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
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
FCC Compliance Statement
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.
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.
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 weee.recycle@thermofisher.com 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.
C
Contents
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
2
MS
Scan and MSn Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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
Thermo Scientific Orbitrap Fusion Series Hardware Manual vii
Contents
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
viii Orbitrap Fusion Series Hardware Manual Thermo Scientific
Contents
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
Thermo Scientific Orbitrap Fusion Series Hardware Manual ix
Contents
x Orbitrap Fusion Series Hardware Manual Thermo Scientific
F
Figures
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
Thermo Scientific Orbitrap Fusion Series Hardware Manual xi
Figures
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
xii Orbitrap Fusion Series Hardware Manual Thermo Scientific
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)
Contents
• Accessing Documentation
• Special Notices, Symbols, and Cautions
• Contacting Us
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.
Thermo Scientific Orbitrap Fusion Series Hardware Manual xiii
Preface
To view the Help
Do the following as applicable:
• Thermo Tune application: Click the Options icon, , and choose Tune H e 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 Ta bl e 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.
xiv Orbitrap Fusion Series Hardware Manual Thermo Scientific
Table 1 . Notices, symbols, labels, and their meanings (Sheet 2 of 2)
Notice, symbol, or label Meaning
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.
Preface
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.
Thermo Scientific Orbitrap Fusion Series Hardware Manual xv
Preface
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.
xvi Orbitrap Fusion Series Hardware Manual Thermo Scientific
Contacting Us
Preface
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 (800) 532-4752 (U.S.) 1 (800) 532-4752
(U.S.) 1 (561) 688-8731 (U.S.) 1 (561) 688-8736
us.customer-support.analyze
@thermofisher.com
To find global contact information or customize your request
us.techsupport.analyze
@thermofisher.com
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 (techpubs-lcms@thermofisher.com).
• Complete a survey at surveymonkey.com/s/PQM6P62.
Thermo Scientific Orbitrap Fusion Series Hardware Manual xvii
Preface
xviii Orbitrap Fusion Series Hardware Manual Thermo Scientific
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.
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
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.”
Thermo Scientific Orbitrap Fusion Series Hardware Manual 1
1
Introduction
Orbitrap Fusion Series Mass Spectrometers
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.
2 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Overview of an LC/MS Analysis
In a typical LC/MS analysis, the liquid chromatograph (LC) portion of the system separates a
mixture into its chemical components. The LC pump produces a solvent stream (the mobile
phase) that passes through an LC column (containing the stationary phase) under high
pressure. An autosampler introduces a measured quantity of sample into this solvent stream.
As the solvent stream passes through the LC column, the sample separates into its chemical
components. The rate at which the components of the sample elute from the column depends
on their relative affinities to the mobile phase and the solid particles that make up the column
packing.
As the separated chemical components exit the LC column, they pass through a sample
transfer line and enter the mass spectrometer for ionization and analysis. As the mass
spectrometer analyzes the ionized components and determines each mass-to-charge ratio
(m/z) and relative intensity, it sends a data stream to the data system computer. In addition to
supplying information about the mass-to-charge ratios of ionized compounds, the mass
spectrometer can also supply structural and quantitative information by performing MS
experiments.
1
Introduction
Overview of an LC/MS Analysis
n
When the system setup includes a syringe pump and divert/inject valve, there are four
additional ways to introduce a sample into the mass spectrometer, as described in Ta bl e 2.
Table 2 . Methods of sample introduction into the mass spectrometer
Method Description
Direct infusion Connect the syringe pump directly to the atmospheric
pressure ionization (API) source of the mass spectrometer.
High-flow infusion Use a union Tee to combine the flow from the syringe pump
with the flow from an LC pump.
Automated loop injection Connect a sample loop, an LC pump, and the syringe pump
to the divert/inject valve. After you connect the plumbing,
specify the flow rate at which the syringe pump fills the
sample loop. After the loop is filled, the data system triggers
an injection.
Manual loop injection Connect a sample loop, a needle port fitting, and an LC
pump to the divert/inject valve. After you fill the sample loop
with sample, switch the position of the divert/inject valve,
which places the contents of the sample loop in the path of
the solvent flow produced by the LC pump.
The Orbitrap Fusion Series MS consists of an API source, ion optics, three mass analyzers,
and an ion detection system. The ion optics, mass analyzers, ion detection system, and part of
the API source are enclosed in a vacuum manifold.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 3
1
Introduction
LC/MS Functional Block Diagram
Ionization of the sample takes place in the API source. The specific method used to ionize the
sample is referred to as the ionization technique. The ion optics transmit the ions produced in
the API source into the user-specified mass analyzer, where the mass-to-charge ratios (of the
ions produced in the API source) are determined. The polarity of the electric potentials
applied to the API source and ion optics determines whether positively charged ions or
negatively charged ions are transmitted to the designated mass analyzer. You can set up data
acquisition methods for the mass spectrometer to analyze positively or negatively charged ions
or to switch between these polarity modes during a single run.
Certain lenses in the API source and ion optics act as gates to start and stop the transmission
of ions from the API source to a mass analyzer. An Automatic Gain Control™ (AGC) process
controls the function of these lenses and sets them to transmit the optimum number of ions to
the mass analyzer.
The data system serves as the user interface to the mass spectrometer, autosampler, LC pump,
and syringe pump. Refer to the Xcalibur Help for more information about the Orbitrap
Fusion Series data processing and instrument control application.
Each sequence of loading a mass analyzer with ions followed by mass analysis of the ions is
called a scan. The mass spectrometer uses several different scan mode and scan type
combinations to load, fragment, and detect ions. The ability to vary not only the ionization
and ion polarity modes, but the scan mode and scan type, provides greater flexibility in the
instrumentation for solving complex analytical problems.
For information about the H-ESI, APCI, and APPI techniques, refer to the Ion Max NG and
EASY-Max NG Ion Sources User Guide. For information about the nanoelectrospray ionization
(nanoESI or NSI) technique, refer to the manual that came with your NSI source.
LC/MS Functional Block Diagram
Figure 1 shows a functional block diagram of the Orbitrap Fusion Series system with
hyperlinks to the applicable sections. A sample transfer line connects the LC to the mass
spectrometer. The LC instrument or modules are usually installed on the left side of the mass
spectrometer. A dedicated holder that sits on top of the mass spectrometer contains the
syringe pump and divert/inject valve.
In a typical analysis by LC/MS, a sample is injected onto an LC column. The sample then
separates into its various components. The components elute from the LC column and pass
into the mass spectrometer for analysis.
4 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Figure 1. Functional block diagram of the Orbitrap Fusion Series MS
Ion
optics
Mass
analyzers
Ion
detection
system
Instrument
control
electronic
assemblies
Vacuum
system
Printer
Computer
Monitor
Mass spectrometer Data systemInlet
Autosampler
(optional)
LC pump
(optional)
Syringe pump
Divert/inject
valve
API
source
1
Introduction
Electronic Assemblies
Electronic Assemblies
Controls and Indicators
The electronic assemblies that control the operation of the mass spectrometer are distributed
among various printed circuit boards (PCBs) and other modules, in the embedded computer,
and on or around the vacuum manifold of the mass spectrometer. You cannot service the
electronic assemblies.
Note If you need assistance, contact your local Thermo Fisher Scientific field service
engineer.
This section describes the following controls and indicators for the Orbitrap Fusion Series
MS:
• LEDs
• Power Entry Module
• Communications Panel
Thermo Scientific Orbitrap Fusion Series Hardware Manual 5
1
Introduction
Controls and Indicators
LEDs
Figure 2 shows the LEDs on the front panel with their descriptions listed in Ta b le 3 .
Figure 2. Orbitrap Fusion Series front panel LEDs
Table 3 . LEDs for the Orbitrap Fusion Series MS
LED State Description
Power Green The mass spectrometer is receiving power.
(The electronics service switch is in the Operating
Mode position.)
Off The mass spectrometer is not receiving power.
(The electronics service switch is in the Service
Mode position.)
Vacuum Green The vacuum is within the allowable operating
range.
Yellow The system bakeout is in progress or the vacuum
is outside the allowable operating range.
Off The mass spectrometer is either off or in the
process of starting up.
Communication Green The mass spectrometer and data system are
communicating.
Yellow The mass spectrometer and data system are trying
to establish a communication link.
Off The mass spectrometer is off.
System Green The mass spectrometer is on.
Yellow The mass spectrometer is in standby mode.
Off The mass spectrometer is off.
Scan Flashing blue The mass spectrometer is on and scanning.
Off The mass spectrometer is not scanning.
6 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Power Entry Module
Power In receptacle
(230 Vac)
Main Power switch
Electronics service switch
SV65 Pump Enable connector
(forepump on/off control)
AC Output receptacle
(reserved for future use)
The mass spectrometer receives line power at 230 Vac ±10%, 15 A, 50/60 Hz through the
right-side power entry module (Figure 3).
Figure 3. Power entry module
1
Introduction
Controls and Indicators
Main Power Switch
In the Off position, the Main Power (circuit breaker) switch removes all power to the mass
spectrometer, including the external forepump or forepumps. In the On position, the mass
spectrometer receives power. In the standard operational mode, the switch stays in the On
position.
CAUTION To shut off all power to the mass spectrometer in an emergency, place the main
power circuit breaker switch (labeled Main Power) in the Off (down) position. Do not use
the electronics service switch.
Electronics Service Switch
The electronics service switch is a circuit breaker. In the Service Mode (down) position, the
switch removes power to all components of the mass spectrometer except for the fans and
vacuum system. This setting allows you to service nonvacuum system components with the
vacuum system still operating. In the Operating Mode (up) position, all components of the
mass spectrometer have power.
SV65 Pump Enable Connector
The mass spectrometer turns the forepump or forepumps on and off by using the relay control
cable that connects to the SV65 Pump Enable connector.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 7
1
Peripheral Control connector
Analog Input connector
USB ports
Ethernet port
Reset button
Introduction
Controls and Indicators
Communications Panel
The communications panel, which is located on the left side of the mass spectrometer,
provides a system Reset button, a contact closure interface (Peripheral Control), an analog
input connector, USB ports for the external syringe pump and divert/inject valve, and a
Gigabit Ethernet connection port for the data system computer.
When you briefly press the reset button, the embedded processing system and digital circuitry
reset and the system software reloads from the data system. For information about resetting
the mass spectrometer, see “Resetting the Mass Spectrometer” on page 55.
Figure 4 shows the communication connectors, and Ta b le 4 lists the pin-out descriptions for
these connectors.
Figure 4. Communication connectors (left side of the MS)
8 Orbitrap Fusion Series Hardware Manual Thermo Scientific
1
Introduction
Controls and Indicators
Table 4 . Pin-out descriptions for the communication connectors (Sheet 1 of 2)
Pin Name Description
– Reset Resets the instrument to a power-up state.
Note Use this button only if the instrument does not
respond to the control program on the data system
computer or if you need to restart the instrument
without turning off the electronics service switch.
Peripheral Control
1Ground Earth ground
2 5V Provides a 5 Vdc, 500 mA output (with pin 1).
4 Start In Receives the start signal from the contact closure
connection of a connected external device.
To activate this signal, the external device must pull the
signal either low (below 0.75 Vdc) or high (above
2.4 Vdc), depending on the polarity, for at least
100 ms by using a relay, an open-collector driver, or a
similar device that connects between pins 4 and 1.
Note In the Instrument Configuration window, set
the contact closure signal to “High-to-low edge” or
“Low-to-high edge,” whichever matches the setting
for the connected external device.
5 Ready Out Provides a relay-driven programmable output signal to
the connected external device. The relay opens when a
method starts and closes when the method finishes.
Output: Maximum 24 Vdc, 3 A
6 Injection Hold Provides a relay-driven programmable output signal to
the connected external device, such as a fraction
collector.
Output: Maximum 24 Vdc, 3 A
8 RO/IH Common (return) connection for the Ready Out and
Injection Hold pins
Thermo Scientific Orbitrap Fusion Series Hardware Manual 9
1
Introduction
Cooling Fans
Table 4 . Pin-out descriptions for the communication connectors (Sheet 2 of 2)
Pin Name Description
Analog Input
The two analog channels connect to two separate 12-bit analog-to-digital converters (ADC)
for on-demand conversion of the input voltage. The conversion rate depends on the mass
spectrometer rate.
1 Chassis Earth ground (for pins 3 and 4)
Cooling Fans
3, 4 2V Max:
+ (positive, pin 3) and
(Channel 2) Provides a connection for an external
device, such as an LC instrument.
– (negative, pin 4)
Input: 0–2 Vdc (voltage clamps at 5 Vdc)
5 Chassis Earth ground (for pins 7 and 8)
7, 8 10V Max:
+ (positive, pin 7) and
(Channel 1) Provides a connection for an external
device, such as an LC instrument.
– (negative, pin 8)
Input: 0–10 Vdc (voltage clamps at 15 Vdc)
Other connectors
– USB (2 ports) Provides a connection for the syringe pump and
divert/inject valve.
– Ethernet 1000 Base T Provides a connection for the Ethernet switch.
Over 20 fans, including those in the power supply subassemblies, provide internal cooling for
the Orbitrap Fusion Series MS. Cooling air enters through the three main air intake fans on
the right side of the mass spectrometer. Exhaust air exits the instrument from the left side
ventilation slots.
