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Orbitrap Fusion Series
Thermo Orbitrap Fusion Series User Manual
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Orbitrap
Fusion Series
Hardware Manual
80011-97004
Revision B
May 2016
2
Table of Contents
Default Chapter
7
Default Chapter
7
Table of Contents
7
Preface
13
Accessing Documentation
13
Special Notices, Symbols, and Cautions
14
Contacting Us
17
Chapter 1 Introduction
19
Introduction
19
Orbitrap Fusion Series Mass Spectrometers
19
Overview of an LC/MS Analysis
21
LC/MS Functional Block Diagram
22
Controls and Indicators
23
Figure 1. Functional Block Diagram of the Orbitrap Fusion Series MS
23
Figure 2. Orbitrap Fusion Series Front Panel Leds
24
Leds
24
Figure 3. Power Entry Module
25
Power Entry Module
25
Communications Panel
26
Figure 4. Communication Connectors (Left Side of the MS)
26
Electronic Assemblies
23
Cooling Fans
28
Chapter 2 Scan Parameters
29
Scan Types
29
MS Scan
29
MS 2 Scan and MS N Scan
30
SIM Scan
30
Scan Rates for the Ion Trap Detector
30
Scan Mass-To-Charge Ratio Ranges
31
Resolutions for the Orbitrap Detector
31
Data Types
32
Ion Polarity Modes
32
Chapter 3 Vacuum System
33
Figure 5. Functional Block Diagram of the Vacuum System
34
Figure 6. Schematic of the Internal Gas Supplies
35
Schematic of the Internal Gas Supply Lines
35
Inlet Gases Hardware
36
Figure 7. Gas Inlet Ports (Back of the Mass Spectrometer)
36
Helium Regulator
37
Nitrogen Gas Valves
37
Vent Valve
38
Vacuum Manifold
38
Vacuum Gauges
39
Vacuum Pumps
39
Figure 8. Placement of the Three Turbomolecular Pumps
40
Atmospheric Pressure Ionization Source
41
Figure 9. EASY-Max NG API Source (H-ESI Mode)
41
API Source Interface
42
Figure 10. API Source Interface (Orbitrap Fusion MS Cross Section)
42
Figure 11. Exit Lens and RF Lens
43
Vacuum System
33
Vacuum System Functional Block Diagram
33
Chapter 4 Ion Transmission and Mass Analysis
45
Workflow for Mass Analysis
45
Figure 12. Workflow for Mass Analysis
46
Ion Optics
47
Figure 13. Schematic of the Orbitrap Fusion Lumos Tribrid MS Ion Transmission Path (Shown with the ETD Source Option)
47
Figure 14. MP00 RF Lens (Orbitrap Fusion and Orbitrap Fusion Lumos Mss)
48
MP00 Ion Optics
48
Figure 15. Lens L0
49
Figure 16. Multipole MP0
49
MP0 Ion Optics
49
Figure 17. TK Lens (both Sides)
50
Figure 18. Multipole MP1 (Orbitrap Fusion and Orbitrap Fusion Lumos Mss)
50
MP1 Ion Optics
50
Curved Linear Trap
51
Figure 19. C-Trap (Orbitrap Fusion and Orbitrap Fusion Lumos Mss)
51
Figure 20. Ion-Routing Multipole (IRM)
51
Ion-Routing Multipole
51
DC Offset Voltages
52
MP3 Ion Optics
52
Mass Analyzers
52
Figure 21. Multipole MP3
52
Figure 22. Quadrupole Q1
53
Figure 23. Dual-Split Gate Lens (both Sides)
53
Quadrupole Mass Analyzer
53
Figure 24. Polarity of the RF and DC Voltages Applied to the Q1 Rods
54
Figure 25. Schematic of the Orbitrap Cell and an Example Stable Ion Trajectory
55
Orbitrap Mass Analyzer
55
Figure 26. Electrodynamic Squeezing of Ions in the Orbitrap Analyzer (R) Versus the
56
Figure 27. Approximate Shape of Ion Packets of Different M/Z after the Voltages
57
Linear Ion Trap Mass Analyzer
57
Figure 28. Linear Ion Trap (LIT) (Orbitrap Fusion MS)
58
Figure 29. Assembly for the Linear Ion Trap
58
