User Operation................................................................................................... 136
6.5.1 Chromeleon User Interface................................................................... 136
6.6 Running Your First Sample ................................................................................. 143
6.6.1 Getting Started...................................................................................... 143

ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 7
6.6.2 Method Editor—Source Settings, Easy View .........................................144
6.6.3 Method Editor—Source Settings, Advanced View ................................146
6.6.4 Method Editor—Scan Settings,..............................................................148
6.6.5 Method Editor—Component Mode.......................................................150
6.6.6 Method Editor—Scan Mode ..................................................................152
6.6.7 Method Development............................................................................154
6.6.8 MS Instrument Data Signal Channels.....................................................156
6.6.9 Custom Variables ...................................................................................156
6.6.10 Chromeleon Audit Trail..........................................................................156
6.7 Shutting Down the MS Instrument .....................................................................157
6.7.1 Short-Term Standby ...............................................................................157
6.7.2 Long-Term Shutdown.............................................................................158
6.7.3 Venting the Mass Spectrometer ............................................................162
6.8 Remote Start Cable .............................................................................................164
6.8.1 Vanquish HPLC-Autosampler .................................................................164
6.8.2 UltiMate 3000 ........................................................................................165
6.8.3 AS-AP Autosampler ................................................................................165
6.8.4 Integrion Autosampler (no AS-AP).........................................................165
7 Maintenance and Service ..............................................................167
7.1 Introduction to Maintenance and Service..........................................................168
7.2 Safety Guidelines for Maintenance and Service .................................................169
7.3 General Rules for Maintenance and Service ......................................................172
7.4 Routine and Preventive Maintenance ................................................................173
7.4.1 Maintenance Plan ..................................................................................173
7.4.2 Preventive Maintenance Schedule ........................................................174
7.4.3 Cleaning or Decontaminating the Instrument .......................................174
7.4.4 Replacing the ESI Probe Capillaries for the ISQ EC and ISQ EM.............176
7.4.5 Replacing the APCI Probe Capillaries for the ISQ EM ............................181
7.4.6 Replacing the APCI Needle.....................................................................189
7.4.7 Cleaning the Front Optics ......................................................................190
7.5 Removing the Instrument from the System Stack..............................................200
7.6 Updating the Mass Spectrometer Firmware ......................................................202
8 Troubleshooting............................................................................205
8.1 General Information about Troubleshooting .....................................................206
8.2 Troubleshooting Problems with Autotune .........................................................208

Page 8 ISQ EC and ISQ EM Mass Spectrometer Operating Manual
8.3 Troubleshooting Leaky Source Gases ................................................................ 210
9 Specifications................................................................................211
9.1 Physical Specifications ....................................................................................... 212
10 Accessories, Consumables and Replacement Parts......................213
10.1 General Information .......................................................................................... 214
10.2 Ship Kit ............................................................................................................... 215
10.3 Replacement Parts ............................................................................................. 217
11 Appendix ....................................................................................221
11.1 Compliance Information .................................................................................... 222
11.1.1 Declarations of Conformity ................................................................... 222
11.1.2 WEEE Compliance ................................................................................. 223
11.1.3 FCC Compliance..................................................................................... 224
11.1.4 Regulatory Compliance ......................................................................... 225
11.1.5 Low Voltage Safety Compliance............................................................ 225
11.1.6 Notice on Lifting and Handling of Thermo Scientific Instruments ........ 225
11.1.7 Notice on the Proper Use of Thermo Scientific Instruments................ 225
11.1.8 Notice on the Susceptibility to Electromagnetic Transmissions ........... 225
11.1.9 Manual Release History ........................................................................ 227
12 Index...........................................................................................228

1Using this Manual
ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 9
1Using this Manual
This chapter provides information about this manual, the conventions used
throughout the manual, and the reference documentation that is available in
addition to this manual.

1Using this Manual
Page 10 ISQ EC and ISQ EM Mass Spectrometer Operating Manual
1.1 About this Manual
This manual describes the functional features and operating principle of
your Thermo Scientific™ ISQ™ EC and ISQ™ EM mass spectrometers and
provides instructions for installation, set up, start up, shut down, operation,
maintenance, and troubleshooting.
The layout of this manual is designed to provide quick reference to the
sections of interest to the user. To obtain a full understanding of your
detector, read this manual thoroughly.
This manual also contains safety messages, precautionary statements, and
special notices that can prevent personal injury, damage to the detector, or
loss of data when followed properly.
Note the following:
The detector configuration may vary; therefore, not all descriptions
necessarily apply to your particular detector.
If some detail applies to only one model or variant, the model or variant
is identified by name.
Illustrations in this manual are provided for basic understanding. They
can vary from the actual model of the detector or component. However,
this does not influence the descriptions. No claims can be derived from
the illustrations in this manual.