API 2000™ LC/MS/MS

System
Service Manual

Document Number: D1000008748 C

June 2005

[Link]
This document is provided to customers who have purchased MDS Sciex equipment to use
in the operation of such MDS Sciex equipment. This document is copyright protected and
any reproduction of this document or any part of this document is strictly prohibited, except
as MDS Sciex may authorize in writing.
Equipment that may be described in this document is protected under one or more patents
filed in the United States, Canada, and other countries. Additional patents are pending.
Software that may be described in this document is furnished under a license agreement. It
is against the law to copy, modify, or distribute the software on any medium, except as
specifically allowed in the license agreement. Furthermore, the license agreement may
prohibit the software from being disassembled, reverse engineered, or decompiled for any
purpose.
Portions of this document may make reference to other manufacturers’ products, which
may contain parts that are patented and may contain parts whose names are registered as
trademarks and/or function as trademarks. Any such usage is intended only to designate
those manufacturers’ products as supplied by Applied Biosystems/MDS SCIEX for
incorporation into its equipment and does not imply any right and/or license to use or permit
others to use such product names as trademarks.
All products and company names mentioned herein may be the trademarks of their
respective owners.
Applied Biosystems/MDS SCIEX makes no warranties or representations as to the fitness
of this equipment for any particular purpose and assumes no responsibility or contingent
liability, including indirect or consequential damages, for any use to which the purchaser
ISO
may put the equipment described herein, or for any adverse circumstances arising
therefrom.
9001
Applied Biosystems/MDS SCIEX is a joint venture between Applera Corporation and REGISTERED
COMPANY
MDS Sciex, the instrument technology division of MDS Inc.

One or more of the following trademarks or registered trademarks may be found in this
document:
API 150EX™, API 2000™, API 3000™, API 4000™, API 5000™, BIOANALYST™,
BIOSPECTROMETRY™, BIOTOOLBOX™, CURTAIN GAS™, EXPLORER™,
INTERROGATOR™, IONSPRAY™, MASSCHROM™, NANOLINK™, OMALDI™, OPTI-
TOF™, RDA™, TOF/TOF™, VOYAGER™, and VOYAGER-DE™ are trademarks owned by
Applera Corporation or its subsidiaries in the United States and certain other countries.
TURBO V™ is a trademark owned by Applied Biosystems.
ANALYST®, DATA EXPLORER®, DELAYED EXTRACTION®, MICROIONSPRAY®,
QSTAR®, SYMBIOT®, and TURBOIONSPRAY® are registered trademarks owned by
Applera Corporation or its subsidiaries in the United States and certain other countries.
API 3200™ , DUO SPRAY™, and QJET™ are trademarks owned by Applied Biosystems/MDS SCIEX
Instruments.
3200 QTRAP®, 4000 Q TRAP®, MICROIONSPRAY®, NANOSPRAY®, PHOTOSPRAY®,
and QTRAP® are registered trademarks owned by Applied Biosystems/MDS SCIEX
Instruments.
MDS SCIEX™ and MDS SCIEX & DESIGN™ are trademarks owned by MDS Inc.
HYPERMASS®, HYPERSPEC®, LINAC®, MALDI TOF/TOF®, and SCIEX® are registered
trademarks owned by MDS Inc. in the United States and certain other countries.
All product and company names mentioned herein may be the trademark of their respective
owners.

Equipment built by MDS Sciex, a division of MDS Inc., at

71 Four Valley Dr., Concord, Ontario, Canada. L4K 4V8.
MDS Sciex and Applied Biosystems are ISO 9001 registered.
© 2005 Edition MDS Sciex, a division of MDS Inc., and Applera Corporation,
Joint Owners. All rights reserved.
Printed in Canada.
 Table of Contents