Figure 30. Visual Representation of the LIT Mass Analyzer Operation
60
Ion Detection Systems
61
Chapter 5 Syringe Pump and Divert/Inject Valve
63
Syringe Pump
63
Divert/Inject Valve
64
Figure 31. Syringe Pump Setup (Top View)
64
Configurations
65
Figure 32. Divert/Inject Valve Positions
65
Controlling the Divert/Inject Valve
66
Figure 33. Divert/Inject Valve Plumbed as a Loop Injector and as a Divert Valve
66
Figure 34. Modular Divert/Inject Valve (Front View)
66
Chapter 6 System Shutdown, Startup, and Reset
67
Shutting down the System in an Emergency
67
Placing the Mass Spectrometer in Standby Mode
68
Figure 35. Thermo Tune Window (Orbitrap Fusion MS)
68
Figure 36. Direct Control Dialog Box (Instrument Setup Window)
69
Turning on the Mass Spectrometer
70
Shutting down the Mass Spectrometer Completely
70
Starting the System after a Complete Shutdown
71
Starting the LC System
71
Starting the Data System
71
Starting the Mass Spectrometer
72
Starting the Autosampler
73
Resetting the Mass Spectrometer
73
Resetting Calibration Parameters
74
Restarting the Data System
75
On/Off Status for MS Components under Varying Power Conditions
76
Chapter 7 Daily Operation
79
Before Operating the Orbitrap Fusion Series System
80
Checking the System Mode
80
Checking the Vacuum Pressure Levels
80
Checking the Gas Supplies
81
After Operating the Orbitrap Fusion Series System
82
Flushing the Inlet Components
82
Purging the Oil in the Forepump
83
Emptying the Solvent Waste Container
83
Placing the System in Standby Mode
83
Chapter 8 Maintenance
85
Maintenance Schedule
86
Guidelines
87
Tools and Supplies
87
Maintaining the API Source Housing
89
Maintaining the API Source Interface
90
Cleaning the Ion Sweep Cone, Spray Cone, and Ion Transfer Tube
90
Figure 37. Direct Control Dialog Box (Instrument Setup Window)
91
Figure 38. Ion Sweep Cone Removed from the MS Mount Assembly
92
Figure 39. Ion Transfer Tube Removal Tool (Orbitrap Fusion MS)
93
Figure 40. Ion Transfer Removal Tool (Orbitrap Fusion Lumos MS)
93
Figure 41. Spray Cone, O-Ring, Ion Transfer Tube, and Ion Sweep Cone
94
Removing the API Source Interface
96
Figure 42. API Source Interface Removed from the Vacuum Manifold
96
Cleaning the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0
97
Figure 43. Lens L0 Removed from the Back of the API Source Interface
97
Figure 44. MP00 RF Lens Assembly Removed from the API Source Interface
98
Figure 45. RF Lens Removed from the API Source Interface Cage
98
Figure 46. Exit Lens Removed from the API Source Interface (Orbitrap Fusion MS)
99
Figure 47. Alignment Slot and Thumbscrew Locations on the MP00 RF Lens
100
Reinstalling the API Source Interface
101
Maintaining the Forepump
101
Maintaining the Air Filter
102
Maintenance
85
Chapter 9 Replaceable Parts
103
Orbitrap Fusion Series Chemicals Kit
103
Calibration Kit
104
MS Setup Kit
105
Performance Specification Kit
105
Single Mechanical Pump Kit
106
Dual Mechanical Pumps Kit
106
API Source Interface
107
Miscellaneous Parts
107
Glossary
109
Index
115
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Thermo Orbitrap Fusion Series Specifications
General
Brand
Thermo
Model
Orbitrap Fusion Series
Category
Laboratory Equipment
Language
English
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