Thermo Orbitrap Fusion Series User manual

Orbitrap Fusion Series
Hardware Manual
80011-97004 Revision B May 2016

© 2016 Thermo Fisher Scientific Inc. All rights reserved.
Automatic Gain Control, EASY-ETD, EASY-IC, EASY-Max NG, Fusion, Lumos, and Orbitrap Fusion Lumos
are trademarks; Unity is a registered service mark; and Accela, Hypersil GOLD AQ, Orbitrap, Orbitrap
Fusion, Pierce, Thermo Scientific, Tribrid, and Xcalibur are registered trademarks of Thermo Fisher Scientific
Inc. in the United States. Fisher Scientific is a registered trademark of Fisher Scientific Co. 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
Corporation. Teflon is a registered trademark of E.I. du Pont de Nemours & Co.
The following are registered trademarks in the United States and possibly other countries: Liquinox is a
registered trademark of Alconox, Inc. MICRO-MESH is a registered trademark of Micro-Surface Finishing
Products, Inc. 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. Tygon is a
registered trademark of the division of Saint-Gobain Performance Plastics Corporation. Upchurch Scientific is
a registered trademark of IDEX Health & Science LLC. Vespel is a registered trademark of E.I. du Pont de
Nemours & Co. Viton is a registered trademark of DuPont Performance Elastomers LLC.
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, July 2015; Rev B, May 2016
Software version: (Thermo) Foundation 3.0 and later, Xcalibur 3.0 and later, Tune 2.0 and later
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 domestic and international regulations. When the system is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described in the next section or sections by product name.
Changes that you make to your system may void compliance with one or more of these EMC and safety 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 EMC and safety standards,
replacement parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific
or one of its authorized representatives.
Regulatory compliance results for the following Thermo Scientific™ products:
•Orbitrap Fusion Lumos MS
•Orbitrap Fusion MS
Orbitrap Fusion Lumos MS
Low Voltage Directive 2006/95/EC
This device complies with Low Voltage Directive 2006/95/EC and the harmonized safety standard IEC/EN/CSA/
UL 61010-1, 3rd Edition.
EMC Directive 2004/108/EC
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: 20103
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 2006/95/EC
This device complies with Low Voltage Directive 2006/95/EC and the harmonized safety standard IEC/EN/CSA/
UL 61010-1, 3rd Edition.
EMC Directive 2004/108/EC
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.

Directive DEEE
2012/19/EU
Thermo Fisher Scientific s'est associé avec une ou plusieurs sociétés de recyclage dans chaque état membre de l’Union
Européenne et ce produit devrait être collecté ou recyclé par celle(s)-ci. Pour davantage d'informations, rendez-vous sur
la page www.thermoscientific.fr/rohs.
WEEE Direktive
2012/19/EU
Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten
getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann. Weitere Informationen
finden Sie unter www.thermoscientific.de/rohs.

Thermo Scientific Orbitrap Fusion Series Hardware Manual vii
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Accessing Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Special Notices, Symbols, and Cautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Orbitrap Fusion Series Mass Spectrometers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Overview of an LC/MS Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
LC/MS Functional Block Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Electronic Assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Controls and Indicators. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
LEDs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Power Entry Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Communications Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Cooling Fans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Chapter 2 Scan Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
MS Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
MS2Scan and MSnScan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
SIM Scan. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Scan Rates for the Ion Trap Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Scan Mass-To-Charge Ratio Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Resolutions for the Orbitrap Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Data Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Ion Polarity Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Chapter 3 Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Vacuum System Functional Block Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Schematic of the Internal Gas Supply Lines. . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Inlet Gases Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Helium Regulator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Nitrogen Gas Valves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Vent Valve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Vacuum Manifold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Contents