Table of Contents
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.1 About This Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.2 International Standards Certifications . . . . . . . . . . . . . . . . . . . . 12
1.3 Servicing the API 2000 Chassis . . . . . . . . . . . . . . . . . . . . . . . . 16
1.3.1 Chassis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.3.2 I/O Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
1.3.3 Gas Connection Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
1.3.4 Interface Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
1.4 Servicing the API 2000 Covers . . . . . . . . . . . . . . . . . . . . . . . . 20
1.5 Instrument Covers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
1.5.1 Front Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
1.5.2 Top Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
1.5.3 Back Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
1.5.4 Power Distribution Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
1.6 Servicing the Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
TurboIonSpray and Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.1 Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.2 TurboIonSpray Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
2.2.1 Droplet Generation and Charging. . . . . . . . . . . . . . . . . . . . . . . 31
2.2.2 Ion Evaporation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
2.2.3 Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
2.2.4 Ion Source Interlocks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
2.3 Source Exhaust System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
2.4 Source Exhaust Venturi Gas Supply. . . . . . . . . . . . . . . . . . . . . 37
2.5 TurboIonSpray Inlet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
2.6 Service Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
2.7 Source Exhaust System Service . . . . . . . . . . . . . . . . . . . . . . . . 52
2.7.1 Venturi Gas Supply. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Vacuum Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
3.1 Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
3.1.1 Gas Curtain Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
3.1.2 Differentially Pumped Interface . . . . . . . . . . . . . . . . . . . . . . . . 55
3.1.3 Entrance Optics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
3.2 Hook-up Schematic. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
3.3 Vacuum Interface Maintenance . . . . . . . . . . . . . . . . . . . . . . . . 59
3.4 Vacuum Interface Service Procedures . . . . . . . . . . . . . . . . . . . 63
Vacuum Chamber . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
4.1 Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
4.1.1 Mass Filter Rail. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.1.2 Quadrupoles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.1.3 Mass Filters (Q1 and Q3) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

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4.1.4 RF-Only Quadrupole (Q0 and Q2) and Stubbies . . . . . . . . . . . 78

4.1.5 Vacuum Feedthroughs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
4.1.6 Collision Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
4.1.7 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
4.1.8 Ion Detector (ETP) and Signal Handling . . . . . . . . . . . . . . . . . 83
4.2 ETP Service Procedures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
4.3 Mass Filter Rail Service Procedures . . . . . . . . . . . . . . . . . . . . . 91
Vacuum Control System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
5.1 Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
5.1.2 Pumping System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
5.1.3 Turbo Pump. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
5.1.4 Turbo Pump Controllers and Gas Control Assembly . . . . . . . 108
5.1.5 Rotary Vane Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
5.1.6 Roughing Pump. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
5.1.7 Anti-Suck Back Valve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
5.1.8 Gas Ballast Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
5.1.9 Smoke Eliminator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
5.1.10 Vacuum Gauge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
5.1.11 Vacuum Gauge Controller . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
5.1.12 Gas Control System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
5.1.13 Safety Interlocks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
5.1.14 Vacuum Control Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
5.2 Gas Control Service Procedures . . . . . . . . . . . . . . . . . . . . . . . 123
5.3 Turbo Pump Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
5.4 Rotary Vane Pump Maintenance . . . . . . . . . . . . . . . . . . . . . . 129
5.5 Vacuum Gauge Service Procedures . . . . . . . . . . . . . . . . . . . . 131
Power and Electronics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
6.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
6.2 Power Distribution Module . . . . . . . . . . . . . . . . . . . . . . . . . . 134
6.2.1 AC Power Distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
6.2.2 DC Power Distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
6.3 System Electronics Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
6.3.1 Motherboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
6.3.2 System Controller Module . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
6.3.3 Internal Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
6.3.4 Windows NT and Mac Users . . . . . . . . . . . . . . . . . . . . . . . . . 143
6.3.5 External Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
6.3.6 Ion Path DACs and Vacuum Gauge Controller Module. . . . . 146
6.3.7 Lens Power Supply Module . . . . . . . . . . . . . . . . . . . . . . . . . . 148
6.3.8 HV Power Supply Module . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
6.4 Quadrupole Power Supply (QPS) . . . . . . . . . . . . . . . . . . . . . . 151
6.4.1 Exciter Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
6.4.2 Amplifier Boards. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153

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6.4.3 Coil Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154

6.5 System Electronics Box Circuit Descriptions. . . . . . . . . . . . . 155
6.5.1 Motherboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
6.5.2 System Controller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
6.5.3 Ion Path DACs and Vacuum Gauge Controller . . . . . . . . . . . . . 162
6.5.4 Lens Power Supply Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
6.5.5 High-Voltage Supply Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
6.5.6 Exciter Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
6.5.7 Amplifier Boards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
6.6 Temperature Controller. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
6.6.1 Temperature Control System . . . . . . . . . . . . . . . . . . . . . . . . . 171
6.7 Q1 and Q3 Coil Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
6.7 Card Cage Blower. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
6.8 Power Distribution Module Service . . . . . . . . . . . . . . . . . . . . 186
6.9 Main Circuit Breaker Switch . . . . . . . . . . . . . . . . . . . . . . . . . 191