The only user-serviceable part is the right-side air filter in front of the air intake fans. For the
recommended maintenance schedule, see Chapter 8, “Maintenance.”
CAUTION To ensure safety and proper cooling, always operate the mass spectrometer with
its covers in place. This is also necessary to comply with product safety and
electromagnetic interference regulations.
10 Orbitrap Fusion Series Hardware Manual Thermo Scientific
2
Scan Parameters
This chapter describes some of the scan parameter settings that you set in the Orbitrap Fusion
Series Tune application.
Contents
• Scan Types
• Scan Rates for the Ion Trap Detector
• Scan Mass-To-Charge Ratio Ranges
• Resolutions for the Orbitrap Detector
• Data Types
• Ion Polarity Modes
Scan Types
The following scan types are available:
• MS Scan
2
• MS
• SIM Scan
Scan and MSn Scan
MS Scan
The full-scan MS (or MS1) scan type corresponds to a single stage of mass analysis—that is, a
scan power of n =1.
With the single-stage full scan, the ions formed in the API source are stored in the ion-routing
multipole (IRM). The mass spectrometer then transfers these ions to either the Orbitrap™ or
linear ion trap (LIT) to produce a full mass spectrum of the observable ions in the specified
mass range at a specific time point in the analysis.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 11
2
Scan Parameters
Scan Rates for the Ion Trap Detector
Single-stage full-scan analysis is a useful tool for qualitative and quantitative analysis. Use
single-stage full-scan experiments to determine the molecular weight and intensity of
compounds present in the mass spectrum.
MS2 Scan and MSn Scan
An MS2 Scan selects the MS/MS mass analysis. An MSn Scan typically involves 2 to 10 stages
of mass analysis (scan power of n =2 to n = 10). Each stage of mass analysis where n >1
includes an ion selection step. As you raise the scan power, you can obtain more structural
information that can be useful in structure elucidation of compounds of interest. The
Orbitrap Fusion Series MS has several advanced features that make its MS
extremely powerful.
In an MS/MS scan, precursor ions fragment into product ions. The MS/MS scan type
experiment can use a full-scan or a defined scan range.
• First stage of mass analysis—You can set either the Quadrupole or the Ion Trap to select
the ions for MS/MS analysis. The mass spectrometer then transfers the selected ions to
the IRM for HCD or to the linear ion trap (LIT) for CID or ETD.
n
capabilities
• Second stage of mass analysis—The mass spectrometer transfers the product ions to either
the Orbitrap or the LIT for detection.
In the n
th
stage of mass analysis, subsequent stages of product ion selection occur in the LIT.
SIM Scan
The selected ion monitoring (SIM) scan type is a single-stage (scan power of n =1) technique
that monitors a particular ion or set of ions. In a SIM scan, the mass spectrometer selects ions
in the defined mass-to-charge ratio range, and ejects all other ions by using either the
quadrupole or the LIT analyzer. The Orbitrap or the LIT then detects the selected ions to
produce a SIM mass spectrum.
Scan Rates for the Ion Trap Detector
With the Orbitrap Fusion Series MS, you can use five scan rates: Turbo, Rapid, Normal,
Enhanced, and Zoom. For information about these scan rates, refer to the Tune Help.
Ta bl e 5 lists the scan rates and their peak widths (resolutions) for the Orbitrap Fusion Series
MS. For additional information about the scan rates, refer to the data system Help.
12 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Table 5 . Ion trap scan rates and peak widths
Scan rate Parameter Value
2
Scan Parameters
Scan Mass-To-Charge Ratio Ranges
Tu r b oa
Scan rate (Da/sec): 125 000
Peak width (FWHM
Rapid (default) Scan rate (Da/sec): 66 666
Peak width (FWHM): 0.6
Normal Scan rate (Da/sec): 33 333
Peak width (FWHM): 0.5
Enhanced Scan rate (Da/sec): 10 000
Peak width (FWHM): 0.35
Zoom Scan rate (Da/sec): 2222
Peak width (FWHM): 0.3
a
The isotopes are partially unresolved. The actual observed peak widths are isotope-abundant dependent.
b
Defined as the peak width at half height.
Scan Mass-To-Charge Ratio Ranges
The Orbitrap Fusion Series MS has two mass-to-charge ratio (m/z) range modes:
b
):
3
•Normal: m/z 50–2000
•High: m/z 100–4000 (ion trap detector type) or m/z 100–6000 (Orbitrap detector type)
with the precursor ion selection up to m/z 4000
Resolutions for the Orbitrap Detector
When you specify the Orbitrap mass analyzer as the detector type, you can choose from seven
resolution levels:
•15000
•30000
•50000
•60000
• 120 000
• 240 000
• 500 000
Thermo Scientific Orbitrap Fusion Series Hardware Manual 13
2
Scan Parameters
Data Types
Data Types
With the Orbitrap Fusion Series MS, you can acquire and display mass spectral data (intensity
versus mass-to-charge ratio) in one of two data types:
•Profile data
With profile data, you can see the inherent shape of the peaks in the mass spectrum. The
mass spectrum divides each atomic mass unit into several sampling intervals. The
intensity of the ion current is determined at each sampling interval. The intensity at each
sampling interval is displayed with the intensities connected by a continuous line.
• Centroid data
With centroid data, you can see the mass spectrum as a bar graph. This scan data type
sums the intensities of each set of sampling intervals. This sum is displayed versus the
integral center of mass of the many sampling intervals. Centroid data requires about
one-tenth the computer disk space of what is required for profile data.
Ion Polarity Modes
The Orbitrap Fusion Series MS can operate in either positive or negative ion polarity mode.
The mass spectrometer controls whether positive ions or negative ions are transmitted to the
mass analyzer for mass analysis by changing the polarity of the voltage potentials applied to
the API source, ion optics, and ion detection system. The ion optics are located between the
API source and the mass analyzer. For a schematic of the ion transmission path, see Figure 13.
14 Orbitrap Fusion Series Hardware Manual Thermo Scientific
3
Vacuum System
This chapter describes the principal components of the vacuum system for the
Orbitrap Fusion Series mass spectrometer.
Contents
• Vacuum System Functional Block Diagram
• Schematic of the Internal Gas Supply Lines
• Inlet Gases Hardware
• Vacuum Manifold
• Vacuum Gauges
• Vacu um Pu mps
• Atmospheric Pressure Ionization Source
• API Source Interface
Vacuum System Functional Block Diagram
The vacuum system evacuates the region around the API source interface, ion optics, mass
analyzers, and ion detection system. Figure 5 shows a functional block diagram of the vacuum
system with hyperlinks to the applicable sections.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 15
3
Nitrogen gas
port
Sweep gas
valve
Sheath gas
valve
Aux gas
valve
Sample
inlet
device
Sample tube
API source
region
RF lens
region
MP00
RF lens
region
MP0
ion guide
region
Quadrupole / MP1 / IRM / C-trap region
Linear ion trap /
MP3 region
Damping gas
restrictor
Helium gas
port
Collision gas
restrictor
Collision gas
port
Orbitrap
region
UHV
pressure
gauge
Vent
valve
Triple-inlet
turbomolecular pump
Foreline
Forepump(s)
Exhaust
Source pressure
gauge
Collision
pressure gauge
Turbomolecular pump
Turbomolecular pump
Ion gauge
Nitrogen gas
Vacuum System
Vacuum System Functional Block Diagram
Figure 5. Functional block diagram of the vacuum system
16 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Schematic of the Internal Gas Supply Lines
Helium open
split inlet
Gas
block
Reagent
ion source
API
source
Ion-routing
multipole
Vent valve
Source PCB
Regulator
UHP nitrogen
gas inlet
UHP helium
gas inlet
HP nitrogen
gas inlet
Linear
ion trap
(Back of the MS)
Figure 6 shows a schematic drawing of the gas lines in the Orbitrap Fusion Series MS where
“Reagent ion source” represents the optional EASY-ETD™ or EASY-IC™ ion source.
Figure 6. Schematic of the internal gas supplies
3
Vacuum System
Schematic of the Internal Gas Supply Lines
Thermo Scientific Orbitrap Fusion Series Hardware Manual 17
3
UHP nitrogen gas inlet
HP nitrogen gas inlet
UHP helium gas inlet
(Orbitrap Fusion MS)
(Orbitrap Fusion Lumos MS)
UHP nitrogen gas inlet
HP nitrogen gas inlet
UHP helium gas inlet
Vacuum System
Inlet Gases Hardware
Inlet Gases Hardware
The inlet gas hardware controls the flow of the helium damping gas; the nitrogen sheath gas,
auxiliary gas, sweep gas, and collision gas; and the nitrogen venting gas into the mass
spectrometer. Figure 7 shows the gas inlets on the back of the mass spectrometer.
• Helium Regulator
• Nitrogen Gas Valves
• Ven t Val ve
Figure 7. Gas inlet ports (back of the mass spectrometer)
18 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Helium Regulator
The helium (damping) regulator controls the flow of helium into the LIT analyzer cavity.
Helium (275 70 kPa [40 10 psi], 99.999% ultra high purity [UHP]) enters the mass
spectrometer through a 1/8 in. port on the back of the mass spectrometer. The mass
spectrometer regulates the flow of helium and delivers it to the ion trap.
Helium in the ion trap cavity dampens ionic motion and improves the performance of the
mass spectrometer. See “Helium Damping Gas” on page 41.
Nitrogen Gas Valves
The valves for the sheath, auxiliary, and sweep gases control the flow of dry nitrogen gas into
the API source (Figure 5). Sheath gas is the inner-coaxial nitrogen gas that helps nebulize the
sample solution into a fine mist as the solution exits the API spray insert nozzle. Auxiliary gas
is the outer-coaxial nitrogen gas that helps the sheath gas in the nebulization and evaporation
of the sample solution by focusing the vapor plume and lowering the humidity in the API
source. Sweep gas is the off-axis nitrogen gas that flows out from behind the optional ion
sweep cone to aid in solvent declustering and adduct reduction. The optional ion sweep cone
has an inlet for the sweep gas.
3
Vacuum System
Inlet Gases Hardware
The data system controls the valves that regulate the nitrogen pressure (see “Checking the Gas
Supplies” on page 63). You can set the gas flow rates on the Ion Source pane in the Tune
application.
High-purity (HP, 99%) and ultra-high-purity (UHP, 99.999%) dry nitrogen enter the back of
the mass spectrometer through two ports:
• 1/4 in. port for the HP nitrogen gas, which functions as the sheath, auxiliary, and sweep
gases
• 1/8 in. port for the UHP nitrogen gas, which functions as the higher energy
collision-induced dissociation (HCD) collision gas and the venting gas. For instruments
with the electron transfer dissociation (ETD) option, the UHP nitrogen gas also
functions as the ETD make-up gas and reagent carrier gas.
For a list of guidelines for the operating parameters, refer to the section “LC Flow Rate
Ranges” in Chapter 1 of the Orbitrap Fusion Series Getting Started Guide.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 19
3
Vacuum System
Vacuum Manifold
Vent Valve
The solenoid-operated vent valve allows the vacuum manifold to be vented with UHP
nitrogen. The vent valve on the vacuum manifold is closed when the solenoid is energized.
The vacuum manifold vents when the mass spectrometer no longer receives external power, as
with a power failure or when you turn off the main power switch. Power is briefly provided to
the vent valve after losing external power to protect against the accidental loss of power. When
power to the vent valve solenoid shuts off for more than a very brief period of time, the vent
valve opens and the manifold vents nitrogen gas.
IMPORTANT After venting the mass spectrometer, remember to turn off the UHP
nitrogen gas supply.
Vacuum Manifold
The vacuum manifold (Figure 8) encloses the API source interface, ion optics, mass analyzers,
and ion detection system assemblies. The vacuum manifold is a thick-walled, aluminum
chamber with multiple removable top cover plates, and various electrical feedthroughs and gas
inlets.
Ta bl e 6 lists the seven vacuum regions, the pumps that evacuate them, and the chamber
pressures. The block diagram in Figure 5 shows the vacuum regions.
Table 6 . Vacuum regions, evacuation devices, and typical pressures
Region Components Evacuated by Pressure
Orbitrap Fusion Orbitrap Fusion Lumos
1API source N/A Atmosphere
2 RF lens Forepump or forepumps Less than 2 Torr Less than 3 Torr
3 MP00 ion optics Triple-inlet turbomolecular pump
50 mTorr 100 mTorr
(first inlet [molecular drag])
4 MP0 ion optics Triple-inlet turbomolecular pump
1 . 5 m To r r 3 m To r r
(second inlet [interstage])
5 Quadrupole mass
analyzer, MP1 ion optics,
Triple-inlet turbomolecular pump
(third inlet [high vacuum])
5×10
–5
Tor r
IRM, C-trap
–5
6 LIT mass analyzer and
MP3 ion optics
Single-inlet turbomolecular
vacuum pump
8×10
7 Orbitrap mass analyzer Single-inlet turbomolecular pump 2 × 10
Tor r 2 × 1 0–5 Tor r
–10
To r r
20 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Vacuum Gauges
The Orbitrap Fusion Series MS contains three types of vacuum gauges that measure the
pressure in specific regions of the vacuum manifold. In the Tune application, you can observe
the readback values for the vacuum gauges on the By Function page in the Status pane (under
Source and FT Vacuum).