Contents
viii Orbitrap Fusion Series Hardware Manual Thermo Scientific
Vacuum Gauges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Vacuum Pumps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Atmospheric Pressure Ionization Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Chapter 4 Ion Transmission and Mass Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Workflow for Mass Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Ion Optics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
MP00 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
MP0 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
MP1 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Curved Linear Trap. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Ion-Routing Multipole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
MP3 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
DC Offset Voltages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Mass Analyzers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Quadrupole Mass Analyzer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Orbitrap Mass Analyzer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Linear Ion Trap Mass Analyzer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Ion Detection Systems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Chapter 5 Syringe Pump and Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Syringe Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Controlling the Divert/Inject Valve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Chapter 6 System Shutdown, Startup, and Reset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Shutting Down the System in an Emergency. . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Placing the Mass Spectrometer in Standby Mode . . . . . . . . . . . . . . . . . . . . . . . 50
Turning On the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Shutting Down the Mass Spectrometer Completely . . . . . . . . . . . . . . . . . . . . . 52
Starting the System after a Complete Shutdown . . . . . . . . . . . . . . . . . . . . . . . . 53
Starting the LC System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Starting the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Starting the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Starting the Autosampler. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Resetting the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Resetting Calibration Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Restarting the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
On/Off Status for MS Components Under Varying Power Conditions. . . . . . . 58

Contents
Thermo Scientific Orbitrap Fusion Series Hardware Manual ix
Chapter 7 Daily Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61
Before Operating the Orbitrap Fusion Series System. . . . . . . . . . . . . . . . . . . . . 62
Checking the System Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Checking the Vacuum Pressure Levels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Checking the Gas Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
After Operating the Orbitrap Fusion Series System . . . . . . . . . . . . . . . . . . . . . . 64
Flushing the Inlet Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Purging the Oil in the Forepump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Emptying the Solvent Waste Container. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Placing the System in Standby Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Chapter 8 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Maintenance Schedule. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Tools and Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Maintaining the API Source Housing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Maintaining the API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Cleaning the Ion Sweep Cone, Spray Cone, and Ion Transfer Tube . . . . . . . 72
Removing the API Source Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Cleaning the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0. . . . . . . . . . . 79
Reinstalling the API Source Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Maintaining the Forepump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Maintaining the Air Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Chapter 9 Replaceable Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
Orbitrap Fusion Series Chemicals Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Calibration Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
MS Setup Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Performance Specification Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Single Mechanical Pump Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Dual Mechanical Pumps Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Miscellaneous Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .97

Contents
xOrbitrap Fusion Series Hardware Manual Thermo Scientific

Thermo Scientific Orbitrap Fusion Series Hardware Manual xi
F
Figure 1. Functional block diagram of the Orbitrap Fusion Series MS . . . . . . . . . . . . . . . . 5
Figure 2. Orbitrap Fusion Series front panel LEDs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Figure 3. Power entry module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Figure 4. Communication connectors (left side of the MS) . . . . . . . . . . . . . . . . . . . . . . . . . 8
Figure 5. Functional block diagram of the vacuum system . . . . . . . . . . . . . . . . . . . . . . . . 16
Figure 6. Schematic of the internal gas supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Figure 7. Gas inlet ports (back of the mass spectrometer) . . . . . . . . . . . . . . . . . . . . . . . . . 18
Figure 8. Placement of the three turbomolecular pumps . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Figure 9. EASY-Max NG API source (H-ESI mode) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Figure 10. API source interface (Orbitrap Fusion MS cross section) . . . . . . . . . . . . . . . . . . 24
Figure 11. Exit lens and RF lens (Orbitrap Fusion and Orbitrap Fusion Lumos
MSs) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Figure 12. Workflow for mass analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Figure 13. Schematic of the Orbitrap Fusion Lumos Tribrid MS ion transmission
path (shown with the ETD source option) . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Figure 14. MP00 RF lens (Orbitrap Fusion and Orbitrap Fusion Lumos MSs) . . . . . . . . . 30
Figure 15. Lens L0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
Figure 16. Multipole MP0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Figure 17. TK lens (both sides) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Figure 18. Multipole MP1 (Orbitrap Fusion and Orbitrap Fusion Lumos MSs) . . . . . . . . 32
Figure 19. C-trap (Orbitrap Fusion and Orbitrap Fusion Lumos MSs) . . . . . . . . . . . . . . . 33
Figure 20. Ion-routing multipole (IRM) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Figure 21. Multipole MP3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Figure 22. Quadrupole Q1 (side and end views, Orbitrap Fusion and Orbitrap Fusion
Lumos MSs) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Figure 23. Dual-split gate lens (both sides) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Figure 24. Polarity of the RF and DC voltages applied to the Q1 rods . . . . . . . . . . . . . . . . 36
Figure 25. Schematic of the Orbitrap cell and an example stable ion trajectory . . . . . . . . . . 37
Figure 26. Electrodynamic squeezing of ions in the Orbitrap analyzer (r) versus the
increased field strength (z) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Figure 27. Approximate shape of ion packets of different m/z after the voltages
stabilize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Figure 28. Linear ion trap (LIT) (Orbitrap Fusion MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Figure 29. Assembly for the linear ion trap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Figure 30. Visual representation of the LIT mass analyzer operation (low pressure
cell, Orbitrap Fusion MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Figure 31. Syringe pump setup (top view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Figures