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List of Figures
Figure 1-1. API 2000 System - Front . . . . . . . . . . . . . . . . . . . . . . . . . 13
Figure 1-2. API 2000 System - Rear . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Figure 1-3. I/O Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Figure 1-4. Gas Connection Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Figure 1-5. Interface Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Figure 1-6. API 2000 - Front Cover . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Figure 1-7. API 2000 - Top Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Figure 1-8. API 2000 Back Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Figure 1-9. API 2000 Power Distribution Cover. . . . . . . . . . . . . . . . . 25
Figure 1-10. Cooling Fan Filter and Cover . . . . . . . . . . . . . . . . . . . . . . 27
Figure 2-1. Illustration of IonSpray and Ion Source . . . . . . . . . . . . . . 29
Figure 2-2. Ion Evaporation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Figure 2-3. TurboIonSpray Inlet and Ion Source . . . . . . . . . . . . . . . . 33
Figure 2-4. TurboIonSpray Unit Plug Connection . . . . . . . . . . . . . . . 34
Figure 2-5. API 2000 - Source Exhaust Pump . . . . . . . . . . . . . . . . . . 37
Figure 2-6. TurboIonSpray Unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Figure 2-7. TurboIon Spray Schematic . . . . . . . . . . . . . . . . . . . . . . . . 42
Figure 2-8. TurboIonSpray X-Y Mechanism . . . . . . . . . . . . . . . . . . . 44
Figure 2-9. TurboIonSpray Assembly . . . . . . . . . . . . . . . . . . . . . . . . . 47
Figure 2-10. Electropolishing Apparatus. . . . . . . . . . . . . . . . . . . . . . . . 51
Figure 3-1. Vacuum Interface - Side View . . . . . . . . . . . . . . . . . . . . . 53
Figure 3-2. Vacuum Interface - Front View . . . . . . . . . . . . . . . . . . . . 55
Figure 3-3. Vacuum Interface Hook-up Schematic. . . . . . . . . . . . . . . 58
Figure 3-4. Vacuum Interface Schematic . . . . . . . . . . . . . . . . . . . . . . 59
Figure 3-5. Vacuum Interface Assembly. . . . . . . . . . . . . . . . . . . . . . . 69
Figure 3-6. Skimmer Plate/Curtain Assembly. . . . . . . . . . . . . . . . . . . 70
Figure 3-7. Interface Plate - Rear View. . . . . . . . . . . . . . . . . . . . . . . . 71
Figure 4-1. API 2000 Mass Filter Rail . . . . . . . . . . . . . . . . . . . . . . . . 74
Figure 4-2. Mechanical and Electrical Configuration of a Quadrupole .
Mass Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Figure 4-3. Vacuum Feedthrough . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Figure 4-4. API 2000 Ion Optics Path . . . . . . . . . . . . . . . . . . . . . . . . . 82
Figure 4-5. ETP Unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Figure 4-6. Response of the Signal Handling Circuit to Pulse Input . 85
Figure 4-7. ETP Replacement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Figure 4-8. ETP Module Assembly. . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Figure 4-9. Feedthrough Installation Schematic . . . . . . . . . . . . . . . . . 92
Figure 4-10. Front Bulkhead . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Figure 4-11. Collision Cell Installation . . . . . . . . . . . . . . . . . . . . . . . . . 95
Figure 4-12. Collision Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Figure 4-13. Q1 Mass Filter and Interconnect PC Board . . . . . . . . . . . 98

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Figure 4-14. Q1 - Q0 RF Connections . . . . . . . . . . . . . . . . . . . . . . . . . 99

Figure 4-15. Q3 - Q2 Connection Schematic . . . . . . . . . . . . . . . . . . . 101
Figure 5-1. Turbo Pump Controller and Gas Control Assembly. . . . 108
Figure 5-2. Vacuum Pump-Down Sequence . . . . . . . . . . . . . . . . . . . 110
Figure 5-3. Roughing Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Figure 5-4. Vacuum Gauge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Figure 5-5. Vacuum Gauge Controller Block Diagram . . . . . . . . . . 115
Figure 5-6. Gas 1/Gas 2 Control Connection Schematic. . . . . . . . . . 118
Figure 5-7. Operating Modes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Figure 5-8. TW 220 Turbo Pump Mount . . . . . . . . . . . . . . . . . . . . . 125
Figure 5-9. Turbo Pump Controller Connections . . . . . . . . . . . . . . . 127
Figure 5-10. Vacuum Gauge Assembly . . . . . . . . . . . . . . . . . . . . . . . 131
Figure 6-1. DC Power Supply Connections . . . . . . . . . . . . . . . . . . . 135
Figure 6-2. System Electronics Box - Layout . . . . . . . . . . . . . . . . . . 137
Figure 6-3. System Controller Interconnect . . . . . . . . . . . . . . . . . . . 139
Figure 6-4. Ion Path/HV System Interconnect . . . . . . . . . . . . . . . . . 147
Figure 6-5. QPS System Interconnect . . . . . . . . . . . . . . . . . . . . . . . . 151
Figure 6-6. Power Supply Enable Logic . . . . . . . . . . . . . . . . . . . . . . 152
Figure 6-7. Motherboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
Figure 6-8. System Controller Block Diagram . . . . . . . . . . . . . . . . . 159
Figure 6-9. Vacuum Gauge Controller Circuit Schematic . . . . . . . . 163
Figure 6-10. Q1 Filter Board Assembly Connections . . . . . . . . . . . . . 174
Figure 6-11. Q3 Feedthrough Installation Schematic . . . . . . . . . . . . . 175
Figure 6-12. Coil Box Connections - Rear and Side View . . . . . . . . . 176
Figure 6-13. Power Connectors Layout. . . . . . . . . . . . . . . . . . . . . . . . 187
Figure 6-14. DC Power Supply AC Input Connection . . . . . . . . . . . . 189
Figure 6-15. DC Power Supply Connections . . . . . . . . . . . . . . . . . . . 190
Figure 6-16. Main Switch Connections . . . . . . . . . . . . . . . . . . . . . . . . 192