3
Vacuum System
Vacuum Gauges
• Convection pressure gauge—Measures pressure down to a fraction of a milliTorr (mT).
The instrument uses two convection gauges:
– Source pressure gauge—Measures the pressure in the RF lens and API ion transfer
tube region in the vacuum manifold and the foreline, which connects the triple-inlet
turbomolecular pump and the forepump or forepumps.
– Collision pressure gauge—Measures the pressure in the IRM.
• Ion gauge—Measures the pressure in the multipole MP3 and LIT region of the vacuum
manifold.
The ion gauge produces energetic electrons that cause the ionization of molecules in the
ion gauge. A collector attracts positive ions formed in the ion gauge. The collector current
is related to the pressure in the vacuum manifold. The ion gauge is also involved in
vacuum protection.
Vacuum Pumps
• Ultra high vacuum (UHV) pressure gauge—A compact cold cathode (inverted
magnetron) gauge measures the pressure in the Orbitrap region of the vacuum manifold.
The Orbitrap Fusion Series MS requires one or two external forepumps and three internal
turbomolecular pumps to provide the vacuum pressures for the seven vacuum regions
(Figure 5).
The forepumps create the vacuum necessary for the proper operation of the turbomolecular
pumps. They also evacuate the ion transfer tube region of the vacuum manifold.
The forepumps’ detachable power supply cords plug into separate, single-phase 230 Vac wall
outlets and the relay control cable connects to the mass spectrometer’s SV65 Pump Enable
connector (Figure 3) so that the mass spectrometer can remotely turn the forepumps on and
off. The Main Power switch controls the SV65 Pump Enable connector, not the electronics
service switch.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 21
3
Triple-inlet turbomolecular
pump (main)
Triple-inlet turbomolecular
pump (UHV)
Turbomolecular
pump (ion trap)
Vacuum System
Vacuum Pumps
As shown in Figure 8, there are three turbomolecular pumps: two triple-inlet pumps that
control the vacuum for multiple vacuum regions and one single-inlet pump that controls the
LIT vacuum region. The turbomolecular pumps also send status information, such as their
temperatures or rotational speeds, to the data system computer.
The Main Power switch turns off the turbomolecular pumps. The electronics service switch
has no effect on these pumps. Power to the turbomolecular pumps automatically shuts off if
the temperatures on the turbomolecular pumps becomes too high.
Figure 8. Placement of the three turbomolecular pumps
22 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Atmospheric Pressure Ionization Source
ESI spray insert
API source housing
Locking lever (locked position)
Sample inlet
The atmospheric pressure ionization (API) source forms gas phase sample ions from sample
molecules that are contained in solution. The API source also serves as the interface between
the LC and the mass spectrometer. You can configure the EASY-Max NG API source, which
is provided with the mass spectrometer, for the following ionization techniques:
heated-electrospray (H-ESI), atmospheric pressure chemical ionization (APCI), and
atmospheric pressure photoionization (APPI).
The Orbitrap Fusion Series MS has a front, built-in drain that routes the solvent waste from
the API source to the solvent waste container connected to the back drain/waste port. For
information about the solvent waste connection, refer to the Orbitrap Fusion Series Getting
Connected Guide.
For information about the API source, refer to Chapter 2 in the Orbitrap Fusion Series Getting
Started Guide. For instructions on how to install the spray insert, refer to the Ion Max NG and
EASY-Max NG Ion Sources User Guide.
Figure 9. EASY-Max NG API source (H-ESI mode)
3
Vacuum System
Atmospheric Pressure Ionization Source
Thermo Scientific Orbitrap Fusion Series Hardware Manual 23
3
Ion transfer tube (not shown)
RF lensVent prevent ball
Ion sweep cone
Heater block
Exit lens
Lens L0
Spray cone (directly
behind the sweep
cone)
Release latch
Vacuum System
API Source Interface
API Source Interface
The API source interface for the Orbitrap Fusion Series MS consists of the components of the
API source that are held under vacuum (except for the atmospheric pressure side of the ion
sweep cone) in a vacuum chamber that the forepump evacuates to a pressure of approximately
1.5 Torr for the Orbitrap Fusion MS and 2.7 Torr for the Orbitrap Fusion Lumos MS. The
API source interface includes an ion sweep cone, an ion transfer tube, two cartridge heaters, a
heater block, a sensor, a vent prevent ball, the RF lens, the exit lens, and lens L0 (Figure 10).
Figure 10. API source interface (Orbitrap Fusion MS cross section)
24 Orbitrap Fusion Series Hardware Manual Thermo Scientific
The ion sweep cone is a metal cone over the ion transfer tube. The ion sweep cone channels
the sweep gas toward the entrance of the ion transfer tube, acts as a physical barrier that
protects the entrance of the ion transfer tube, and increases source robustness. The net result
is a significant increase in the number of samples to analyze without a loss of signal intensity.
In addition, keeping the ion transfer tube entrance as clean as possible reduces the need for
frequent maintenance. Install the ion sweep cone to improve ruggedness when analyzing
complex matrices such as plasma or nonvolatile salt buffers. Remove the ion sweep cone
before performing NSI experiments.
The ion transfer tube is a metal, cylindrical tube that assists in desolvating ions produced by
the API spray insert while transferring them into the vacuum system.
The heater block contains two heater cartridges, surrounds the ion transfer tube, and heats the
tube to temperatures up to 400 °C (752 °F). A thermocouple measures the temperature of the
heater block. Typical temperatures of the ion transfer tube are 270 °C (518 °F) for H-ESI and
250 °C (482 °F) for APCI, but these temperatures vary with the flow rate and the mobile
phase composition. A decreasing pressure gradient draws ions into the ion transfer tube in the
3
Exit lens
RF lens
Orbitrap Fusion MS
Orbitrap Fusion Lumos MS
Vacuum System
API Source Interface
atmospheric pressure region and transports them to the API source interface region of the
vacuum manifold. The mass spectrometer applies the same electrical potential (positive for
positive ions and negative for negative ions) to the ion transfer tube and the RF lens, which
assists in transporting the ions from the tube to the RF lens. When you remove the ion
transfer tube (after it has cooled to room temperature), the vent prevent ball drops into place
to stop air from entering the vacuum manifold. Therefore, you can remove the ion transfer
tube for cleaning or replacement without venting the system.
Ions from the ion transfer tube pass through the RF lens and then the exit lens (Figure 11).
The RF lens is an ion transmission device consisting of progressively spaced, stainless-steel
electrodes. The RF lens differs slightly between the Orbitrap Fusion Lumos MS and the
Orbitrap Fusion MS. The mass spectrometer applies an RF voltage to the electrodes, and
adjacent electrodes have voltages of opposite phase. As the RF amplitude increases, ions of
progressively higher mass-to-charge ratios pass through to the exit lens and move toward the
MP00 RF lens. The exit lens acts as a vacuum baffle between the higher pressure API source
interface region and the lower pressure MP00 RF lens region of the vacuum manifold. The
RF lens and exit lens mount to the API source interface cage.
Figure 11. Exit lens and RF lens (Orbitrap Fusion and Orbitrap Fusion Lumos MSs)
Thermo Scientific Orbitrap Fusion Series Hardware Manual 25
3
Vacuum System
API Source Interface
26 Orbitrap Fusion Series Hardware Manual Thermo Scientific
4
Ion Transmission and Mass Analysis
This chapter provides a workflow chart that shows the paths for mass analysis through the
Orbitrap Fusion Series mass spectrometer. It also provides descriptions of the ion optics
elements, the three mass analyzers, and the ion detection system.
Contents
• Workflow for Mass Analysis
• Ion Optics
• Mass Analyzers
• Ion Detection Systems
Workflow for Mass Analysis
Figure 12 shows the possible mass analysis paths through the Orbitrap Fusion Series MS.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 27
4
Ion-routing multipole
activation (optional)
Further
processing?
Send to linear
ion trap?
Ion-routing
multipole
activation?
Ion-routing multipole
C-trap
LIT high-pressure
trap
Yes
No
Further
processing?
Yes
LIT low-pressure
analysis
Yes
No
Send to linear
ion trap?
No
CID activation
(optional)
Orbitrap
analysis
Q1 isolation
(optional)
Ions pass through C-trap
to ion-routing multipole.
High-pressure cell
isolation
Ions exit the
API source.
Yes
No
Yes
No
Ion Transmission and Mass Analysis
Workflow for Mass Analysis
Figure 12. Workflow for mass analysis
28 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Ion Optics
Dual-pressure linear
ion trap (LIT)
Conversion
dynode
Lens TL1
MP3
Lenses L3-1 and L3-2
Ion-routing multipole
C-trap, trap lens
C-trap
C-trap, gate lens
Ultra-high field Orbitrap
mass analyzer
Orbitrap
transfer lens
MP1
Split gate
Lens L2
Q1 quadrupole
mass analyzer
Lenses TK1
and TK2
MP0 (90 degrees)
Lens L0
MP00 RF lens
Exit lens or reagent ion
source
1
(shown)
RF lens
EASY-ETD or -IC
ion source
(Drawing is not to scale)
High capacity ion
transfer tube
4
Ion Transmission and Mass Analysis
Ion Optics
Figure 13 shows a schematic of the ion transmission path through the Orbitrap Fusion Series
MS with hyperlinks to the applicable sections.
Figure 13. Schematic of the Orbitrap Fusion Lumos Tribrid MS ion transmission path (shown with the ETD source option
1
)
1
For the Orbitrap Fusion Series MS with the Internal Calibration (IC) or ETD configuration, the ETD/IC source heater interface replaces the
exit lens.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 29
4
Orbitrap Fusion MS Orbitrap Fusion Lumos MS
Ion Transmission and Mass Analysis
Ion Optics
The ion optics focus and accelerate the gas-phase sample ions into the designated mass
analyzer, where they are isolated and ejected according to their mass-to-charge ratios. This
section describes the following:
• MP00 Ion Optics
• MP0 Ion Optics
• MP1 Ion Optics
• Curved Linear Trap
• Ion-Routing Multipole
• MP3 Ion Optics
• DC Offset Voltages
MP00 Ion Optics
Ions pass through the exit lens and move toward the MP00 ion optics, which are located
between the API source interface and the MP0 ion optics. The MP00 ion optics include the
MP00 RF lens and the L0 lens. See Figure 13 for the location of these components.
For the Orbitrap Fusion MS, the square-metal elements of the MP00 RF lens act as an
ion-focusing device (first image in Figure 14). For the Orbitrap Fusion Lumos MS, the MP00
RF lens is an array of four cylindrical metal elements (second image in Figure 14). The mass
spectrometer applies an RF voltage to the elements, generating an electric field that guides the
ions along the axis of the lens.
Figure 14. MP00 RF lens (Orbitrap Fusion and Orbitrap Fusion Lumos MSs)
30 Orbitrap Fusion Series Hardware Manual Thermo Scientific
MP0 Ion Optics
4
Ion Transmission and Mass Analysis
Ion Optics
The lens L0 is a metal disk with a small hole in the center through which the ion beam passes
(Figure 15). The mass spectrometer applies an electrical potential (positive for positive ions
and negative for negative ions) to lens L0 to aid in ion transmission. (The system ground is
referenced to the C-trap potential, not earth ground.) Lens L0, which mounts to the MP00
RF lens, also acts as a vacuum baffle between the MP00 and MP0 ion optics chambers.
Figure 15. Lens L0
The MP0 ion optics, also called the active beam guide (ABG), transmits ions from the MP00
ion optics through a 90-degree arc along the central axis to quadrupole Q1. The curved
design reduces noise by preventing neutral species and high-velocity clusters from entering
Q1. The MP0 ion optics include multipole MP0 and lenses TK1 and TK2 (Turner-Kruger
lenses). See Figure 13 for the location of these components.
Multipole MP0 consists of a pair of PCBs arranged parallel to each other and separated by a
small distance (Figure 16). The multipole’s design of individual electrode segments allows the
mass spectrometer to implement a DC gradient in addition to the RF voltage. This provides
an axial field along the length of the device to provide fast and consistent ion flight times
through the device.
Figure 16. Multipole MP0
Thermo Scientific Orbitrap Fusion Series Hardware Manual 31
4
Orbitrap Fusion MS Orbitrap Fusion Lumos MS
Ion Transmission and Mass Analysis
Ion Optics
The TK1 and TK2 lenses are metal discs with a circular hole in the center through which the
ion beam passes (Figure 17). The mass spectrometer applies an electrical potential to the lens
to accelerate (or decelerate) ions as they approach each lens and to focus the ion beam as it
passes through each lens. Lens TK1 acts as vacuum baffle between the MP0 multipole and the
Q1 quadrupole mass analyzer. It also shields MP0 from the RF voltage that the mass
spectrometer applies to Q1, and vice versa.
Figure 17. TK lens (both sides)
MP1 Ion Optics
The MP1 ion optics transmit ions from quadrupole Q1 to the C-trap. The MP1 ion optics
include multipole MP1 and the C-trap gate lens. For the location of these components, see
the schematic in Figure 13.
