Thermo Scientific Orbitrap Fusion Lumos MS User manual

Orbitrap Fusion Series
Getting Connected Guide
80011-97002 Revision C June 2017

© 2017 Thermo Fisher Scientific Inc. All rights reserved.
EASY-Max NG, Fusion, Ion Max NG, and Lumos are trademarks, and Orbitrap Fusion, Orbitrap Fusion
Lumos, Thermo Scientific, Tribrid, and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in
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The following are registered trademarks in the United States and possibly other countries: Nalgene is a
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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
the Crawford Fitting Company. Tygon is a registered trademark of the division of Saint-Gobain Performance
Plastics Corporation.
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The contents of this document are subject to change without notice. All technical information in this
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This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
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Release history: Rev A, July 2015; Rev B, May 2016; Rev C, June 2017
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.
Changes that you make to your system might void compliance with one or more of these regulatory standards. Changes
to your system include replacing a part or adding components, options, or peripherals not specifically authorized and
qualified by Thermo Fisher Scientific. To ensure continued compliance with the regulatory standards, order
replacement parts and additional components, options, and peripherals directly from Thermo Fisher Scientific or an
authorized representative.
Regulatory compliance results for the following Thermo Scientific™ products:
•Orbitrap Fusion Lumos MS
•Orbitrap Fusion MS
Orbitrap Fusion Lumos MS
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 MS
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 Fusion Series Getting Connected Guide vii
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Accessing Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Special Notices, Symbols, and Cautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Chapter 1 Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Connecting the Forepumps to the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . 1
Connecting the Forepumps to the Lab Exhaust System. . . . . . . . . . . . . . . . . . . . 3
Chapter 2 Gas Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Chapter 3 API Source and Waste Container Connections. . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Installing the API Source. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Connecting the Solvent Waste Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Chapter 4 Syringe Pump and Modular Valve Assembly. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Chapter 5 Electrical Connections. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
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
MS Setup Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Power Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Contents

Contents
viii Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide ix
P
Preface
The Orbitrap Fusion Series Getting Connected Guide is intended for the following Thermo
Scientific™ mass spectrometers (MSs):
• Orbitrap Fusion™ (also known as Fusion™) (requiring one forepump)
• Orbitrap Fusion Lumos™ (also known as Lumos™) (requiring two forepumps)
Use the information in this guide 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.
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
• Special Notices, Symbols, and Cautions
•ContactingUs
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.
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 Orbitrap Fusion Series Preinstallation Requirements Guide.

Preface
xOrbitrap Fusion Series Getting Connected Guide Thermo Scientific
Accessing Documentation
The Orbitrap Fusion Series MS includes complete documentation. For system requirements,
refer to the release notes on the software DVD.
To view the product manuals
From the Microsoft™ Windows™ taskbar, choose Start > All Programs > Thermo
Instruments > model x.x, and then open the applicable PDF file.
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.
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 (Sheet 1 of 2)
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.

Preface
Thermo Scientific Orbitrap Fusion Series Getting Connected Guide xi
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 Fusion 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.
Table 1. Notices, symbols, labels, and their meanings (Sheet 2 of 2)
Notice, symbol, or label Meaning

Preface
xii Orbitrap Fusion Series Getting Connected Guide Thermo Scientific
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]).

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide 1
1
Vacuum System
To connect the forepump or forepumps to the Orbitrap Fusion 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
Connecting the Forepumps to the Mass Spectrometer
Before you begin, lift up and remove the workbench’s front panel.
CAUTION In addition to reading the forepump’s operating and maintenance instructions,
do the following:
• Prevent the forepump from overheating by ensuring that there is sufficient air
clearance around the pump.
• Maintain the exhaust pressure from atmospheric pressure minus 15 mbar to
1.15 bar absolute (0.15 bar relative).
• 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.
IMPORTANT For optimal performance of the forepumps, place them as follows:
• For the Orbitrap Fusion Lumos MS, place the forepumps under the workbench.
• For the Orbitrap Fusion MS, place the forepump under the workbench or within
2.4 m (8 ft) of the instrument.

1Vacuum System
Connecting the Forepumps to the Mass Spectrometer
2Orbitrap Fusion 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
Orbitrap Fusion Lumos MS
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
Orbitrap Fusion MS

1 Vacuum System
Connecting the Forepumps to the Lab Exhaust System
Thermo Scientific Orbitrap Fusion 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.
• 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)

1Vacuum System
Connecting the Forepumps to the Lab Exhaust System
4Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide 5
2
Gas Connections
To connect the gas lines to the back of the Orbitrap Fusion Series MS, follow the next
procedure. 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 Fusion 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
Note 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.
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.

2Gas Connections
6Orbitrap Fusion Series Getting Connected Guide Thermo Scientific
To connect the gas lines to the back of the MS
IMPORTANT
• After you start using the MS, do not shut off the gases. Optimum performance requires a continuous gas
flow.
• Do not shut off the UHP nitrogen gas unless you have vented the MS.
• If you intend to use helium for sparging your LC solvents, you must have a second tank and regulator.
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)

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide 7
3
API Source and Waste Container Connections
To install the Thermo Scientific EASY-Max NG™ API source and the solvent waste container
to the Orbitrap Fusion Series MS, follow these procedures.
Contents
• Installing the API Source
• Connecting the Solvent Waste Container
Installing the API Source
All the wiring and gas plumbing for the API source are internal. This means you can install or
remove the API source or change the ionization mode1(H-ESI, APCI, or APPI) by changing
the spray insert—all without the use of tools. For information about the spray inserts,
optional interface kits, and switching ionization modes, refer to the Ion Max NG and
EASY-Max NG Ion Sources User Guide.
1APCI and APPI modes require that you purchase and install the applicable kits.

3API Source and Waste Container Connections
Connecting the Solvent Waste Container
8Orbitrap Fusion Series Getting Connected Guide Thermo Scientific
To install the API source onto the MS
Connecting the Solvent Waste Container
The MS internally routes the solvent waste from the bottom of the API source to the back
drain/waste port. Use the provided Tygon™ tubing to connect the solvent waste container to a
fume exhaust system. To prevent solvent waste from backing up into the instrument, make
sure that all Tygon tubing is above the level of liquid in the waste container as follows:
• From the MS to the solvent waste container
• From the waste container to the exhaust system
Equip your lab with at least two fume exhaust systems:
• The analyzer optics become contaminated if the drain/waste tubing and the exhaust
tubing from the forepump connect to the same fume exhaust system. Route the exhaust
tubing from the forepump to a dedicated fume exhaust system.
• Do not vent the Tygon drain tube (or any vent tubing connected to the waste container)
to the same fume exhaust system that connects to the forepump. Vent the waste container
to a dedicated fume exhaust system. The exhaust system for the API source must
accommodate a flow rate of up to 30 L/min (64 ft3/h).
Install the ion sweep
cone on the MS.
Align the source mounting holes with the MS pins and carefully
attach the source. Then, lock the source levers.
Unlock the source
locking levers.
3
21