Thermo Scientific ISQ EC User manual

ISQ EC and ISQ EM
Mass Spectrometer
Preinstallation Requirements Guide
1R120591-0001 Revision B • October 2018

Copyright © 2018 Thermo Fisher Scientific Inc. All rights reserved.
Preinstallation Requirement Guide
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without notice, in future revisions.
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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.
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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 Preinstallation Requirements Guide 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

ISQ EC and ISQ EM Mass Spectrometer Preinstallation Requirements Guide Page 4

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Contents
Contacting Us...................................................................................... 3
1 Using this Manual ............................................................................ 7
1.1 About this Manual ..................................................................................................8
1.2 Conventions ............................................................................................................9
1.2.1 Safety Messages.........................................................................................9
1.2.2 Special Notices and Informational Notes...................................................9
1.2.3 Typographical Conventions......................................................................10
1.3 Reference Documentation....................................................................................12
2 Safety..............................................................................................14
2.1 Safety Symbols and Signal Words.........................................................................15
2.1.1 Safety Symbols and Signal Words in This Manual ...................................15
2.1.2 Observing this Manual .............................................................................16
2.1.3 Safety Symbols on the Detector ..............................................................16
2.2 Intended Use.........................................................................................................18
2.3 Safety Precautions ................................................................................................19
2.3.1 General Safety Information .....................................................................19
2.3.2 Qualification of the Personnel .................................................................19
2.3.3 Personal Protective Equipment ...............................................................20
2.3.4 Electrical Safety Precautions....................................................................21
2.3.5 General Residual Hazards ........................................................................21
2.4 Solvent and Additive Information.........................................................................26
2.5 Compliance Information .......................................................................................27
3 Site Preparation ..............................................................................28
3.1 Entrance Requirements ........................................................................................29
3.2 Workbench and Space Requirements ..................................................................30

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3.3 Lighting Requirements..........................................................................................34
3.4 Power Requirements ............................................................................................35
3.5 Environmental Requirements...............................................................................40
3.6 Gas Requirements.................................................................................................42
3.6.1 Nitrogen Gas Supply.................................................................................42
3.7 Exhaust Requirements..........................................................................................45
1.1.1 Foreline Pump Exhaust ............................................................................45
1.1.2 Ion Source Exhaust...................................................................................45
3.8 Solvents and Sample Preparation.........................................................................47
3.8.1 Standard Installation................................................................................47
3.9 Receiving Requirements .......................................................................................48
3.10 What Happens Next? ............................................................................................49
4 Appendix.........................................................................................50
4.1 Compliance Information .......................................................................................51
4.1.1 Declarations of Conformity......................................................................51
4.1.2 WEEE Compliance ....................................................................................52
4.1.3 FCC Compliance .......................................................................................53
4.1.4 Regulatory Compliance ............................................................................54
4.1.5 Low Voltage Safety Compliance...............................................................54
4.1.6 Notice on Lifting and Handling of Thermo Scientific Instruments...........54
4.1.7 Notice on the Proper Use of Thermo Scientific Instruments...................54
4.1.8 Notice on the Susceptibility to Electromagnetic Transmissions..............54
4.1.9 Manual Release History ...........................................................................56

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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.

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1.1 About this Manual
This guide contains detailed instructions to prepare your site for
installation of a Thermo Scientific™ ISQ™ EC or a Thermo Scientific™
ISQ™ EM mass spectrometer.
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.

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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.

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NOTICE Indicates that failure to take note of the accompanying
information could cause wrong results or may result in damage to the
device.
TIP Highlights information of general interest or helpful information that
can make a task easier or optimize the performance of the detector.
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
•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.

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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

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1.3 Reference Documentation
In addition to this operating manual, other documentation is available
for reference.
Hardware Documentation
Additional hardware documentation includes the following:
•ISQ EC and ISQ EM Mass Spectrometer Operating Manual
Operating manuals for the other modules of the LC or IC system
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.
TIP The Chromeleon Help and documents are included in the software
shipment. The ISQ EC and ISQ EM do not support Chromeleon software
versions before 7.2.6.

