Thermo Scientific Orbitrap Fusion User manual

Orbitrap Tribrid Series
Getting Connected Guide
80000-97025 Revision A June 2018

© 2018 Thermo Fisher Scientific Inc. All rights reserved.
Fusion, ID-X, Lumos, and Orbitrap ID-X are trademarks, and Orbitrap Fusion, Orbitrap Fusion Lumos,
Thermo Scientific, Tribrid, and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the
United States.
The following are registered trademarks in the United States and other countries: COMBICON is a registered
trademark of Phoenix Contact GmbH & Co. Microsoft and Windows are registered trademarks of Microsoft
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The following are registered trademarks in the United States and possibly other countries: Nalgene is a
registered trademark of Nalge Nunc International Corporation. Oerlikon Leybold Vacuum is a registered
trademark of OC Oerlikon Corporation AG. Rheodyne is a registered trademark of IDEX Health & Science,
LLC. SOGEVAC is a registered trademark of Oerlikon Leybold Vacuum. Swagelok is a registered trademark of
Swagelok Company. Tygon is a registered trademark of the division of Saint-Gobain Performance Plastics
Corporation.
Chemyx is a trademark of Chemyx Inc. MX Series II is a trademark of IDEX Health & Science, LLC.
All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.
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, June 2018
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.
Regulatory compliance results for the following Thermo Scientific™ mass spectrometers:
•Orbitrap Fusion Lumos
•Orbitrap Fusion and Orbitrap ID-X
Orbitrap Fusion Lumos
Low Voltage Directive 2014/35/EU
This device complies with Low Voltage Directive 2014/35/EU and the harmonized safety standard IEC/EN/CSA/
UL 61010-1, 3rd Edition.
EMC Directive 2014/30/EU and other EMC test standards
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 61000-3-2: 2006 + A1 + A2 EN 61000-4-5: 2006
CISPR 11: 2009 + A1 EN 61000-3-3: 2008 EN 61000-4-6: 2009
ICES-003: 2014 EN 61000-4-2: 2009 EN 61000-4-8: 2010
EN 55011: 2009 + A1 EN 61000-4-3: 2006 + A1 + A2 EN 61000-4-11: 2004
EN 61326-1: 2013 EN 61000-4-4: 2004 + A1

Orbitrap Fusion and Orbitrap ID-X
FCC Compliance Statement
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.
Low Voltage Directive 2014/35/EU
This device complies with Low Voltage Directive 2014/35/EU and the harmonized safety standard IEC/EN/CSA/
UL 61010-1, 3rd Edition.
EMC Directive 2014/30/EU and other EMC test standards
This device was tested by TÜV Rheinland of North America and complies with the following EMC standards:
47 CFR 15, Subpart B, Class A: 2012 EN 61326-1: 2013 EN 61000-4-4: 2004 + A1
CISPR 11: 2009 + A1 EN 61000-3-2: 2006 + A1 + A2 EN 61000-4-5: 2006
AS/NZS CISPR 22: 2009 + A1 EN 61000-3-3: 2008 EN 61000-4-6: 2009
ICES-003: 2012 EN 61000-4-2: 2009 EN 61000-4-8: 2010
EN 55011: 2009 + A1 EN 61000-4-3: 2006 + A1 + A2 EN 61000-4-11: 2004
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.

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 [e-mail] 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 Orbitrap Tribrid Series Getting Connected Guide vii
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Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Accessing Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Viewing the Product Manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Viewing Online User Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Providing Documentation Feedback. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Special Notices, Symbols, and Cautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Model Differences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Chapter 1 Connecting the Forepump for the Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . .1
Connecting the Forepumps to the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . 1
Connecting the Forepumps to the Lab Exhaust System. . . . . . . . . . . . . . . . . . . . 3
Locking the Workbench Wheels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Chapter 2 Connecting the Nitrogen and Helium Gases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Gas Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Connecting the Instrument Gas Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Chapter 3 Connecting the API Source and Waste Container . . . . . . . . . . . . . . . . . . . . . . . . . .9
Installing the API Source. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Setting Up the Fume Exhaust Connections. . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Connecting the Solvent Waste Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Chapter 4 Installing the Syringe Pump and Modular Valve. . . . . . . . . . . . . . . . . . . . . . . . . . .13
Chapter 5 Connecting the Cables and Power Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Chapter 6 External Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Contact Closure Signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Communication Connectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Appendix A Installation Kits and Power Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Syringe Pump and Modular Valve Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Single Mechanical Pump Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Dual Mechanical Pumps Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Contents

Contents
viii Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific
MS Setup Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Power Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide ix
P
Preface
The Orbitrap Tribrid Series Getting Connected Guide is intended for the following Thermo
Scientific™ mass spectrometers (MSs):
• Orbitrap Fusion™ (also known as Fusion™)
• Orbitrap Fusion Lumos™ (also known as Lumos™)
• Orbitrap ID-X™(also known as ID-X™)
This guide describes how to install the MS system in your laboratory and connect any external
liquid chromatography (LC) devices. External devices include those that are controlled from
or are independent of Thermo Scientific mass spectrometry applications, such as the Thermo
Xcalibur™ data system. For a list of hardware differences for this MS series, see Model
Differences.
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
• Special Notices, Symbols, and Cautions
• Model Differences
•ContactingUs
IMPORTANT Thermo Fisher Scientific field service engineers access internal components
by opening the top cover. Ensure that the instrument location allows for a vertical
clearance of at least 92 cm (36 in.) above the instrument. For additional clearance
guidelines, refer to the Preinstallation Requirements Guide.

Preface
xOrbitrap Tribrid Series Getting Connected Guide Thermo Scientific
Accessing Documentation
The Orbitrap Tribrid Series MS includes complete documentation.
•Viewing the Product Manuals
•Viewing Online User Documentation
For system requirements, refer to the release notes on the software DVD.
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.
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.
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.