Multipole MP1 is an array of circular rods that act as an ion transmission device (Figure 18).
The mass spectrometer applies an RF voltage to the rods, generating an electric field that
guides the ions along the axis of the multipole. The C-trap gate lens focuses the ions as they
enter the C-trap.
Figure 18. Multipole MP1 (Orbitrap Fusion and Orbitrap Fusion Lumos MSs)
32 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Curved Linear Trap
Orbitrap Fusion MS Orbitrap Fusion Lumos MS
4
Ion Transmission and Mass Analysis
For Orbitrap mass analysis, the mass spectrometer always passes the ions through the gas-free
multipole MP1 and the gas-filled curved linear trap (C-trap) before trapping them in the
IRM. The mass spectrometer then passes the ions back to the C-trap (Figure 19) before
injecting them into the Orbitrap mass analyzer.
Ions that enter the C-trap lose their kinetic energy by colliding with the nitrogen collision gas,
which dissipates their kinetic energy and cools them down to the center axis of the C-trap. See
Figure 13 for its location.
Figure 19. C-trap (Orbitrap Fusion and Orbitrap Fusion Lumos MSs)
Ion Optics
Ion-Routing Multipole
The ion-routing multipole (Figure 20) consists of a straight multipole that is mounted inside
a metal tube and has a direct line-of-sight to the C-trap. The mass spectrometer supplies the
IRM with the nitrogen collision gas to increase the multipole’s gas pressure. The C-trap
attaches to the multipole, so part of the collision gas also flows into the C-trap.
To perform HCD, ions pass through the C-trap into the IRM. The offset voltage between the
C-trap and multipole accelerates the precursor ions into the gas-filled multipole. The mass
spectrometer applies a potential gradient to the multipole to provide fast extraction of the
ions. The spectrum of the fragments generated in the IRM and detected in the Orbitrap mass
analyzer shows a fragmentation pattern comparable to the pattern of a typical triple
quadrupole spectrum.
Figure 20. Ion-routing multipole (IRM)
Thermo Scientific Orbitrap Fusion Series Hardware Manual 33
4
Ion Transmission and Mass Analysis
Mass Analyzers
MP3 Ion Optics
The MP3 ion optics transmit ions from the IRM to the dual-pressure LIT. The MP3 ion
optics include multipole MP3 and the transfer lens TL1, which is also known as the front
lens. For the location of these components, see Figure 13.
Multipole MP3 is an array of circular rods that act as an ion transmission device (Figure 18).
The mass spectrometer applies an RF voltage to the rods, generating an electric field that
guides the ions along the axis of the multipole. The transfer lens TL1 focuses the ions as they
enter the LIT.
Figure 21. Multipole MP3
DC Offset Voltages
Mass Analyzers
The mass spectrometer controls the ion transmission through the ion optics by applying DC
offset voltages to each of the ion optics. The DC voltage, offset from the system ground
(defined at the C-trap), increases the translational kinetic energy (TKE) of the ions emerging
from each of the exit lenses through the ion optic path. Increasing the offset voltage increases
the TKE of the ions. The voltages (for positive ions) go from more positive to more negative
as you move from the API source to the mass analyzers.
This section describes the components of the three mass analyzers, voltages applied to the
mass analyzer electrodes, helium damping gas in the mass analyzer cavity, and mass analyzer
operation during mass analysis. Ion manipulation and mass analysis occur in a mass analyzer.
The Orbitrap Fusion Series MS can provide multiple levels of mass analysis. Each level of
mass analysis adds a new dimension of specificity for unequivocal compound identification.
The Orbitrap Fusion Series MS contains the following mass analyzers:
• Quadrupole Mass Analyzer
• Orbitrap Mass Analyzer
• Linear Ion Trap Mass Analyzer
34 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Quadrupole Mass Analyzer
Orbitrap Fusion MS
Orbitrap Fusion Lumos MS
The quadrupole mass analyzer (Q1) transmits ions from the MP0 ion guide. This mass
analyzer includes quadrupole Q1, lens L2, and the dual-split gate lens. For the location of
these components, see Figure 13.
Quadrupole Q1 is a square array of circular rods (Figure 22). Quartz spacers act as electrical
insulators between adjacent rods. The mass spectrometer applies an RF voltage to the rods,
generating an electric field that guides the ions along the axis of the quadrupole. The mass
spectrometer applies the DC quadrupole offset voltage to the quadrupole rods in addition to
the resolving DC voltage. The offset voltage accelerates (or decelerates) ions and, therefore,
sets the TKE of the ions as they enter the quadrupole rod assembly.
Figure 22. Quadrupole Q1 (side and end views, Orbitrap Fusion and Orbitrap Fusion Lumos MSs)
4
Ion Transmission and Mass Analysis
Mass Analyzers
The lens L2 is a metal disk with a small hole in the center through which the ion beam passes.
Lens L2 focuses the ions coming from the quadrupole into the MP1 ion optics.
The dual-split gate lens (Figure 23) starts and stops the injection of ions into the multipole
MP1 by deflecting the beam at high speeds at the appropriate times. The voltages on the
dual-split gate lens depend on the calibration of the system. The voltage to deflect the beam is
typically 50 Vdc.
Figure 23. Dual-split gate lens (both sides)
Thermo Scientific Orbitrap Fusion Series Hardware Manual 35
4
RF voltage + DC voltage
RF voltage 180° out of phase – DC voltage
Ion Transmission and Mass Analysis
Mass Analyzers
Applied RF and DC Fields
In a quadrupole rod assembly, because rods opposite each other in the array connect
electrically, the four rods are considered two pairs of two rods each. The mass spectrometer
applies RF and DC voltages to the rods. As shown in Figure 24, although the RF voltages
applied to the four rods are the same, the two pairs are 180 degrees out of phase (that is, one
pair has a positive voltage and the other is negative).
Figure 24. Polarity of the RF and DC voltages applied to the Q1 rods
Mass Filtering
The quadrupole coil module provides the voltages for operating the quadrupole. The RF
voltage applied to the quadrupole rods is of constant frequency (approximately 1.1 MHz) and
varies from 0 to 10 000 Vac peak-to-peak amplitude. The DC voltage varies from 0 to
±800 V.
When the mass spectrometer applies both RF and DC voltages, quadrupole Q1 acts as a mass
filter. When it applies only the RF voltage, the quadrupole acts as ion transmission devices. In
the ion transmission mode, the quadrupole allows ions in a wide window of mass-to-charge
ratios to pass.
The variable amplitude of RF and DC voltages applied to the quadrupole rods generates an
electric field that gives stable oscillations to ions with a specific mass-to-charge ratio and
unstable oscillations to all others. When the mass spectrometer applies one particular set of
RF and DC voltages to the quadrupole, only ions of one mass-to-charge ratio (for example,
m/z 609) are maintained within bounded oscillations as their velocity carries them through
the mass filter. At the same time, all other ions undergo unbounded oscillations. These ions
strike one of the rod surfaces, become neutralized, and are pumped away, or they are ejected
from the rod assembly.
The more closely the electrostatic field generated by a set of quadrupole rods approximates a
hyperbolic geometry, the better their operating characteristics are. As a result, the precision
quadrupole rods of the Orbitrap Fusion Series MS provide excellent sensitivity, peak shape,
resolution, and high mass transmission.
36 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Orbitrap Mass Analyzer
r
Z
The core of the Orbitrap mass analyzer is an axially-symmetrical mass analyzer. It consists of a
spindle-shaped central electrode surrounded by a pair of bell-shaped outer electrodes
(Figure 25). The Orbitrap analyzer employs electrostatic fields, without an RF or magnetic
component, to capture and confine ions.
Figure 25. Schematic of the Orbitrap cell and an example stable ion trajectory
• Extraction of Ion Packets
4
Ion Transmission and Mass Analysis
Mass Analyzers
Extraction of Ion Packets
For ion extraction, the mass spectrometer ramps off the RF voltage to the C-trap rods and
applies a pulsing extracting voltage to the electrodes, which pushes the ions orthogonally
through a slot in the inner electrode toward the curved axis. Because of the initial curvature of
the C-trap and its lenses, the ion beam converges on the entrance into the Orbitrap analyzer.
The lenses that follow the C-trap form differential pumping slots and cause spatial focusing of
the ion beam into the entrance of the Orbitrap analyzer. Ions are electrostatically deflected
away from the gas jet, thereby eliminating gas carryover into the Orbitrap analyzer.
Because of the fast ion pulsing from the C-trap, ions of each mass-to-charge ratio arrive at the
Orbitrap analyzer’s entrance as short packets that are only a few millimeters long. For each
mass-to-charge population, this corresponds to a spread of flight times of only a few hundred
nanoseconds for mass-to-charge ratios of a few hundred daltons per charge. Such durations
are considerably shorter than a half-period of axial ion oscillation in the C-trap. When the
mass spectrometer injects the ions into the Orbitrap analyzer at a position offset from its
equator (Figure 26), these packets start coherent axial oscillations without the need for any
additional excitation cycles.
• Measuring Principle
• Ion Detection
Thermo Scientific Orbitrap Fusion Series Hardware Manual 37
4
z
m
----
k=
Ion Transmission and Mass Analysis
Mass Analyzers
Figure 26. Electrodynamic squeezing of ions in the Orbitrap analyzer (r) versus the increased field
Figure 26 shows a schematic of the development of an ion packet with the increased electric
field. When the injected ions approach the opposite electrode for the first time, the increased
electric field (from the change of the voltage on the central electrode) contracts the radius of
the ion cloud. A further increase of the electric field continues to move the trajectory closer to
the axis, which allows additional ions (normally with a higher mass-to-charge ratio) to enter
the Orbitrap. After the ions of all mass-to-charge ratios enter the Orbitrap analyzer and move
far enough from the outer electrodes, the voltage on the central electrode is kept constant and
image current detection takes place.
strength (z)
Measuring Principle
Ion Detection
In the mass analyzer (Figure 25), stable ion trajectories combine rotation around an axial
central electrode with harmonic oscillations that run along it. The frequency of these
harmonic oscillations along the z axis depends only on the ion mass-to-charge ratio (m/z) and
the instrumental constant k:
The Orbitrap analyzer’s two split halves of the outer electrode detect the image current that
the oscillating ions produce. By using a fast fragment ion algorithm of the amplified image
current, the instrument measures the frequencies of these axial oscillations and the
mass-to-charge ratios of the ions.
To avoid mass drift during ion detection, the mass spectrometer maintains very stable voltages
on the central electrode and the additional electrode. Both electrodes deflect ions during
injection and compensate for electric field imperfections during the mass measurement
(Figure 26). The outer electrode is split in half at z = 0, which allows for the detection of the
ion motion in the axial direction through the induced image current. The image current on
each half of the outer electrode is differentially amplified and then undergoes analog-to-digital
conversion before processing by using the fast Fourier transform (FT) algorithm.
38 Orbitrap Fusion Series Hardware Manual Thermo Scientific
4
Lower m/z Higher m/z
Ion Transmission and Mass Analysis
Mass Analyzers
As previously mentioned, stable ion trajectories within the Orbitrap analyzer combine axial
oscillations along the z axis with rotation around the central electrode and vibrations in the
radial direction (Figure 25). For any given mass-to-charge ratio, only the frequency of axial
oscillations is completely independent of the initial ion parameters, whereas rotational and
radial frequencies exhibit strong dependence on the initial radius and energy. Therefore, ions
of the same mass-to-charge ratio continue to oscillate along the z axis together, remaining
in-phase for many thousands of oscillations.
In contrast to the axial oscillations, the frequencies of radial and rotational motion vary for
ions with slightly different initial parameters. This means that in the radial direction, the
dephasing of ions is faster than in the axial direction, and the process occurs in a period of
only 50–100 oscillations. After this, the ion packet of a given mass-to-charge ratio assumes the
shape of a thin ring, with ions uniformly distributed along its circumference (Figure 27).
Because of this angular and radial smearing, radial and rotational frequencies cannot appear in
the measured spectrum. Meanwhile, axial oscillations persist, with axial thickness of the ion
ring remaining small compared with the axial amplitude. Moving from one half of an outer
electrode to the other, this ring induces opposite currents on these halves, which creates a
signal detectable by differential amplification.
Figure 27. Approximate shape of ion packets of different m/z after the voltages stabilize
Linear Ion Trap Mass Analyzer
The Orbitrap Fusion Series MS contains a dual-cell, two-dimensional LIT mass analyzer that
consists of a front transfer lens (TL1), a high pressure LIT cell, a center transfer lens (TL2), a
low pressure LIT cell, and a back transfer lens (TL3) (Figure 28). The front, center, and back
transfer lenses are metal plates with a circular hole in the center through which the ion beam
passes. These transfer lenses provide conductance limits.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 39
4
High pressure cell
Low pressure cell
Lens TL3
Lens TL2
Lens TL1
Y
X
Z
Back section
Center section
Front section
Ion Transmission and Mass Analysis
Mass Analyzers
Figure 28. Linear ion trap (LIT) (Orbitrap Fusion MS)
Inside the mass analyzer cells are square arrays of precision-machined and precision-aligned
hyperbolic rods that have three sections (Figure 29). Ions are ejected only through slots in the
X-rods during scan-out.
