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
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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
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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
C
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.

Preface
Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide xi
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 1.
Table 1. Notices, symbols, labels, and their meanings
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.
Heavy object: The Orbitrap Tribrid Series MS, excluding its
workbench, weighs over 227 kg (500 lb). Never try to detach
and move the instrument from its workbench; you can suffer
personal injury or damage the instrument.
Pinch point: Keep hands away from the specified areas.
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.
Trip obstacle: Be aware of cords, hoses, or other objects located
on the floor.

Preface
xii Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific
Model Differences
This table lists the required number of forepumps and the available options for the
Orbitrap Tribrid Series MSs.
Instrument Number of
forepumps
Available options
EASY-IC
ion source
EASY-ETD
ion source
Advanced
peak
determination
1M Orbitrap
resolution
UVPD
laser module
Orbitrap Fusion Lumos 2    
Orbitrap Fusion 1  
Orbitrap ID-X 1 

Preface
Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide xiii
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 [e-mail] (U.S.) 1 [phone]
U.S. Customer Service
and Sales
[e-mail] (U.S.) 1 [phone]
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 ([e-mail]).

Preface
xiv Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 1
1
Connecting the Forepump for the Vacuum System
To connect the forepump or forepumps to the Orbitrap Tribrid Series MS and the lab exhaust
system, follow these procedures.
Contents
• Connecting the Forepumps to the Mass Spectrometer
• Connecting the Forepumps to the Lab Exhaust System
• Locking the Workbench Wheels
Connecting the Forepumps to the Mass Spectrometer
Before you begin, lift up and remove the workbench’s front panel. To determine which
instrument requires two forepumps, see Model Differences.
CAUTION In addition to reading the forepump’s operating and maintenance instructions,
follow the instructions for adding and changing the oil.
CAUTION Possible pinch points. Be aware where you place your hands when you
remove or attach the workbench’s front panel.

1Connecting the Forepump for the Vacuum System
Connecting the Forepumps to the Mass Spectrometer
2Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific
To attach the vacuum hose assembly
Using a hose clamp, a hose adapter, a centering ring, and a
swing clamp, connect the other end of the vacuum hose to
the plumbing elbow on the forepump.
(Optional) Place each forepump on an oil tray. Then,
move them under the MS.
4
2
Using a centering ring and a swing clamp, attach the
plumbing elbow to the forepump’s inlet port.
3
Two-pump MS System
Using a centering ring and a swing
clamp, connect a 90-degree
plumbing elbow to the MS’s back
vacuum port with the open end
facing toward the side, not the
floor (as shown). Then, using a
center ring and swing clamp from
the vacuum hose assembly,
connect the hose to the elbow.
1
Using the stainless steel clamp, connect the short
tubing on the vacuum hose assembly to the
vacuum port located under the workbench (front,
left corner).
1
Single-pump MS System
IMPORTANT For optimal performance of the forepumps, place them as follows:
• For a two-forepump MS system, place the forepumps under the workbench.
• For a single-forepump MS system, place the forepump under the workbench or
within 2.4 m (8 ft) of the instrument.
• Prevent the forepump from overheating by ensuring that there is sufficient air
clearance around each forepump.

1 Connecting the Forepump for the Vacuum System
Connecting the Forepumps to the Lab Exhaust System
Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 3
Connecting the Forepumps to the Lab Exhaust System
Most atmospheric pressure ionization (API) applications contribute to solvents accumulating
in the forepump. Choose an exhaust system that can accommodate the periodic purging of
these solvents. The frequency of the purging depends on the throughput of the system—never
operate the pump continuously with the gas ballast valve open.
To connect the forepumps to the exhaust system
CAUTION
• Run the exhaust hose at floor level for at least 2 m (79 in.). This hose acts as a trap for
exhaust fumes that would otherwise recondense in the forepump oil.
• Maintain the exhaust pressure from atmospheric pressure minus 15 mbar to
1.15 bar absolute (0.15 bar relative).
• Although Thermo Fisher Scientific recommends that you periodically open the gas
ballast valve for at least 30 minutes (on the side of the pump) to purge the
accumulated solvents, opening the valve might allow a large volume of volatile solvent
waste to enter the fume exhaust system.
• The forepump exhaust is a health hazard. The dedicated exhaust system must be
actively vented and be able to accommodate the periodic purging of the accumulated
solvents in the forepump.
Connect one end of the exhaust tubing to the forepump exhaust
ports. Then, secure the other end to the lab exhaust system.
If you removed the workbench’s front
panel (as shown), reattach it.
1
2
(Orbitrap Fusion Lumos MS)