Figures
xii Orbitrap Fusion Series Hardware Manual Thermo Scientific
Figure 32. Divert/inject valve positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Figure 33. Divert/inject valve plumbed as a loop injector and as a divert valve . . . . . . . . . . 48
Figure 34. Modular divert/inject valve (front view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Figure 35. Thermo Tune window (Orbitrap Fusion MS) . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Figure 36. Direct Control dialog box (Instrument Setup window) . . . . . . . . . . . . . . . . . . . 51
Figure 37. Direct Control dialog box (Instrument Setup window) . . . . . . . . . . . . . . . . . . . 73
Figure 38. Ion sweep cone removed from the MS mount assembly (Orbitrap Fusion
MS). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Figure 39. Ion transfer tube removal tool (Orbitrap Fusion MS) . . . . . . . . . . . . . . . . . . . . 75
Figure 40. Ion transfer removal tool (Orbitrap Fusion Lumos MS) . . . . . . . . . . . . . . . . . . . 75
Figure 41. Spray cone, O-ring, ion transfer tube, and ion sweep cone
(Orbitrap Fusion MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Figure 42. API source interface removed from the vacuum manifold (Orbitrap Fusion
MS). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Figure 43. Lens L0 removed from the back of the API source interface
(Orbitrap Fusion MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Figure 44. MP00 RF lens assembly removed from the API source interface
(Orbitrap Fusion MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Figure 45. RF lens removed from the API source interface cage (Orbitrap Fusion
MS). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Figure 46. Exit lens removed from the API source interface (Orbitrap Fusion MS) . . . . . . 81
Figure 47. Alignment slot and thumbscrew locations on the MP00 RF lens
(Orbitrap Fusion MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

Thermo Scientific Orbitrap Fusion Series Hardware Manual xiii
P
Preface
The Orbitrap Fusion Series Hardware Manual describes the modes of operation and hardware
components for the Thermo Scientific™ Orbitrap Fusion™ Series Tribrid ™ system. It also
provides the instrument’s cleaning and maintenance procedures.
This guide is intended for the following Thermo Scientific mass spectrometers (MSs):
• Orbitrap Fusion (also known as Fusion™) (requires one forepump)
• Orbitrap Fusion Lumos™ (also known as Lumos™) (requires two forepumps)
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.
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.
Contents
•Accessing Documentation
•Special Notices, Symbols, and Cautions
•Contacting Us

