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.
Trademarks
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All other trademarks are property of Thermo Fisher Scientific and its subsidiaries.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to
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of Thermo Fisher Scientific Inc.
This manual is provided "as is." The contents of this manual are subject to being changed,
without notice, in future revisions.
Thermo Fisher Scientific Inc. makes no representations that this document is complete,
accurate, or error-free. Thermo Fisher Scientific Inc. assumes no responsibility and will not be
liable for any errors, omissions, damage, or loss that might result from any use of this document,
even if the information in the document is followed properly.
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.
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.

1Using this Manual
ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 11
1.2 Conventions
This section describes the conventions that are used throughout this
manual.
1.2.1 Safety Messages
The safety messages and precautionary statements in this manual appear as
follows:
Safety messages or precautionary statements that apply to the entire
manual and all procedures in this manual are grouped in the Safety
chapter.
Safety messages or precautionary statements that apply to an entire
section or to multiple procedures in a section appear at the beginning of
the section to which they apply.
Safety messages that apply to only a particular section or procedure
appear in the section or procedure to which they apply. They appear
different from the main flow of text.
Safety messages are often preceded by an alert symbol and/or alert word.
The alert word appears in uppercase letters and in bold type.
Make sure that you understand and follow all safety messages presented in
this manual.
1.2.2 Special Notices and Informational Notes
Special notices and informational notes in this manual appear different from
the main flow of text. They appear in boxes and a note label identifies them.
The label text appears in uppercase letters and in bold type.
WARNING Indicates that failure to take note of the accompanying
information may result in personal injury.

1Using this Manual
Page 12 ISQ EC and ISQ EM Mass Spectrometer Operating Manual
AVERTISSEMENT Indique que ne pas tenir compte de l’information jointe
peut entraîner des blessures corporelles.
NOTICE Indicates that failure to take note of the accompanying information
could cause wrong results or may result in damage to the device.
ATTENTION Indique que ne pas tenir compte de l’information jointe peut
conduire aux résultats faux ou endommager l’appareil.
TIP Highlights information of general interest or helpful information that can
make a task easier or optimize the performance of the detector.
TIP Veuillez noter Signale des informations d’intérêt général ou utiles qui
peuvent simplifier l’exécution d’une tâche ou optimiser le fonctionnement du
détecteur.
1.2.3 Typographical Conventions
These typographical conventions apply to the descriptions in this manual:
Data Input and Output
The following appears in bold type:
Input that you enter by the keyboard or that you select with the
mouse
Buttons that you click on the screen
Commands that you enter by the keyboard
Names of, for example, dialog boxes, properties, and parameters

1Using this Manual
ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 13
For brevity, long expressions and paths appear in the condensed form,
for example: Click Start > All Programs > Thermo Chromeleon 7 >
Services Manager > Start Instrument Controller.
References and Messages
References to additional documentation appear italicized.
Messages that appear on the screen are identified by quotation marks.
Viewpoint
If not otherwise stated, the expressions left and right in this manual always
refer to the viewpoint of a person that is facing the detector from the front.
Particularly Important Words
Particularly important words in the main flow of text appear italicized.
Electronic Manual Version (PDF)
The electronic version (PDF) of the manual contains numerous links that you
can click to go to other locations within the manual. These include:
Table of contents entries
Index entries
Cross-references (in blue text), for example, to sections and figures

1Using this Manual
Page 14 ISQ EC and ISQ EM Mass Spectrometer Operating Manual
1.3 Reference Documentation
In addition to this operating manual, other documentation is available for
reference.
Hardware Documentation
Additional hardware documentation includes the following:
Operating manuals for the other modules of the LC or IC system
Instrument Installation Qualification Operating Instructions
TIP Electronic versions of these manuals are available as PDF (Portable
Document Format) files. To open and read the PDF files, Adobe™ Reader™
or Adobe™ Acrobat™ is required.
Software Documentation
Additional software documentation includes the following:
Chromeleon™7 Help and documents
The Chromeleon 7 Help provides extensive information and
comprehensive reference material for all aspects of the software. For
basic information about device installation and configuration, refer to
the Installation Guide; for specific information about a certain device,
refer to the Instrument Configuration Manager Help. In Chromeleon 7,
devices are called modules.
For information about the main elements of the user interface and step-
by-step guidance through the most important workflows, refer to the
Quick Start Guide.
For a concise overview of the most important workflows, refer to the
Reference Card.
Chromeleon™6.8 Help
The Chromeleon 6.8 Help provides extensive information for all aspects
of the software, including device installation and configuration.