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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
optional gas supply, as applicable:
♦User documentation for the nitrogen generator

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2Safety
This chapter provides general and specific safety information and informs
about the intended use of the detector.

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2.1 Safety Symbols and Signal Words
2.1.1 Safety Symbols and Signal Words in This Manual
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.

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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.
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.
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.
|Ο
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.
˜

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Symbol Description
Indications 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.

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2.2 Intended Use
The instrument is intended for use in liquid chromatography (LC) and ion
chromatography (IC) mass spectrometry (MS) applications. The system is
for use by qualified personnel and in laboratory environment only.
The instrument is intended for laboratory research use only. It is not
intended for use in diagnostic procedures.
Laboratory Practice
Thermo Fisher Scientific recommends that the laboratory in which the
MS system is used follow best practices for LC-MS and IC-MS analyses.
This includes among others:
♦Using appropriate standards
♦Regularly running calibration
♦Establishing shelf life limits and following them for all consumables
used with the system
♦Running the system according to the laboratory's verified and
validated 'lab developed test' protocol

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2.3 Safety Precautions
2.3.1 General Safety Information
All users must observe the general safety information presented in this section
and all specific safety messages and precautionary statements
elsewhere in this manual during all phases of installation, operation,
troubleshooting, maintenance, shutdown, and transport of the detector.
If the instrument is used in a manner not specified by Thermo Fisher Scientific,
the protection provided by the detector could be impaired. Observe the
following:
•Operate the instrument only within its technical specifications.
•Use only the replacement parts and additional components, options, and
peripherals specifically authorized and qualified for the detector by Thermo
Fisher Scientific.
•Perform only the procedures that are described in this operating manual
and in supporting documents for the detector.
Follow all instructions step by step and use the tools recommended for the
procedure.
•Open the enclosure of the detector and other components only if
specifically instructed to do so in this manual.
•Thermo Fisher Scientific cannot be held liable for any damage, material or
otherwise, resulting from inappropriate or improper use of the detector. If
there is any question regarding appropriate usage, contact Thermo Fisher
Scientific before proceeding.
Safety Standard
This device is a Safety Class I instrument (provided with terminal for
protective grounding). The device has been manufactured and tested
according to international safety standards.
2.3.2 Qualification of the Personnel
Observe the information below on the proper qualification of the
personnel installing and/or operating the detector.

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Installation
Only skilled personnel are permitted to install the detector and to establish the
electrical connections according to the appropriate regulations. Thermo Fisher
Scientific recommends always having service personnel certified by Thermo
Fisher Scientific perform the installation (for brevity, referred to as Thermo
Fisher Scientific service engineer).
If a person other than a Thermo Fisher Scientific service engineer installs and
sets up the module, the installer is responsible for ensuring the safety of the
module and system.
General Operation
The detector is designed to be operated only by trained and qualified personnel
in a laboratory environment.
All users must know the hazards presented by the detector and the substances
they are using. All users should observe the related Safety Data Sheets (SDSs).
2.3.3 Personal Protective Equipment
Wear personal protective equipment and follow good laboratory
practice to protect you from hazardous substances. The appropriate
equipment depends on the hazard. For advice on the hazards and the
equipment required for the substances you are using, refer to the
material handling and safety data sheet provided by the vendor.
An eyewash facility and a sink should be available nearby. If any substance
contacts your skin or eyes, wash the affected area and seek medical attention.
Protective Clothing
To protect you from chemical splashes, harmful liquids, or other
contamination, when performing any work on or near the LC-MS or IC-
MS system put on appropriate protective clothing, such as a lab coat. For
information about the proper handling of a particular substance and for
advice on specific hazards, refer to the safety data sheet (SDS) for the
substance you are using.