Axial Trapping Voltages
Figure 29. Assembly for the linear ion trap
The Orbitrap Fusion Series MS uses six DC axial trapping voltages, one for each rod section
on both cells. These voltages establish axial trapping by creating potential wells. These DC
axial trapping voltages allow the mass analyzer to perform its storage and scan-out functions.
40 Orbitrap Fusion Series Hardware Manual Thermo Scientific
AC Voltages Applied to the X-Rods
The Orbitrap Fusion Series MS applies ion isolation waveform voltage, resonance excitation
RF voltage, and resonance ejection RF voltage to the X-rods to stimulate motion of the ions in
the direction of the ion detection system. When the AC frequency applied to the rods equals
the frequency of the motion of the trapped ion (which depends on its mass), the ion gains
kinetic energy. If the magnitude of the applied voltage is large enough or the ion is given
sufficient time, the mass analyzer ejects the ion in the direction (that is, X direction) of the ion
detection system.
4
Ion Transmission and Mass Analysis
Mass Analyzers
Helium Damping Gas
The ion isolation waveform voltage is a multifrequency resonance ejection waveform that acts
during the ion isolation step of SIM or MS
n
(n > 1) applications. The ion isolation waveform
voltage, combined with the main RF voltage, ejects all ions except those of a selected
mass-to-charge ratio or narrow ranges of mass-to-charge ratios.
During the collision-induced dissociation (CID) step of MS
n
(n > 1) applications, the
Orbitrap Fusion Series MS applies a resonance excitation AC voltage to the X-rods to
fragment precursor ions into product ions. Ion motion is enhanced and the ion gains kinetic
energy. After many energetic collisions with the helium damping gas, which is present in the
mass analyzer, the ion gains enough internal energy to cause it to dissociate into product ions.
The mass analyzer then analyzes the product ions.
During ion scan-out, the resonance ejection AC voltage allows for the ejection of ions from
the mass analyzer, which improves mass resolution and sensitivity. The mass spectrometer
applies resonance ejection AC voltage during the ramp of the main RF voltage. Ions
consecutively move into resonance with the resonance ejection RF voltage. When an ion
approaches resonance, it moves farther away from the center of the mass analyzer and is
subsequently ejected.
The LIT mass analyzer cavity contains helium that is used as a damping gas and a collision
activation partner. The collisions of the ions entering the LIT with the helium slow the ions so
that the RF field in the LIT can more efficiently trap them.
The presence of helium in the LIT cavity significantly enhances sensitivity and mass spectral
resolution. Before their ejection from the mass analyzer cavity, sample ions collide with
helium atoms. These collisions reduce the kinetic energy of the ions, which results in damping
the amplitude of their oscillations. The mass analyzer then focuses the ions to the axis of the
cavity rather than allow them to spread throughout the cavity, which would spread their
ejection times and degrade the mass spectral resolution.
Helium in the LIT mass analyzer cavity also serves as a collision activation partner. During the
CID step of an MS
n
(n > 1) analysis, the resonance excitation AC voltage that is applied to the
X-rods drives precursor ions energetically into the helium atoms. After gaining sufficient
internal energy from the resulting collisions, the precursor ion dissociates into one or more
product ions.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 41
4
Dynode in the ion
detection system
Ion Transmission and Mass Analysis
Mass Analyzers
Summary of Linear Ion Trap Mass Analyzer Operation
The processes that occur in the LIT mass analyzer can be broken down into four steps:
1. Ion storage
2. Ion isolation (SIM or MS
n
3. CID (MS
[n >1])
n
[n >1])
4. Ion scan-out (the ion detection step)
n
For MS/MS applications, the quadrupole typically performs the ion isolation. For MS
(n > 1) applications, the LIT mass analyzer performs the ion isolation and CID steps n–1
times.
n
For SIM or MS
(n > 1) analyses, the LIT mass analyzer applies the ion isolation waveform
voltage to the X-rods, in combination with a ramp of the main AC voltage to a new storage
voltage, to eject all ions except those of the selected mass-to-charge ratio.
n
For MS
(n > 1) analyses, the LIT mass analyzer applies the resonance excitation AC voltage
to the X-rods to cause CID. Product ions with a mass-to-charge ratio of less than the
minimum storage mass-to-charge ratio are not stored.
Finally, the sample ions or product ions are either scanned out or sent to the Orbitrap mass
analyzers. To scan out the ions, the main RF voltage ramps up from low voltage to high
voltage, and simultaneously the mass spectrometer applies the resonance ejection AC voltage
to the X-rods to facilitate ejection. As the main RF voltage increases, ions of increasing
mass-to-charge ratios become unstable and eject through the slots in the X-rods. Most of these
ions are focused toward the ion detection system where they are detected. The scan-out step
can only occur in the LIT’s low pressure trap, while initial trapping, isolation, and dissociation
of the ions occur in the high pressure trap.
Figure 30 illustrates the ion scan-out process.
Figure 30. Visual representation of the LIT mass analyzer operation (low pressure cell,
Orbitrap Fusion MS)
42 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Ion Detection Systems
The Orbitrap Fusion Series MS has a high-sensitivity, off-axis ion detection system with two
conversion dynodes and one electron multiplier (Figure 30). The ion detection system
produces a high signal-to-noise ratio (S/N), which is proportional to the number of ions
detected, and enables voltage polarity switching between positive and negative ion modes of
operation. The electron multiplier is located under the LIT. The conversion dynodes are
located on each side of the LIT.
A conversion dynode is a concave metal surface located at a right angle to the ion beam. The
ion detection system applies to the conversion node a high positive potential (12 kVdc) for
negative-ion detection or a high negative potential (–12 kVdc) for positive-ion detection.
Both conversion dynodes are physically connected and operate at the same voltage. An ion
striking the surface of the conversion dynode produces one or more secondary particles. The
curved surface of the conversion dynode focuses these secondary particles and the voltage
gradient accelerates them into the electron multiplier. The conversion dynode shields protect
the vacuum manifold from the electric field that the conversion dynode produces.
4
Ion Transmission and Mass Analysis
Ion Detection Systems
The electron multiplier samples the signal and includes an anode that collects the electrons
produced by the cathode. The data system records the current that leaves the electron
multiplier through the anode.
Because of the off-axis orientation of the ion detection system relative to the LIT, neutral
molecules from the trap tend not to strike the conversion dynode or electron multiplier. As a
result, the noise from neutral molecules is reduced.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 43
4
Ion Transmission and Mass Analysis
Ion Detection Systems
44 Orbitrap Fusion Series Hardware Manual Thermo Scientific
5
Syringe Pump and Divert/Inject Valve
This chapter describes the external syringe pump and divert/inject valve that ship with the
Orbitrap Fusion Series mass spectrometer. For information about installing these
components, refer to the Orbitrap Fusion Series Getting Connected Guide.
Contents
• Syringe Pump
• Divert/Inject Valve
Syringe Pump
The external Chemyx™ Fusion 100T syringe pump delivers sample solution from an installed
syringe, through the sample transfer line (red PEEK), and into the API source. The motorized
pusher block (Figure 31) depresses the syringe plunger at the flow rate specified in the data
system. (The default flow rate for calibration is 3 μL/min.)
You can start and stop the syringe pump from the data system; refer to the data system Help
for instructions. You can also start and stop the syringe pump by pressing the syringe pump
buttons.
Note If you choose to provide a syringe pump other than the Fusion 100T, ensure that it
can provide a steady, continuous flow of 1–5 μL/min.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 45
5
Teflon™
tubing
Fingertight
fittings
LC union, internal view Red PEEK
tubing
Pusher blockSyringe pump
Release
knob
Syringe
holder
Syringe
Syringe Pump and Divert/Inject Valve
Divert/Inject Valve
Figure 31. Syringe pump setup (top view)
Divert/Inject Valve
The external Rheodyne™ MX Series II™ divert/inject valve is a 6-port motorized valve that
switches between two positions. In the first position, port 1 connects internally to port 2,
port 3 connects to port 4, and port 5 connects to port 6. In the second position, the valve
rotates one position so that port 1 connects internally to port 6, port 2 connects to port 3,
and port 4 connects to port 5. Figure 32 shows the valve’s internal flow paths for both
positions.
The Method Editor in the Xcalibur application identifies the valve’s two positions as “1–2”
(port 1 to 2) and “1–6” (port 1 to 6).
46 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Figure 32. Divert/inject valve positions
Internal connection path
(light gray)
Port 1 internally switches between port 2
(position 1–2) and port 6 (position 1–6, shown).
Position 1–2 Position 1–6
Valve screw
5
Syringe Pump and Divert/Inject Valve
Divert/Inject Valve
Configurations
2
3
4
1
6
5
2
3
4
1
6
5
You can configure (plumb) the divert/inject valve as a loop injector (for flow injection
analysis) or as a divert valve. The divert valve can switch the solvent front, gradient endpoint,
or any portion of the LC run to waste. Figure 33 shows both of these configurations.
In the loop injector valve configuration, the valve switches between these two positions:
• Load (position 1–2)—The sample loop is isolated from the solvent stream. Solvent flow
from the LC pump enters and exits the valve through ports 5 and 6, respectively. When
you load the sample into port 2, the sample enters and exits the sample loop through
ports 1 and 4, respectively. As you overfill the sample loop, the excess sample exits the
valve through port 3 to waste.
• Inject (position 1–6)—The sample loop is open to the solvent stream. The solvent flow
from the LC pump flushes sample out of the sample loop, and then exits through port 6
into the API source.
In the divert valve configuration, the valve switches between these two positions:
• Detector (position 1–2)—Solvent flow from the LC pump enters the valve through
port 5 and exits through port 6 into the API source.
• Waste (position 1–6)—Solvent flow from the LC pump enters the valve through port 5
and exits through port 4 to waste.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 47
5
Waste Waste
API sourceLC pump
LC pump
API source
Loop injector
(Position 1–2 with load configuration)
Sample input
Divert valve
(Position 1–2 with detector configuration)
Sample loop
Valve control buttons
Valve position indicator
Six-port, two-position valve
Syringe Pump and Divert/Inject Valve
Divert/Inject Valve
Figure 33. Divert/inject valve plumbed as a loop injector and as a divert valve
2
3
4
Controlling the Divert/Inject Valve
You can control the divert/inject valve as follows:
• Use the MS’s data system to specify the parameters in the Divert Valve Properties pane in
the Method Editor. For instructions, refer to the Method Editor Help.
• Use the valve’s control buttons (Figure 34) to divert the LC flow between the mass
spectrometer and waste when the valve is in the divert valve configuration, or switch
between load and inject modes when the valve is in the loop injector configuration. For
instructions, refer to the manufacturer’s manual.
1
6
5
2
3
4
1
6
5
Figure 34. Modular divert/inject valve (front view)
48 Orbitrap Fusion Series Hardware Manual Thermo Scientific
6
System Shutdown, Startup, and Reset
When you are not using the Orbitrap Fusion Series system for short periods of time, place the
mass spectrometer in standby mode. For longer periods, for example, two or more months,
you can shut it down completely. In addition, many maintenance procedures for the
Orbitrap Fusion Series system require shutting down the mass spectrometer completely.
Contents
• Shutting Down the System in an Emergency
• Placing the Mass Spectrometer in Standby Mode
• Turning On the Mass Spectrometer
• Shutting Down the Mass Spectrometer Completely
• Starting the System after a Complete Shutdown
• Resetting the Mass Spectrometer
• Resetting Calibration Parameters
• Restarting the Data System
• On/Off Status for MS Components Under Varying Power Conditions
Shutting Down the System in an Emergency
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 (Figure 3). This switch turns off all
power to the mass spectrometer, including the forepump, without harming components
within the instrument. However, do not use this method as part of the standard shutdown
procedure. Instead, see “Shutting Down the Mass Spectrometer Completely.”
To turn off the LC, autosampler, and data system computer in an emergency, use their
respective on/off switch or button.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 49
6
System readback statusThree power mode icons
(on/standby/off])
System Shutdown, Startup, and Reset
Placing the Mass Spectrometer in Standby Mode
Placing the Mass Spectrometer in Standby Mode
If you are temporarily not using the Orbitrap Fusion Series MS, you do not need to shut it
down completely. Instead, place the mass spectrometer in standby mode.
To place the mass spectrometer in Standby mode
1. Complete all data acquisition, if any.
2. On the Windows taskbar, choose Start > All Programs > Thermo Instruments >
model x.x > model Tun e to open the Tune window (Figure 35).
Figure 35. Thermo Tune window (Orbitrap Fusion MS)
50 Orbitrap Fusion Series Hardware Manual Thermo Scientific
6
Select this
check box.
Start and Stop
buttons
System Shutdown, Startup, and Reset
Placing the Mass Spectrometer in Standby Mode
3. If your LC/MS system includes an LC pump, turn off the liquid flow to the API source.
When controlling the LC pump through the Xcalibur data system, use the Direct Control
dialog box to turn off the solvent flow. For example, to turn off the solvent flow from an
Accela™ pump, do the following:
a. In the Xcalibur Instrument Setup window, click the icon for the LC pump.
b. In the menu bar, choose pump model > Direct Control to open the Direct Control
dialog box (Figure 36).