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List of Tables
Table 1-1. API 2000 Connection Panel Locations . . . . . . . . . . . . . . . . 16
Table 3-1. Entrance Optics Functions . . . . . . . . . . . . . . . . . . . . . . . . . 56
Table 3-2. Entrance Optics Standard Voltage Settings . . . . . . . . . . . . 57
Table 4-1. Ion Optics Standard Voltage Settings . . . . . . . . . . . . . . . . . 81
Table 4-2. ETP Voltage and Limitations . . . . . . . . . . . . . . . . . . . . . . . 83
Table 4-3. Continuity Check Pins . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Table 6-1. System Controller Digital I/O. . . . . . . . . . . . . . . . . . . . . . 140
Table 6-2. Miscellaneous Parallel I/O . . . . . . . . . . . . . . . . . . . . . . . . 140
Table 6-3. Scan Timing and Control (STC) Signals . . . . . . . . . . . . . 142
Table 6-4. Lens Power Supply Ranges . . . . . . . . . . . . . . . . . . . . . . . 148
Table 6-5. Coil Box Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
Table 6-6. Power Distribution Board - Fuse Distribution . . . . . . . . . 188

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000 I'M INVISIBLE

1 Overview
1.1 About This Manual
This service manual contains information required to maintain the API 2000
instrument. It contains detailed descriptions of the system components, as
well as preventive maintenance and corrective maintenance procedures.
The service manual is part of a set of manuals that also includes the
API 2000 Operator’s Manual and the API 2000 Qualified Operator’s Service
Manual. Other related documents include the API 2000 LC/MS/MS Triple
Quadrupole Products Site Guide, Instrument and Operations Qualification
Manual, the TUNE Software Manual, the Sample Control Software Manual
and the MultiView Manual.
Within the scope of this manual, the following conventions are used:

WARNING Indicates an operation that may cause personal injury if

precautions are not followed.

Caution Indicates an operation that may cause damage to the

instrument if precautions are not followed.

Note Emphasizes significant information in a procedure or description.

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Overview

1.2 International Standards Certifications

This instrument and its components have been certified by the following
international agencies. Applicable labels for these qualifications have been
attached to various components of the instruments.
FCC
The API 2000 comply with FCC Part 15, Subpart B, Class A.

Note This equipment has been tested and found to comply with the
limits for a Class A digital device, pursuant to Part 15 of the FCC
Rules. These limits are designed to provide reasonable protection
against harmful interference when the equipment is operated in a
commercial environment. This equipment generates, uses, and
can radiate radio frequency energy and, if not installed and used
in accordance with the instruction manual, may cause harmful
interference to radio communications. Operation of this equipment
in a residential area is likely to cause harmful interference in which
case the user will be required to correct the interference at the
user’s own expense.

CISPR
The API 3000 complies with Class A of CISPR publication
22 (1993)/British Standard BSI EN 55022 (1987).
IEC
The API 3000 is certified to comply with the ‘Low Voltage Directive
(73/23/EEC & 93/68/EEC)’, standard EN61010-1 and the ‘EMC Directive
(89/336/EEC & 93/68/EEC)’, and its standards EN50081-1 & EN50082-1

CE
Certificate of CE compliance is included with the instrument.

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 Overview

Figure 1-1. API 2000 System - Front

13
Overview

Figure 1-2. API 2000 System - Rear

14
 Overview

The rest of this manual is divided into service procedures based on

instrument assemblies.
All procedures should be strictly followed to ensure safety in the servicing
of this instrument.

WARNING All standard safety precautions regarding high voltages,

vacuum systems, and electrostatic discharge must be
followed to prevent personal injury or damage to the
instrument.