Preface
xiv Orbitrap Fusion Series Hardware Manual Thermo Scientific
To view the Help
Do the following as applicable:
• Thermo Tune application: Click the Options icon, , and choose Tun e He l p .
• Thermo Xcalibur™ Method Editor: Choose an option from the Help menu (or press
the F1 key).
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 Hardware Manual xv
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.
Hot surface: Before touching the API source assembly, allow
heated components to cool.
Pinch point: Keep hands away from the specified areas.
Risk of electric shock: This instrument uses voltages that can
cause electric shock and personal injury. Before servicing the
instrument, shut it down and disconnect it from line power.
While operating the instrument, keep covers on.
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.
Sharp object: Avoid handling the tip of the syringe needle.
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
xvi Orbitrap Fusion Series Hardware Manual Thermo Scientific
Read and understand the following cautions that are specific to the shutdown of the mass
spectrometry system or to the removal of parts for cleaning.
CAUTION If you must turn off the mass spectrometer in an emergency, turn off the
main power switch located on the right-side power panel. This switch turns off all
power to the mass spectrometer, including the forepump, without harming components
within the system. However, do not use this method as part of the standard shutdown
procedure. Instead, see “Shutting Down the Mass Spectrometer Completely” on page 52.
To turn off the LC, autosampler, and data system computer in an emergency, use their
respective on/off switch or button.
CAUTION To avoid an electrical shock, be sure to follow the instructions in “Shutting
Down the Mass Spectrometer Completely” on page 52.
CAUTION Do not turn the instrument on if you suspect that it has incurred any kind of
electrical damage. Instead, disconnect the power supply cord and contact Thermo Fisher
Scientific technical support for a product evaluation. Do not attempt to use the
instrument until it has been evaluated. (Electrical damage might have occurred if the
system shows visible signs of damage, or has been transported under severe stress.)
CAUTION Do not disconnect the power supply cord at the mass spectrometer while the
other end is still plugged into the electrical outlet.
CAUTION Do not place any objects (for example, the syringe pump or other containers
with liquids) on top of the instrument, unless instructed to in the documentation.
Leaking liquids might contact the electronic components and cause an electrical short
circuit.
CAUTION Hot surface. Allow heated components to cool to room temperature
(approximately 20 minutes) before servicing them.

Preface
Thermo Scientific Orbitrap Fusion Series Hardware Manual xvii
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need. You
can use your smartphone to scan a QR code, which opens your email application or browser.
Contact us Customer Service and Sales Technical Support
(U.S.) 1 [phone] (U.S.) 1 [phone]
(U.S.) 1 [phone] (U.S.) 1 [phone]
us.customer-support.analyze
@thermofisher.com
us.techsupport.analyze
@thermofisher.com
To find global contact information or customize your request
1. Go to thermofisher.com.
2. Click Contact Us 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:
• Send an email message to Technical Publications ([e-mail]).
• Complete a survey at surveymonkey.com/s/PQM6P62.

Preface
xviii Orbitrap Fusion Series Hardware Manual Thermo Scientific

Thermo Scientific Orbitrap Fusion Series Hardware Manual 1
1
Introduction
The Orbitrap Fusion Series Tribrid mass spectrometer is part of the Thermo Scientific family
of mass spectrometers. The Orbitrap Fusion Series system consists of the mass spectrometer, a
syringe pump, a divert/inject valve, and the Thermo Xcalibur™ data system.
Orbitrap Fusion Series Mass Spectrometers
The Orbitrap Fusion Series includes the Orbitrap Fusion MS and Orbitrap Fusion Lumos
MS. For descriptions of the various hardware components, see Chapter 3, “Vacuum System,”
Chapter 4, “Ion Transmission and Mass Analysis,” and Chapter 5, “Syringe Pump and
Divert/Inject Valve.”
Note The “Glossary” defines some of the terms used in this manual.
Contents
•Overview of an LC/MS Analysis
•LC/MS Functional Block Diagram
•Electronic Assemblies
•Controls and Indicators
•Cooling Fans

1Introduction
Orbitrap Fusion Series Mass Spectrometers
2Orbitrap Fusion Series Hardware Manual Thermo Scientific
Orbitrap Fusion MS
The Orbitrap Fusion is a mass spectrometer that contains three mass analyzers and includes
an external syringe pump, a divert/inject valve, and the Thermo Scientific EASY-Max NG™
API source. The instrument requires one forepump.
Orbitrap Fusion Lumos MS
The Orbitrap Fusion Lumos is a mass spectrometer that contains three mass analyzers and
includes an external syringe pump, a divert/inject valve, and the EASY-Max NG API source.
The instrument requires two forepumps.