Figure 36. Direct Control dialog box (Instrument Setup window)
c. Click the tab for the LC pump, and then select the Tak e Pu mp Un d e r C o n tr o l
check box.
d. Click the Stop button.
4. In the Tune window, place the mass spectrometer in Standby mode.
The center of the selected power mode icon changes from white to green. The System
LED on the front panel turns yellow. To keep the API source clean, the mass spectrometer
reduces the auxiliary and sheath gas flows to their standby default settings (2 arbitrary).
The mass spectrometer turns off the electron multiplier, conversion dynodes, 8 kV power
to the API source, main RF voltage, and ion optic RF voltages. For a more complete list,
see “On/Off Status for MS Components Under Varying Power Conditions.”
CAUTION Hot surface. Allow heated components to cool to room temperature
(approximately 20 minutes) before you touch or service them.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 51
6
System Shutdown, Startup, and Reset
Turning On the Mass Spectrometer
Turning On the Mass Spectrometer
To turn on the mass spectrometer
1. Open the Tune window.
2. Click the On icon to place the mass spectrometer in On mode.
The center of the selected power mode icon changes from white to green. The System
LED on the front panel turns green. The high voltage to the electron multiplier turns on.
Shutting Down the Mass Spectrometer Completely
Shut down the Orbitrap Fusion Series MS completely only when you are not using it for an
extended period of time or when you must shut it down for maintenance or service. You do
not need to shut down the system completely if you are not going to use it temporarily, such
as overnight or through the weekend. Instead, place the system in standby mode as described
in “Placing the Mass Spectrometer in Standby Mode.”
CAUTION Hot surface. Allow heated components to cool to room temperature
(approximately 20 minutes) before you touch or service them.
To shut down the mass spectrometer completely
1. Follow the procedure, “Placing the Mass Spectrometer in Standby Mode.”
2. Place the electronics service switch in the Service Mode (down) position.
This turns off the power to the nonvacuum system electronics.
3. Turn off the Main Power switch.
The following occurs:
• All power to the mass spectrometer, including the turbomolecular pumps and the
one or two forepumps, turn off. All LEDs on the front panel are off.
• After approximately 5 seconds, power to the vent valve solenoid shuts off, the vent
valve opens, and the vacuum manifold vents with dry nitrogen. You can hear a
hissing sound.
• After about 2 minutes, the vacuum manifold is at atmospheric pressure.
4. Unplug the mass spectrometer’s power supply cord from the electrical outlet.
CAUTION Do not disconnect the power supply cord at the mass spectrometer while
the other end is still plugged into the electrical outlet.
52 Orbitrap Fusion Series Hardware Manual Thermo Scientific
6
System Shutdown, Startup, and Reset
Starting the System after a Complete Shutdown
5. (Optional) Follow the next procedure, “To turn off the LC, gases, data system, and
autosampler.”
Tip If you only plan to perform routine or preventive system maintenance on the
mass spectrometer, you do not need to turn off the LC, gases, data system, and
autosampler. In this case, the shutdown procedure is complete. However, if you plan
to have the system off for an extended period of time, Thermo Fisher Scientific
recommends that you also turn off these other parts of the LC/MS system.
To turn off the LC, gases, data system, and autosampler
1. If included, turn off the LC system as described in the LC manual.
2. Turn off the helium and nitrogen gas supplies at their tanks.
3. Shut down the data system computer, and turn off the monitor and printer, if provided.
4. If included, turn off the autosampler by using its On/Off switch.
Starting the System after a Complete Shutdown
To start the Orbitrap Fusion Series system after it has been shut down completely, follow these
procedures:
• Starting the LC System
• Starting the Data System
• Starting the Mass Spectrometer
• Starting the Autosampler (if this is a part of the system)
Starting the LC System
To start the LC system, follow the startup procedure described in the manufacturer’s manual.
Note Do not turn on the liquid flow to the mass spectrometer at this point in the
procedure.
Starting the Data System
To start the data system
Turn on the computer, monitor, and printer, if provided.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 53
6
System Shutdown, Startup, and Reset
Starting the System after a Complete Shutdown
Starting the Mass Spectrometer
Make sure that the data system is running before starting the mass spectrometer. The mass
spectrometer does not operate until it receives instructions from the data system.
To start the mass spectrometer
1. Turn on the flows for the helium and nitrogen gases at their tanks, if they are off.
2. Turn off the Main Power switch and place the electronics service switch in the Service
Mode (down) position.
3. Plug in the power supply cord for the mass spectrometer.
4. Turn on the Main Power switch.
This turns on the forepump and the turbomolecular pumps. All LEDs on the front panel
are off.
5. If the mass spectrometer was turned off for an extended period of time, follow the
procedures in section “Pumping Down the Mass Spectrometer,” in Chapter 5 of the
Orbitrap Fusion Series Getting Started Guide. Otherwise, wait at least 1 hour to allow the
mass spectrometer to pump down.
6. Place the electronics service switch in the Operating Mode (up) position.
The following occurs:
• The Power LED on the front panel turns green to indicate that the electronics have
power. However, the electron multiplier, conversion dynodes, 8 kV power to the API
source, main RF voltage, and ion optic RF voltage remain off.
• After several more seconds, the Communication LED turns green to indicate that the
mass spectrometer and the data system are communicating. Make sure that the
instrument console window is active. The data system transfers operational software
to the mass spectrometer.
54 Orbitrap Fusion Series Hardware Manual Thermo Scientific
6
System Shutdown, Startup, and Reset
Resetting the Mass Spectrometer
• After 3 minutes, the System LED turns yellow to indicate the software transfer from
the data system to the mass spectrometer is complete and that the mass spectrometer
is in standby mode. When you change the mode from standby to on, the System
LED turns green to indicate that the mass spectrometer is functional and the high
voltages are on.
IMPORTANT On the front panel, the Vacuum LED illuminates green only when
these gauges are on and register below the indicated pressure threshold:
• Source Pressure gauge—Below 3.0 Torr (Orbitrap Fusion MS) or 4.5 Torr
(Orbitrap Fusion Lumos MS) as applicable
• Ion Gauge Pressure gauge—Below 1.5 × 10
• UHV Pressure gauge (Orbitrap)—Below 5 × 10
Although you can calibrate the mass spectrometer after the vacuum LED turns
green, you must allow the mass spectrometer’s vacuum system to stabilize
completely, which takes approximately 15–24 hours of continuous pumping, to
ensure that the calibrations are correct.
Starting the Autosampler
Turn on the autosampler by using its on/off power switch. If necessary, configure the
autosampler. For procedures for placing sample vials, preparing solvent and waste containers,
installing syringes, and so on, refer to the autosampler manual. The Orbitrap Fusion Series
Getting Connected Guide provides procedures for connecting the mass spectrometer to the
autosampler by using a contact closure cable.
Resetting the Mass Spectrometer
In the unlikely event that communication is lost between the mass spectrometer and data
system computer, you can reset the mass spectrometer by using the reset button located on the
left-side communications panel.
–4
Torr
–8
Tor r
The following procedure assumes that power to the mass spectrometer and data system
computer are on and that both are operational. If the mass spectrometer, data system
computer, or both are off, see “Starting the System after a Complete Shutdown.”
Thermo Scientific Orbitrap Fusion Series Hardware Manual 55
6
System Shutdown, Startup, and Reset
Resetting Calibration Parameters
To reset the mass spectrometer
Hold down the reset button for 3 seconds.
The following occurs:
• The embedded computer restarts. All LEDs on the front panel turn off except the
Power LED.
• After several more seconds, the Communication LED turns green to indicate that the
mass spectrometer and the data system are communicating. The data system transfers
operational software to the mass spectrometer.
• After 3 minutes, the System LED turns yellow to indicate that the software transfer
from the data system to the mass spectrometer is complete and that the mass
spectrometer is in standby mode. Or, the System LED turns green to indicate that the
mass spectrometer is functional and the high voltages are on.
Resetting Calibration Parameters
If you must reset the calibration parameters to their factory default values, contact your local
Thermo Fisher Scientific service engineer for assistance.
IMPORTANT
• Before resetting the instrument parameters to their default values, make sure that the
system problems you are experiencing are not due to improper API source settings
(such as spray voltage, sheath and auxiliary gas flow, or ion transfer tube temperature).
• If you reset the instrument to the factory calibration settings, always repeat the
calibration of the internal electronic devices as specified in the Orbitrap Fusion Series
Getting Started Guide. Otherwise, all instrument calibrations might produce incorrect
results.
56 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Restarting the Data System
If possible, use the Windows restart procedure to shut down and restart the data system so
that Windows can properly close applications and save changes to any open Thermo
application.
Note After you reset the data system, the communications link between the data system
and the mass spectrometer is automatically reestablished. When this occurs, the
Communication LED turns yellow and then green. If the system is unable to reestablish
the communications link, hold down the reset button for 3 seconds.
To restart the data system by using Windows
1. On the Windows taskbar, choose Start, and then click the arrow next to Shut Down.
2. Choose Restart, and then click OK.
To restart the data system by using the power button
6
System Shutdown, Startup, and Reset
Restarting the Data System
1. Press the power button on the data system computer.
2. Wait at least 20 seconds after the computer shuts down.
3. Press the power button again.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 57
6
System Shutdown, Startup, and Reset
On/Off Status for MS Components Under Varying Power Conditions
On/Off Status for MS Components Under Varying Power Conditions
Ta bl e 7 summarizes the on/off status of mass spectrometer components, voltages, and API gas
flows.
Table 7 . On/off status of mass spectrometer components, voltages, and API gas flows (Sheet 1 of 2)
Mass spectrometer component
Standby
mode
Off
mode
Electronics
service switch,
Service Mode position
Main Power switch,
Off (O) position
Vent valve Closed Closed Closed Open (5 sec)
APPI lamp
On On
APCI corona discharge needle
Conversion dynode
Off
Electron multiplier
Spray voltage
Vaporizer temperature
Gas, nitrogen (collision)
Gases, auxiliary, sheath, and sweep
Gauge, linear ion trap chamber
a
Off
Ion optics lenses DC offset voltages
Ion optics multipoles DC offset voltages
Ion optics multipoles RF voltages
Off
Ion transfer tube DC offset
Off
Ion transfer tube temperature
Mass analyzers (all), DC offset voltages
Mass analyzers (Q1 and LIT),
On
RF/waveform voltages
Power supply, 300 Vdc
Fans, RF coils
Gauge, Orbitrap (UHV) chamber
Gauges, source and ion-routing multipole
Power supply, PS1
On
Fans, electronics tower
OnFans, internal
Fans, turbomolecular pumps
58 Orbitrap Fusion Series Hardware Manual Thermo Scientific
6
System Shutdown, Startup, and Reset
On/Off Status for MS Components Under Varying Power Conditions
Table 7 . On/off status of mass spectrometer components, voltages, and API gas flows (Sheet 2 of 2)
Mass spectrometer component
Standby
mode
Off
mode
Electronics
service switch,
Service Mode position
Main Power switch,
Off (O) position
Forepump (one or two)
Power supply, PS2
Turbomolecular pumps
On On On
Turbomolecular pump controller
Gas, helium On
a
In standby mode, the Tune application sets the API gases to their standby default settings (2 arbitrary) to keep the API source clean.
Off
Thermo Scientific Orbitrap Fusion Series Hardware Manual 59
6
System Shutdown, Startup, and Reset
On/Off Status for MS Components Under Varying Power Conditions
60 Orbitrap Fusion Series Hardware Manual Thermo Scientific
7
Daily Operation
To ensure the proper operation of the Orbitrap Fusion Series system, Thermo Fisher
Scientific recommends that you perform daily preventive maintenance. This chapter specifies
the items to check before operating the system and the cleaning procedures to perform after
completing the analyses.
Clean the ion sweep cone, the spray cone, and the ion transfer tube on a regular basis to
prevent corrosion and to maintain optimum performance of the API source; see “Cleaning
the Ion Sweep Cone, Spray Cone, and Ion Transfer Tube” on page 72. If you use a mobile
phase that contains a nonvolatile buffer or inject high concentrations of sample, you might
need to clean these parts more often. It is not necessary to vent the system to flush the ion
sweep cone and ion transfer tube.
Note You do not need to calibrate the Orbitrap Fusion Series system as part of your daily
routine. Generally, you must calibrate the mass spectrometer every one to three months of
operation for optimum performance over the entire mass range of the mass detector.
For information about calibration, refer to the Orbitrap Fusion Series Getting Started
Guide.
Contents
• Before Operating the Orbitrap Fusion Series System
• After Operating the Orbitrap Fusion Series System
Thermo Scientific Orbitrap Fusion Series Hardware Manual 61
7
Daily Operation
Before Operating the Orbitrap Fusion Series System
Before Operating the Orbitrap Fusion Series System
Follow these preventive maintenance procedures every day before beginning the first analysis:
• Checking the System Mode
• Checking the Vacuum Pressure Levels
• Checking the Gas Supplies
Checking the System Mode
Make sure that the system is turned on. See “Turning On the Mass Spectrometer” on page 52.
Checking the Vacuum Pressure Levels
Before beginning your daily operation, check the vacuum pressure levels in the system and
check for major air leaks in the system. If there is a major air leak, the system does not pump
down to sufficient levels to turn on the system. In the Tune window, a green square, ,
indicates that the readback value is good.