WARNING Verify with the operator that no biohazardous materials were

run through the instrument. If these materials have been
used, ask the operator to use the proper cleaning methods
before maintenance.

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Overview

1.3 Servicing the API 2000 Chassis

1.3.1 Chassis
The chassis is the main physical support for the instrument components,
and the main path for grounding the instrument's electrical components. All
the electrical components are grounded to the chassis. The chassis is
connected directly to the AC power supply ground circuit.
The chassis base is a steel tubular frame on which the API 2000 main
console is assembled. The vacuum chamber that houses the mass filter rail
and supports both the vacuum interface and the Ion Source, is fastened to
the chassis base.
All connections to external sources are made through bulkheads attached
to the chassis. The external power supply, IEEE connection to the host
computer, the AUX I/O and the serial port connections are made through
the back panel. See the table below.

Table 1-1. API 2000 Connection Panel Locations

Panel Location
I/O Panel rear of the chassis, centre
Gas Supply Panel rear of the chassis, right hand side
Ion Source Panel chassis front, left side
Main Power rear of the chassis, right side

16
 Overview

1.3.2 I/O Panel

The external power supply, the IEEE-488 connection to the Applications
Computer, the AUX I/O and the serial port connections are made through
the I/O Panel on the rear centre of the chassis as shown below.

Figure 1-3. I/O Panel

17
Overview

1.3.3 Gas Connection Panel

The vacuum lines to the Backing Pump are connected through the Gas
Connection Panel on the rear right-hand corner of the chassis. The panel
also houses on the left-hand side, the GAS 1/GAS 2 and Curtain Gas
supply connections and the external connections for the Source Exhaust
System. It also shows the connections for the Exhaust and Valve Waste.

Figure 1-4. Gas Connection Panel

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 Overview

1.3.4 Interface Assembly

The Interface Assembly is located at the left-hand side of the instrument. It
is connected to the vacuum chamber and supports connections for
Gas 1, Gas 2, and Gas 3 and the electrical connections.

Figure 1-5. Interface Assembly

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Overview

1.4 Servicing the API 2000 Covers

This procedure should be followed before performing any maintenance on
the instrument to minimize the potential for exposure to the instrument's
high-operating voltages.
When shutting down the instrument, care must be taken to prevent the
rotary vane pump’s exhaust from being drawn into the vacuum chamber via
the turbo pump exhaust ports. The likelihood of this happening is reduced
because the rotary vane pump has a valve that isolates the pump exhaust
from the pump intake when the pump is shut off or fails.
Shutting down the API 2000 instrument
1. Complete any ongoing scans or select the abort scan command from
the TUNE or Sample Control application.

Note Windows NT and MAC users should choose Stop Sample from
the Acquire menu. The queue stops after the current scan in the
selected sample.

2. Shut off the sample flow to the Ion Source.

Caution The sample flow must be turned off before shutting down the
instrument.

3. Perform an overnight quit from the TUNE or Sample Control

application to disengage the Data Acquisition Computer from the
instrument.

Note Windows NT and MAC users should choose Standby from the
Acquire menu.

4. Shut off the Main Power switch to the instrument from the bulkhead at
the back right corner of the chassis.

Caution If the instrument is going to be shut down for any length of

time, it is recommended that the vacuum chamber be vented
to prevent the Rotary Vane Pump exhaust from being sucked
back into the vacuum chamber (follow steps 5 and 6).

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 Overview

Caution If the vacuum chamber is not going to be vented while the

instrument is shut down, it is recommended that the Backing
Pumps remain turned on to prevent the rotary vane pump’s
exhaust from being sucked back into the vacuum chamber
(skip steps 5 and 6).

5. Shut off the backing pump. This pump is located outside the main
console. The power switch is located beside the power supply input
attachment.
6. To vent the vacuum chamber, remove the venting screw with a 5mm
socket wrench from the front of the chamber.
Powering Up the API 2000 Instrument
1. Replace the venting screw on the front of the vacuum chamber and
tighten if the instrument was vented.
2. Replace the instrument covers.
3. Switch on the Backing Pump, if it was turned off.

Note The pump has it own power toggle switch and must be turned on
manually. It is not controlled remotely by the System Controller.

4. Ensure that the Curtain Gas supply is flowing to the instrument. The
pressure should be regulated to 60 psig.
5. Ensure that the 207V to 242V main power supply is plugged into the
electrical connections panel.
6. Turn on the main power switch.
7. Ensure that the Graphical Purpose Interface Bus (GPIB) box is turned
on and is connected to both the API 2000 instrument and the
Applications Computer.
8. Turn on the Applications Computer.