1Using this Manual
ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 15
TIP The Chromeleon Help and documents are included in the software
shipment.
Third-Party Documentation
Refer also to the user documentation provided by the manufacturers of
third-party components and materials, for example, Safety Data Sheets
(SDSs).
Third-party documentation includes the user documentation for the gas
supply, as applicable:
User documentation for the nitrogen generator

2Safety
Page 16 ISQ EC and ISQ EM Mass Spectrometer Operating Manual
2Safety
This chapter provides general and specific safety information and informs
about the intended use of the detector.

2Safety
ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 17
2.1 Safety Symbols and Signal Words
2.1.1 Safety Symbols and Signal Words in This Manual (Symboles de sécurité et
mentions d’avertissement utilisés dans ce manuel)
This manual contains safety messages to prevent injury of the persons using the
detector. The safety symbols and signal words in this manual include the following:
Always be aware of the safety information. Do not proceed until you
have fully understood the information and consider the consequences of
what you are doing.
CAUTION Indicates a hazardous situation that, if not avoided, could
result in minor or moderate injury.
WARNING Indicates a hazardous situation that, if not avoided, could
result in serious injury.
Ce manuel contient des messages de sécurité visant à prévenir les blessures
chez les utilisateurs du détecteur. Les symboles de sécurité et les mentions
d’avertissement utilisés dans ce manuel sont les suivants :
Soyez toujours au fait des informations de sécurité. N’entreprenez rien
avant d’avoir bien compris toutes les informations et considéré les
conséquences de vos actes.
ATTENTION Indique une situation dangereuse qui, si elle n’est pas évitée,
peut aboutir à des blessures mineures à modérées.

2Safety
Page 18 ISQ EC and ISQ EM Mass Spectrometer Operating Manual
AVERTISSEMENT Indique une situation dangereuse qui, si elle n’est pas
évitée, peut entraîner de graves blessures.

2Safety
ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 19
2.1.2 Observing this Manual
Observe the following:
Before installing or operating the instrument, read this manual carefully
to be familiar with the instrument and this manual. The manual contains
important information with regard to user safety as well as use and care
of the instrument.
Always keep the manual near the instrument for quick reference.
Save this manual and pass it on to any subsequent user.
Read, understand, and comply with all safety messages and
precautionary statements presented in this manual.
Il est important de lire, de comprendre et de respecter tous les messages
et consignes de sécurité présentés dans ce manuel.
2.1.3 Safety Symbols on the Instrument
The table lists the safety symbols that appear on the instrument or on labels
affixed to the instrument. Follow the safety notices in this manual to
prevent the risk of operator injury or damage to the instrument.

2Safety
Page 20 ISQ EC and ISQ EM Mass Spectrometer Operating Manual
Symbol
Description
Indicates a potential hazard. Refer to this manual to avoid the risk of
personal injury and/or to prevent damage to the device.
|

Power supply is on
Power supply is off
Indicates alternating current.
Indicates a terminal for protective grounding.
Indicates that an electrical shock could or might occur
Alerts you to the presence of a hot surface that could or might cause
burn injuries.
Indicates that eye damage could or might occur.
Alerts you to carefully read your instrument’s documentation to
ensure your safety and the instrument’s operation ability. Failing to
carefully read the documentation could or might put you at risk for a
physical injury.
Indicates that physical injury could or might occur if two or more
people do not lift an object.
˜