CAUTION For proper performance, operate the Orbitrap Fusion Series system at the
proper vacuum levels. Operating the system with poor vacuum levels can cause reduced
sensitivity and reduced electron multiplier life.
To check the vacuum pressures
Make sure that the Vacuum LED on the front of the mass spectrometer is green, which
indicates that the pressure gauges are within their threshold values.
IMPORTANT
•See page 55 for the gauges’ threshold values. If the readback values are higher
than normal, there might be an air leak or the helium flow might be insufficient.
–8
• If the UHV pressure is above 5 × 10
restarted within the last 30 to 60 minutes, wait another 30 minutes and recheck
the pressure. If the pressure decreases with time, check the pressure periodically
until it is within the typical range for the mass spectrometer.
• If the pressure remains high, the system might have an air leak.
To check the system for major air leaks
Listen for a rush of air or a hissing sound coming from the mass spectrometer.
Torr in the analyzer region and the system
Possible causes of a major leak might be a loose or disconnected fitting, an improperly
positioned O-ring, or an open valve.
62 Orbitrap Fusion Series Hardware Manual Thermo Scientific
To fix an air leak
1. Shut down the system (see “Shutting Down the Mass Spectrometer Completely” on
page 52).
2. Visually inspect the vacuum system and vacuum lines for leaks.
3. Check each fitting and flange on the system for tightness, and tighten the fittings or
flanges that are loose.
Do not tighten fittings indiscriminately. Pay particular attention to fittings that have been
changed recently or to fittings that have been subjected to heating and cooling.
Checking the Gas Supplies
Check the helium gas tank’s regulator. Make sure that there is sufficient gas for the analysis,
which is a minimum of 3447 kPa (500 psi) on the high pressure gauge of the regulator. If
necessary, replace the tank. Verify that the pressure of helium gas reaching the mass
spectrometer is 275 ±70 kPa (40 ±10 psi). If necessary, adjust the pressure with the tank
pressure regulator.
7
Daily Operation
Before Operating the Orbitrap Fusion Series System
Check the nitrogen gas supply on the regulator of the nitrogen gas tank or liquid nitrogen
boil-off tank. Make sure that there is sufficient gas for the analysis. If necessary, replace the
tank. Verify that the pressures of nitrogen gases reaching the mass spectrometer are as follows:
• 690 ±140 kPa (100 ±20 psi) for the HP nitrogen gas pressure
• 345 ±70 kPa (50 ±10 psi) for the UHP nitrogen gas pressure
If necessary, adjust the pressures with the tank pressure regulators.
Note When operating 24 hours and 7 days a week, typical daily consumption of nitrogen
gas is as follows:
3
• UHP nitrogen: approximately 46 L/day (1.62 ft
• HP nitrogen: 11500–26 700 L (406–943 ft
)
3
)
For more information about gas requirements, refer to the Orbitrap Fusion Series
Preinstallation Requirements Guide.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 63
7
Daily Operation
After Operating the Orbitrap Fusion Series System
After Operating the Orbitrap Fusion Series System
Follow these preventive maintenance procedures every day after operating the system:
• Flushing the Inlet Components (as needed)
• Purging the Oil in the Forepump
• Emptying the Solvent Waste Container
• Placing the System in Standby Mode
Flushing the Inlet Components
This section describes how to flush the syringe and the inlet components (sample transfer line,
sample tube, and spray insert) at the end of each work day (or more often if you suspect they
are contaminated). You can also use an LC pump to flush the 50:50 methanol/water solution
through the inlet components to the API source at a flow rate of 200–400 μL/min for
approximately 15 minutes.
Tip You do not need to flush the inlet components daily. However, if a mass spectrum
shows unwanted contamination peaks, follow this procedure.
CAUTION When the mass spectrometer’s ion transfer tube is installed, do not flush it with
cleaning solution, which flushes the residue into the mass spectrometer.
To flush the inlet components
1. Turn off the liquid flow from the syringe pump.
2. Place the mass spectrometer in Standby mode.
3. Remove the syringe from the syringe pump as follows:
a. Lift the syringe holder off of the syringe.
b. Press the pusher block’s release knob and slide the block to the left.
c. Remove the syringe from the holder.
d. Carefully remove the syringe needle from the Teflon tube on the syringe adapter
assembly.
4. Clean the syringe as follows:
a. Rinse the syringe with a solution of 50:50 methanol/water.
b. Rinse the syringe with acetone several times.
64 Orbitrap Fusion Series Hardware Manual Thermo Scientific
5. Flush the sample transfer line, sample tube, and spray insert as follows:
a. Load the cleaned syringe with a solution of 50:50 methanol/water (or another
appropriate solvent).
b. Carefully reinsert the syringe needle into the Teflon tube on the syringe adapter
assembly.
c. Slowly depress the syringe plunger to flush the solution through the sample transfer
line, sample tube, and spray insert.
d. Remove the syringe needle from the syringe adapter assembly.
This completes the procedure to flush the inlet components.
Purging the Oil in the Forepump
Purge (decontaminate) the oil in the forepump daily to remove water and other dissolved
chemicals, which can cause corrosion and decrease the lifetime of the forepump. For
instructions, refer to the forepump’s documentation.
7
Daily Operation
After Operating the Orbitrap Fusion Series System
The best time to purge the oil is at the end of the working day after you flush the inlet
components. Remember to close the purge valve before continuing normal operation.
Emptying the Solvent Waste Container
Check the solvent level in the solvent waste container daily. If necessary, empty the container
and dispose of the solvent waste in accordance with local and national regulations.
Placing the System in Standby Mode
After you complete the daily maintenance procedures, place the mass spectrometer in standby
mode as described in “Placing the Mass Spectrometer in Standby Mode” on page 50.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 65
7
Daily Operation
After Operating the Orbitrap Fusion Series System
66 Orbitrap Fusion Series Hardware Manual Thermo Scientific
8
Maintenance
This chapter provides routine maintenance procedures that you must perform to ensure
optimum performance of the Orbitrap Fusion Series MS. Optimum performance depends on
the maintenance of all parts of the instrument. You are responsible for maintaining the system
properly by performing the system maintenance procedures on a regular basis.
For a list of replaceable parts, see Chapter 9, “Replaceable Parts.”
Note The following components are slightly different between the Orbitrap Fusion MS
and the Orbitrap Fusion Lumos MS: sweep cone, ion transfer tube, API source interface,
RF lens, MP00 RF lens, lens L0. Unless otherwise noted, use the Orbitrap Fusion MS
procedures.
CAUTION 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. For additional
information, contact your local Thermo Fisher Scientific field service engineer.
Contents
• Maintenance Schedule
• Guidelines
• Tools and Supplies
• Maintaining the API Source Housing
• Maintaining the API Source Interface
• Maintaining the Forepump
• Maintaining the Air Filter
Thermo Scientific Orbitrap Fusion Series Hardware Manual 67
8
Maintenance
Maintenance Schedule
Maintenance Schedule
Ta bl e 8 lists the maintenance procedures and their recommended frequency.
Table 8 . Mass spectrometer maintenance procedures and frequency
MS component Procedure Recommended frequency Reference
API source
(EASY-Max NG)
Flush (clean) the sample transfer
line, sample tube, and spray insert.
Clean the API source housing.
Clean the APPI fan filter.
Replace the APPI lamp.
Replace the H-ESI needle insert. If the metal needle is obstructed
Replace the APCI fused-silica
tubing.
API source interface Clean the ion sweep cone and spray
cone.
Remove and clean the ion transfer
tube.
Replace the ion transfer tube. If the bore becomes corroded or
Clean the exit lens
a
or RF lens.
Clean the MP00 RF lens and lens
L0.
Daily page 64
page 71
As needed
Ion Max NG and
EASY-Max NG
Ion Sources User
If the tubing is obstructed
Guide
Daily, or more often depending on
analytical conditions
Weekly, or if the ion transfer tube
bore is contaminated or
page 72
obstructed
blocked
As needed, depending on
analytical conditions
page 79
As needed, depending on
analytical conditions
Forepump (each) Purge (decontaminate) the oil and
Daily
check for leaks.
Add oil. As needed, based on oil level
Manufacturer’s
manual
Change the oil. Every 12 months of typical use, or
if the oil is cloudy or discolored
Cooling fans Clean the air filter. Every 4 months page 84
a
The exit lens is not installed in instruments with the Internal Calibration or ETD option.
For instructions about maintaining the LC modules, refer to that instrument’s manual.
68 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Guidelines
8
Maintenance
Guidelines
For optimal results, follow these guidelines when performing the procedures in this chapter:
• Always wear a new pair of lint- and powder-free gloves when handling internal
components. Never reuse gloves after you remove them because the surface contaminants
on them recontaminate clean parts.
• Always place the components on a clean, lint-free work surface.
• Have nearby the necessary tools, supplies, and replacement parts (when applicable).
• Never overtighten a screw or use excessive force.
• Proceed methodically.
IMPORTANT
• Put on a new pair of lint- and powder-free gloves before starting each removal,
cleaning, and reinstallation procedure.
• Make sure that you do not introduce any scratches or surface abrasions while
Tools and Supplies
The Orbitrap Fusion Series MS requires very few tools to perform routine maintenance
procedures. You can remove and disassemble many of the components by hand. Tab l e 9 lists
the necessary chemicals, tools, and equipment for maintaining the instrument. (One of the
tools is in the Calibration Kit.) In addition, you can use the contents of the PM Cleaning Kit
(P/N 70111-62112).
handling the API source interface components. Even small scratches can affect
performance if they are close to the ion transmission path. Avoid using tools, such as
metal pliers, that might scratch these components.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 69
8
Maintenance
Tools and Supplies
CAUTION Avoid exposure to potentially harmful materials.
By law, producers and suppliers of chemical compounds are required to provide their
customers with the most current health and safety information in the form of Material
Safety Data Sheets (MSDSs) or Safety Data Sheet (SDS). The MSDSs and SDSs must be
freely available to lab personnel to examine at any time. These data sheets describe the
chemicals and summarize information on the hazard and toxicity of specific chemical
compounds. They also provide information on the proper handling of compounds, first
aid for accidental exposure, and procedures to remedy spills or leaks.
Read the MSDS or SDS for each chemical you use. Store and handle all chemicals in
accordance with standard safety procedures. Always wear protective gloves and safety
glasses when you use solvents or corrosives. Also, contain waste streams, use proper
ventilation, and dispose of all laboratory reagents according to the directions in the MSDS
or SDS.
Table 9 . Chemicals, tools, and equipment (Sheet 1 of 2)
Description Part number
Chemicals
Acetone
HPLC grade Fisher Scientific™ A949
GC Resolv Fisher Scientific A928-4
(amber glass, 4L)
Detergent (for example, Liquinox™) (Liquinox) Fisher Scientific:
• 50-821-299 (1 quart)
• 50-821-298 (1 gallon)
Methanol, UHPLC/MS-grade Fisher Scientific A458-1
Nitrogen gas, clean and dry –
Water, LC/MS-grade Fisher Scientific W8-1
Tools
Ion transfer tube removal toolsa:
• Orbitrap Fusion MS
• Orbitrap Fusion Lumos MS
70111-20258
70005-20972
Screwdriver, Phillips #2 (M3) –
(Optional) Toothbrush, soft (or similar tool) –
(Optional) Tweezers, plastic (or similar tool) –
70 Orbitrap Fusion Series Hardware Manual Thermo Scientific
8
Maintenance
Maintaining the API Source Housing
Table 9 . Chemicals, tools, and equipment (Sheet 2 of 2)
Description Part number
Equipment
Beaker or graduated cylinder (for use with methanol) –
Chamois-tipped swabs 00725-01-00028
Gloves, lint-free and powder-free Fisher Scientific 19-120-2947
Unity Lab Services:
• 23827-0008 (size medium)
• 23827-0009 (size large)
Industrial tissues, lint-free –
Magnification device –
b
MICRO-MESH™ polishing swabs, 6000 grit (light
purple color), 2.25 in. long
Sonicator –
a
Provided in the Source Installation Kit
b
Multiple sizes are available.
Maintaining the API Source Housing
Only Thermo Fisher Scientific service engineers can service the API source housing, while
user maintenance is limited to cleaning the housing as necessary. Follow all safety precautions
in the Ion Max NG and EASY-Max NG Ion Sources User Guide regarding the installation and
removal of the API source. For any additional service, contact your local Thermo Fisher
Scientific service engineer.
IMPORTANT Prevent damage: Remove or install the API source’s drain insert by pressing
a small, slotted screwdriver against the insert’s tab.
To clean the API source housing
1. After the API source cools to room temperature, remove it from the mass spectrometer.
00725-01-00027
2. Put on appropriate eye-wear and gloves.
3. In an appropriate fume hood, rinse the interior of the housing with LC/MS-grade
methanol.
4. Allow the housing to dry before you install it on the mass spectrometer.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 71
8
Maintenance
Maintaining the API Source Interface
Maintaining the API Source Interface
While you or the service engineer can remove and service the API source interface, only the
service engineer may service the other internal components.