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Overview

1.5 Instrument Covers

There are four covers that enclose the operating modules of the API 2000.
The covers can be opened to allow access to the instrument's component
modules, the System Electronics Box, and the operational parameter check
points. The covers are designed to prevent access to the instrument when
high-operating voltages are engaged.

1.5.1 Front Cover

The front cover is the main cover that must be removed before you can
open the remaining covers.

Figure 1-6. API 2000 - Front Cover

Opening the front cover exposes the main components of the API 2000,
including many of the system test points. The cover is secured at the top by
three screws that are mounted on top of the card cage and coil box. It is
inserted to the chassis on the bottom with three tabs. It is not hinged to the
chassis and must be removed to access the front of the API 2000.
1. Shut off the instrument.
2. Remove the Ion Source.

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 Overview

WARNING Do not open the API 2000 covers unless the Ion Source is
removed first. Failure to follow this sequence will expose the
operator to the operating voltages.

3. Unscrew the three captured bolts that secure the Front Cover to the
instrument.
4. Grasp the top corners of the Front Cover and gently pull and lift the
cover to remove it.

1.5.2 Top Cover

Figure 1-7. API 2000 - Top Cover

1. Remove the Front Cover.

WARNING Do not open the API 2000 covers unless the Ion Source is
removed first. Failure to follow this sequence will expose the
operator to the operating voltages.

2. Unscrew the two captured bolts that secure the top cover to the back
of the instrument.
3. Tilt the front end of the cover up and gently pull towards the rear. Lift
the cover to remove it.

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Overview

1.5.3 Back Cover

The back cover encloses most of the systems cabling. It is not hinged and
must be removed to access the back of the API 2000.

Figure 1-8. API 2000 Back Cover

1. Remove the front cover.

2. Remove the top cover.

WARNING Do not open the API 2000 covers unless the Ion Source is
removed first. Failure to follow this sequence will expose the
operator to the operating voltages.

3. Unscrew the two captured bolts that secure the back cover to the back
of the instrument.
4. Gently lift the cover to remove it.

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 Overview

1.5.4 Power Distribution Cover

Figure 1-9. API 2000 Power Distribution Cover

WARNING There are no operator serviceable items located behind the

power distribution cover.

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Overview

1.6 Servicing the Filters

Removing and Replacing the Handles
1. Shut down the instrument.
2. Unscrew and remove the three bolts that connect the handles at each
end of the instrument.
3. To replace the handles, reattach them at both ends of the chassis.
Removing and Replacing the Card Cage Blower Filter
A cooling fan housed inside the instrument chassis blows air over the circuit
boards housed in the system electronics box and the turbo pump that is
attached to the vacuum chamber. An air filter, which filters the cooling fan’s
intake air, is mounted to the chassis in front of the fan.

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

Caution This filter should be replaced every three months of

operation or when it becomes dirty. Use correct replacement
filter or the instrument may burn out.

The card cage blower filter can be replaced easily without opening or
removing any of the instrument’s covers. The filter is accessed via a filter
cover located on the chassis in the back corner.

Caution The API 2000 instrument must be turned off before removing
the filter cover, otherwise the filter can be pulled into the fan
assembly.

1. Shut off the Instrument.

2. With a flat head screwdriver, loosen the screws that secure the filter
cover plate.
3. Remove the filter cover and the filter from the frame.

26
 Overview

Figure 1-10. Cooling Fan Filter and Cover

4. Place the replacement filter on the filter cover plate.

5. Mount the filter cover and filter to the chassis by tightening the two
screws you loosened in step 2.
6. Turn on the instrument.

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Overview

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100 I'M INVISIBLE

2 TurboIonSpray and Ion Source

2.1 Overview
TurboIonSpray is an atmospheric pressure ion source in which pre-formed
ions in a solution are emitted into the gas phase without applying heat. In
this way, quasi-molecular ions can be generated from very labile and high
molecular weight compounds with no thermal degradation. It is the
technique by which a liquid sample is pumped by a liquid chromatograph
(LC) pump or syringe drive through a sprayer tube that is maintained at a
high voltage, and is nebulized into the Ion Source creating a mist of highly
charged droplets (see the figure below). Once inside the Ion Source, the
droplets evaporate causing the ions to enter the gas phase by a low energy
process called Ion Evaporation.
The use of an orthogonal heated gas extends the rugged and versatile
technique of TurboIonSpray to accept higher flow rate with improved
sensitivity. TurboIonSpray will accept flows from 5 to 1000 µL/min of solvent
compositions from 100% aqueous to 100% organic, such as acetonitrile,
without splitting. This allows the use of 1mm, 2mm, and 4.6mm analytical
columns with or without splitting.