1Connecting the Forepump for the Vacuum System
Locking the Workbench Wheels
4Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific
Locking the Workbench Wheels
After you position the forepumps and workbench, lock the workbench wheels.
To lock the workbench wheels
1. Lift up the workbench’s front panel to remove it, and set it aside.
2. Lock the front wheels by moving the locking levers forward to the upright position.
The locking levers have three positions. To fully unlock the roll and swivel movements,
push the levers back to the third position (almost horizontal).
3. Reattach the front panel when you are ready.
CAUTION Possible pinch points. Be aware where you place your hands when you
remove or attach the workbench’s front panel.

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 5
2
Connecting the Nitrogen and Helium Gases
Connections and gas delivery systems might vary. You are responsible for supplying any
additional fittings or connections necessary during installation. If your system includes
additional devices that require their own gas connections, refer to those instruments’ manuals.
Contents
• Gas Specifications
• Connecting the Instrument Gas Lines
Gas Specifications
Make sure that the ultra-high-purity (UHP) and high-purity (HP) supply gases are delivered
with the necessary pressure and purity as listed in Table 2.
Table 2. Summary of the required gases for the Orbitrap Tribrid Series MS
Type Recommended purity Required
pressure
Typical daily
consumptiona
aApproximate value when operating 24 hours and 7 days a week
Function
Helium UHP (99.999%)—Has less than
1.0 ppm each of water, oxygen,
and total hydrocarbons.
275 ±70 kPa
(40 ±10 psi)
9.22 L
(0.325 ft3)
Linear ion trap damping gas
and collision gas
Nitrogen UHP (99.999%)—Has less than
3.0 ppm each of water, oxygen,
and total hydrocarbons.
345 ±70 kPa
(50 ±10 psi)
46 L (1.62 ft3) Venting gas, ion routing
multipole (IRM) collision
gas, and make-up gas and
reagent carrier gas for the IC
and ETD configurations
HP (99%) 690 ±140 kPa
(100 ±20 psi)
11 500–26 700 L
(406–943 ft3)
API source auxiliary gas,
sheath gas, and sweep gas

2Connecting the Nitrogen and Helium Gases
Connecting the Instrument Gas Lines
6Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific
Connecting the Instrument Gas Lines
To connect the gas lines to the back of the MS
CAUTION You must use either copper (provided) or stainless steel for the UHP gas lines.
CAUTION After completing these connections, route the tubing so that they are not a trip
hazard.
Swagelok fittings, 1/8 in. ID
(UHP helium gas) Repeat Step 2 with another length
of copper tubing, except connect it between the
Helium In inlet and your UHP helium gas supply.
3
(UHP nitrogen gas) Cut a length of the copper tubing,
attach the 1/8 in. ID Swagelok™-type nut and ferrule
set, and then connect it to the UHP Nitrogen inlet until
fingertight. On the other end, connect an appropriate
fitting that connects to your UHP nitrogen gas supply.
Note Use an open wrench to tighten the fitting on the
gas inlet another 1/8- to 1/4-turn.
(HP nitrogen gas) Cut a length of the
Teflon™ PFA tubing and push it into the
Nitrogen In inlet. On the other end,
connect an appropriate fitting that
connects to your HP nitrogen gas supply.
1
2
(Orbitrap Fusion Lumos MS)