To maintain the API source interface, follow these procedures:
• Cleaning the Ion Sweep Cone, Spray Cone, and Ion Transfer Tube
• Removing the API Source Interface
• Cleaning the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0
• Reinstalling the API Source Interface
Note Before you continue, read the precautions in “Special Notices, Symbols, and
Cautions” on page xiv.
IMPORTANT
• Prepare a clean work surface by covering the area with lint-free paper.
• Put on a new pair of lint- and powder-free gloves before starting each of these
removal, cleaning, and reinstallation procedures.
Cleaning the Ion Sweep Cone, Spray Cone, and Ion Transfer Tube
Because buffer salts or high concentrations of sample can cause blockages, you must clean the
bore of the ion transfer tube. If pressure in the ion transfer tube and RF lens region (as
measured by the Source Pressure gauge) drops considerably below 1 Torr, a blocked ion
transfer tube is likely.
Tip You do not have to vent the system to remove the ion transfer tube.
Follow these procedures:
1. To remove the ion transfer tube
2. To clean the spray cone and O-ring
3. To clean the ion transfer tube
4. To clean the ion sweep cone
72 Orbitrap Fusion Series Hardware Manual Thermo Scientific
8
Select this
check box.
Start and Stop
buttons
Maintenance
Maintaining the API Source Interface
To remove the ion transfer tube
CAUTION Hot surface. The external surface of the spray insert and API source
housing can become hot enough to burn your skin. Before you touch or remove
heated parts, allow the part to cool to room temperature (approximately 20 minutes)
before you touch it.
1. If your LC/MS system includes an LC pump, turn off the liquid flow to the API source as
follows:
a. In the Xcalibur Instrument Setup window, click the icon for the LC pump.
b. In the menu bar, choose pump model > Direct Control to open the Direct Control
dialog box (Figure 37).
Figure 37. Direct Control dialog box (Instrument Setup window)
c. Click the tab for the LC pump, and then select the Tak e Pu mp Un d e r C o n tr o l
check box.
d. Click the Stop button.
2. Place the mass spectrometer in Off mode.
You can observe the readback temperature for the ion transfer tube on the Ion Source
page in the Ion Source pane.
3. Place the mass spectrometer’s electronics service switch in the Service Mode (down)
position to turn off the nonvacuum system voltages.
The electronics service switch is located on the right side of the instrument.
CAUTION To avoid an electric shock, make sure that the electronics service switch is
in the Service Mode (down) position before proceeding.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 73
8
Release lever for the
API source interface
API cone seal
Ion sweep cone
Maintenance
Maintaining the API Source Interface
4. After the API source cools to room temperature, remove it.
5. Remove the ion sweep cone by grasping its outer ridges and pulling it off of the API cone
seal (Figure 38).
CAUTION
• Make sure that you do not accidentally lift the release lever located at the top of
the API source interface, which will vent the mass spectrometer.
• To avoid contaminating the ion transfer tube, do not touch its exposed entrance.
Figure 38. Ion sweep cone removed from the MS mount assembly (Orbitrap Fusion MS)
74 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Maintaining the API Source Interface
Fit this end of the tool around the
exposed ion transfer tube.
API source interface
6. To remove the ion transfer tube, do one of the following:
• (Orbitrap Fusion MS) Align the flat edges (hook) of the custom removal tool with
the flat edges on the exposed tip of the ion transfer tube (Figure 39), and then rotate
the tool counterclockwise. When the tube is free of the spray cone, use the hook on
the tool to pull it straight out of the API source interface.
Figure 39. Ion transfer tube removal tool (Orbitrap Fusion MS)
–or–
8
Maintenance
• (Orbitrap Fusion Lumos MS) Turn the ion transfer tube with the custom removal
tool (Figure 40) until you can pull it free from the API source interface.
Tip If necessary, insert a hex key through a side hole for leverage.
Figure 40. Ion transfer removal tool (Orbitrap Fusion Lumos MS)
Thermo Scientific Orbitrap Fusion Series Hardware Manual 75
8
Spray cone
Ion transfer tube
API cone seal
Gas inlet on the ion
sweep cone
Vespel™ O-ring
Maintenance
Maintaining the API Source Interface
To clean the spray cone and O-ring
1. Soak the lint-free tissues or chamois-tipped swabs in a 50:50 solution of methanol/water,
2. (Orbitrap Fusion MS) Remove and inspect the O-ring located in the spray cone under
Note The Orbitrap Fusion Lumos MS does not have an O-ring behind its ion
transfer tube.
and then clean the exterior surface of the spray cone.
the entrance end of the ion transfer tube (Figure 41).
Figure 41. Spray cone, O-ring, ion transfer tube, and ion sweep cone (Orbitrap Fusion MS)
3. (Orbitrap Fusion MS) Clean the O-ring with methanol or replace it if necessary.
4. Using a magnification device, inspect the components for any residual lint or particulates.
5. (Orbitrap Fusion MS) Reinstall the O-ring in the spray cone.
To clean the ion transfer tube
1. If there is extreme contamination, follow these steps. If not, start with step 2.
Note Inspect the inside surfaces and edges to confirm that no lint or particulates are
present. Use plastic tweezers or a similar tool to remove the lint or particulate.
IMPORTANT Always use LC/MS-grade methanol and LC/MS-grade water.
a. Overnight, sonicate the component in a 10% solution of Liquinox in water.
b. Rinse the component with water, and then for 2 minutes force a strong stream of
water through the orifice.
c. For 30 minutes, sonicate the component in water.
76 Orbitrap Fusion Series Hardware Manual Thermo Scientific
8
Maintenance
Maintaining the API Source Interface
2. For 30 minutes, sonicate the component in a 50:50 solution of methanol/water that
contains 20% formic acid.
3. Rinse the component thoroughly with water.
4. For 15 minutes, sonicate the component in deionized water.
5. Rinse the component with methanol.
6. For 15 minutes, sonicate the component in methanol.
7. Dry the component with nitrogen gas until it is dry.
Replace the ion transfer tube if the bore becomes corroded or blocked.
CAUTION When you reinstall the ion transfer tube into the heater block, take these
precautions:
• Put on a new pair of lint- and powder-free gloves.
• Verify that everything is properly aligned to prevent stripping the threads on the ion
transfer tube.
• Do not bend the ion transfer tube. Rotate it as you insert it.
To clean the ion sweep cone
1. Soak lint-free tissues or chamois-tipped swabs in a 50:50 solution of methanol/water, and
then clean both sides of the ion sweep cone.
2. For 10 minutes, sonicate the component in either a 50:50 solution of methanol/water or
a 1% solution of Liquinox in water.
3. Rinse the component thoroughly with water.
4. Sonicate the component in water for 10 minutes.
5. Sonicate the component in methanol for 10 minutes.
6. Rinse the component with methanol.
7. Dry the component with nitrogen gas to make sure that all the solvent evaporates.
8. Using a magnification device, inspect the component for any residual lint or particulates.
After you clean and reinstall these components, turn on the nonvacuum system voltages by
placing the mass spectrometer's electronics service switch in the Operating Mode (up)
position.
Tip If you successfully unblocked the ion transfer tube, check that the Source Pressure
reading has increased to a normal value (approximately 1.5–2.5 Torr). If trying this
method does not clear the blockage, replace the ion transfer tube.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 77
8
Release latch on the
API source interface
Vacuum manifold
Viton™ O-ring
Maintenance
Maintaining the API Source Interface
Removing the API Source Interface
To remove the API source interface
CAUTION To avoid an electrical shock, be sure to follow the instructions in “Shutting
Down the Mass Spectrometer Completely” on page 52 before continuing with this
procedure.
1. Shut down and vent the system, and let it cool to room temperature.
Venting the mass spectrometer can take several minutes.
CAUTION Hot surface. Allow heated components to cool to room temperature
(approximately 20 minutes) before you touch or service them.
2. Unplug the mass spectrometer’s power supply cord from the electrical outlet.
CAUTION Do not disconnect the power supply cord at the mass spectrometer while
the other end is still plugged into the electrical outlet.
3. Remove the API source housing.
4. Lift up the release latch, grasp the API source interface with your fingers, and then
carefully pull it out of the vacuum manifold (Figure 42).
Figure 42. API source interface removed from the vacuum manifold (Orbitrap Fusion MS)
78 Orbitrap Fusion Series Hardware Manual Thermo Scientific
Cleaning the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0
Lens L0
Chemicals can accumulate on the surfaces of the RF lens, exit lens, MP00 RF lens, and lens
L0. However, the use of an RF lens that incorporates an RF electric field minimizes the
harmful effects of this contamination. The lenses require cleaning less often than the ion
sweep cone and the ion transfer tube. How frequently you clean these lenses depends on the
type and quantity of the compounds that you analyze. Remove the lenses from the API source
interface cage before cleaning them. No tools are needed to remove or install these
components.
Note The exit lens is not installed in instruments with the Internal Calibration or ETD
option.
To clean the RF lens, exit lens, MP00 RF lens, and lens L0, follow these procedures:
1. To remove the RF lens, exit lens, MP00 RF lens, and lens L0
2. To clean the RF lens, exit lens, MP00 RF lens, and lens L0
8
Maintenance
Maintaining the API Source Interface
3. To reinstall the RF lens and exit lens
4. To reinstall the MP00 RF lens and lens L0
5. To reinstall the API source interface
To remove the RF lens, exit lens, MP00 RF lens, and lens L0
1. Remove the API source interface (see page 78).
2. Using the plastic tweezers along the outer edge of lens L0, rotate the lens
counterclockwise to remove it (Figure 43).
Figure 43. Lens L0 removed from the back of the API source interface (Orbitrap Fusion MS)
Thermo Scientific Orbitrap Fusion Series Hardware Manual 79
8
MP00 RF lens
Thumbscrews
Exit lensAPI source interface cage
RF lens assembly
Maintenance
Maintaining the API Source Interface
3. Loosen and extend the two thumbscrews on the back of the API source interface, and
then remove the MP00 RF lens (Figure 44).
Figure 44. MP00 RF lens assembly removed from the API source interface (Orbitrap Fusion
MS)
4. Continue to loosen the two thumbscrews and use them to carefully pull out the RF lens
assembly from the API source interface cage (Figure 45).
Figure 45. RF lens removed from the API source interface cage (Orbitrap Fusion MS)
80 Orbitrap Fusion Series Hardware Manual Thermo Scientific
8
Exit lens
Lead pin through the exit lens
RF lens
Lead pin socket
Maintenance
Maintaining the API Source Interface
5. Loosen the two thumbscrews even further and use them to pull out the exit lens
(Figure 46).
Figure 46. Exit lens removed from the API source interface (Orbitrap Fusion MS)
To clean the RF lens, exit lens, MP00 RF lens, and lens L0
CAUTION Do not clean the lenses with abrasives, acidic or caustic substances, or
detergents not stated in this chapter.
IMPORTANT Always use LC/MS-grade methanol and LC/MS-grade water.
1. Using a magnification device, inspect the components for any lint, particulates, and
sample buildup or coatings.
2. For 10 minutes, sonicate the components in either a 50:50 solution of methanol/water or
a 1% solution of Liquinox in water.
3. If a sonicator is not available, do the following:
• To clean the RF lens, use chamois-tipped swabs with a 1% solution of Liquinox in
water. To clean the areas that you cannot reach with the swab, use the 6000 grit
MICRO-MESH polishing swabs.
• To clean the exit lens, use a soft toothbrush with a 1% solution of Liquinox in water.
4. For the exit lens, MP00 RF lens, and lens L0, use the 6000 grit MICRO-MESH
polishing swabs to clean the bore.
5. Rinse the components thoroughly with water.
6. Sonicate the components in water for 10 minutes.
7. Sonicate the components in methanol for 10 minutes.
8. Rinse the components with methanol.
Thermo Scientific Orbitrap Fusion Series Hardware Manual 81
8
Thumbscrew location
Slot for the lead pin
Maintenance
Maintaining the API Source Interface
9. Dry the components with nitrogen gas to make sure that the solvent evaporates.
10. Using a magnifying device, inspect the components for any residual lint or particulates.
To reinstall the RF lens and exit lens
1. Align the lead pin on the exit lens with the lead pin socket on the RF lens (Figure 46),
2. Tighten the two thumbscrews a few turns into the RF lens.
3. Orient the RF lens as shown in Figure 45, and then carefully slide it into the API source
4. Tighten the two thumbscrews a few turns into the API source interface cage.
To reinstall the MP00 RF lens and lens L0
Note Inspect the orifices to confirm that no lint or particulates are present in the bore
of the orifices. Use plastic tweezers or a similar tool to remove the lint or particulate.
and then firmly press the lens until it snaps into place.
interface cage.
1. Align the MP00 RF lens’s bottom slot (Figure 47) with the lead pin on the exit lens
(Figure 46), and then carefully push the MP00 RF lens onto the exit lens.
Figure 47. Alignment slot and thumbscrew locations on the MP00 RF lens (Orbitrap Fusion
MS)
2. Tighten the two thumbscrews so that they touch the MP00 RF lens.
3. Place lens L0 on the MP00 RF lens.
4. Using the plastic tweezers along the outer edge of lens L0, rotate the lens clockwise to lock
it in place.
82 Orbitrap Fusion Series Hardware Manual Thermo Scientific
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