Figure 2-1. Illustration of IonSpray and Ion Source

The heater probe directs a jet of heated dry gas (up to a maximum of
500°C) at the mist produced by the sprayer. The gas is sprayed across the
orifice at an angle of approximately 45° with respect to the Curtain Plate.
The liquid spray emerging from the TurboIonSpray is directed at an angle
of about 45° from the opposite direction (or 135°). The TurboIonSpray
effluent and the heated dry gas intersect at an angle of approximately 90°

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TurboIonSpray and Ion Source

near the orifice. This interaction helps focus the TurboIonSpray stream and
increases the rate of droplet evaporation resulting in an increased ion
signal.
TurboIonSpray is ideally suited for LC/MS/MS quantitative analyses. The
sensitivity increases that are achieved with this technique are both flow rate
and analyte dependent. In the conventional TurboIonSpray, source
sensitivity decreases with increased flow rate, while the heated
TurboIonSpray process increases ionization efficiency, especially at the
higher flow rates. This results in improved sensitivity. Sensitivity is
compound dependent and compounds of extremely high polarity and low
surface activity usually show the greatest sensitivity increases. The
TurboIonSpray technique is mild enough to be used with labile compounds
such as peptides, proteins, and thermally liable pharmaceuticals.

Note The difference between conventional IonSpray and

TurboIonSpray is that in the TurboIonSpray, the ionization of the
sample is achieved with additional heater gas delivered to aid in
the desolvation of the spray. Typically the TurboIonSpray is used
at higher flow rates (greater than or equal to 40 µL/min).

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 TurboIonSpray and Ion Source

2.2 TurboIonSpray Theory

This section describes the theory of TurboIonSpray, including the formation
of charged droplets and ion evaporation mechanism.

2.2.1 Droplet Generation and Charging

WARNING All during normal operation, high voltages exist in the

TurboIonSpray inlet. Do not operate the instrument without
the viewing glass in place in the TurboIonSpray inlet casing.

A high-velocity flow of nebulizer gas shears droplets from the liquid sample
stream In the TurboIonSpray inlet. Using the variable high voltage applied
to the sprayer, a net charge is applied to each droplet and aids in the droplet
dispersion. Ions of a single polarity are preferentially drawn into the droplets
by the high voltage as they are separated from the liquid stream. The
separation, however, is incomplete, therefore each droplet contains many
ions of both polarities. Ions of one polarity are predominant in each droplet,
and the difference between the number of positively or negatively-charged
ions results in the net charge. Only the excess ions of the predominant
polarity are available for ion evaporation, and only a fraction of these
actually evaporate.
The polarity and concentration of excess ions depends on the magnitude
and polarity of the high-voltage potential applied to the sprayer tip. For
example, when a sample contains arginine in water/acetonitrile, and a
positive potential is applied to the sprayer, the excess positive ions will be
H+ and MH+ arginine.
TurboIonSpray can generate multiple-charged ions from compounds that
have multiple charge sites, such as peptides and oligonucleotides. This is
useful when observing high-molecular weight species, where the multiple
charges produce ions of a mass-to-charge (m/z) value within the mass
range of the instrument. This allows routine molecular weight
determinations of compounds in the kilodalton (KDa) range.

2.2.2 Ion Evaporation

Each charged droplet contains solvent and both positive and negative ions,
with ions of one predominant polarity. A simple view of the droplet as a
conducting medium suggests that excess charges reside at the droplet’s
surface (see the next figure). As the solvent evaporates, the electrical field
at the surface of the droplet increases due to the decreasing radius of the
droplet.

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TurboIonSpray and Ion Source

If the droplet contains excess ions, and evaporates enough, a critical field
is reached at which ions are emitted from the surface. Eventually, all of the
solvents will evaporate from the droplet, leaving a dry particle consisting of
the non-volatile components of the sample solution.

Figure 2-2. Ion Evaporation

Only compounds that ionize in the liquid solvent can be generated as gas
phase ions in the Ion Source. The efficiency and rate of ion generation
depends on the solvation energies of the specific ions. Ions with lower
solvation energies are more likely to evaporate than ions with higher
solvation energies.
Given that the solvation energies for most organic molecules are unknown,
the sensitivies of any given organic ion to ion evaporation is difficult to
predict. The importance of solvation energy is shown by the observation
that surfactants that concentrate at the surface of a liquid tend to very
sensitively detected.

2.2.3 Ion Source

“Ion Source” refers to the area where sample ions are generated. In the
context of this manual, it refers to the round chamber that houses the
sample inlet. The Ion Source is located at the left-most end of the main
console as viewed from the front of the instrument (see the TurboIonSpray
Inlet and Ion Source figure).
The Ion Source housing mounts to the front end of the Vacuum Chamber,
and is held in position by two locking arms. A Plexiglass window on the side
of the housing allow you to observe the TurboIonSpray Inlet. The Ion
Source and housing can be quickly and easily removed without tools to
allow you access to the Vacuum Interface.

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 TurboIonSpray and Ion Source

Figure 2-3. TurboIonSpray Inlet and Ion Source

Gas, High Voltage, and the Source Identification key are made through the
front plate of the interface. LC inlet and splitter connections are on the front
and front side of the Ion Source. A sample waste tube connected to the
bottom of the Ion Source allows the venting of sample waste via the Source
Exhaust System.

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TurboIonSpray and Ion Source

2.2.4 Ion Source Interlocks

WARNING Do not rely solely on the Interlocks to ensure your safety from
the instrument’s high voltage. When performing routine
maintenance, ensure that the main circuit breaker is off and
the main power supply is disconnected.

The Source Interlock Assembly is connected to the Source Cover beneath

on the Ion Source Housing (see the TurboIonSpray Unit Plug Connection
figure). Direct wiring attached to the bottom of the Ion Source Housing is
used to trigger the interlock microswitches on a PC board inside the Source
Interlock Assembly. When a valid Ion Source is properly installed, an
electrical field is generated that closes the interlock switches. If a valid Ion
Source is not installed or installed incorrectly, the switches open, activating
the interlocks. This interrupts a signal from the System Controller, disabling
the high voltages and setting the ion optic voltages to zero. For more
information on the system’s power supplies, refer to the Power and
Electronics section in this manual.
Restricting tool access to the Front and Back covers ensures that they
cannot be taken off while the system’s high voltages are applied.

Figure 2-4. TurboIonSpray Unit Plug Connection

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 TurboIonSpray and Ion Source

The circuit board inside the Source Interlock Assembly also contains
circuits that recognize the type of Ion Source installed. The Ion Source
housings for the Heated Nebulizer and TurboIonSpray inlets trigger
different sets of switches in the Interlock Assembly that sends information
to the System Controller indicating the type of Ion Source installed. The
System Controller uses this information to control the Source Exhaust
System, a safety feature that isolates the Ion Source Exhaust products from
the laboratory equipment.

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TurboIonSpray and Ion Source

2.3 Source Exhaust System

Each of the Ion Sources produces both ions and solvents vapours. As the
Ion Source is opened to the atmosphere, these vapours represent a
potential hazard to the laboratory equipment. The Source Exhaust System
is designed to safely remove and service the Ion Source exhaust products.
The Source Exhaust System is a venturi system that uses a flow of gas
through a venturi tube to draw the Ion Source exhaust from the Ion Source.
The exhaust, along with the air used to drive the venturi, is delivered to the
gas connections panel at the rear of the instrument, where an external
connection is available to remove the exhaust from the laboratory. The
exhaust gas can be connected to a fume hood or to some other means to
remove the gas safely from the laboratory.

WARNING Take all necessary precautions to ensure the safe disposal of

the Source Exhaust Gases.

The TurboIonSpray and the Heated Nebulizer sources produce greater

volumes of exhaust products because both use additional volumes of gas
and heat to produce ions. As a result, using the Source Exhaust System is
an essential component of these Ion Sources. In fact, when either the
TurboIonSpray or the Heated Nebulizer source is installed, the firmware will
not enable the instrument’s electronics unless the Source Exhaust system
is operating.

WARNING If you are analyzing gases containing toxic or highly volatile

chemicals or solvents, it is highly recommended that you use
the Source Exhaust System.

Note The Source Exhaust System slightly reduces the pressure in the
Ion Source. The reduction in pressure has proven to be beneficial
for the ionization performance of both the Heated Nebulizer and
TurboIonSpray Ion Sources.

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 TurboIonSpray and Ion Source

2.4 Source Exhaust Venturi Gas Supply

The venturi system is driven by an external supply of gas regulated to a
maximum pressure of 60 psig. The gas has no chemical requirements
because it is isolated from the Vacuum Chamber and is used solely to drive
the Source Exhaust Venturi. The gas, normally compressed air, can be
supplied by a “house supply”, a cylinder, or from a compressor (available
as an option) from a 3rd-party vendor.
The external venturi gas supply is connected to the Exhaust Supply
Connector on the gas interface panel and is fed directly to a solenoid valve
that controls the gas flow to the venturi tube. The venturi output is
connected to the “Exhaust Waste Out” connection on the Gas Interface
panel. A third connection from the tube connects to the Source Exhaust
Tube in the Interlock Assembly below the Ion Source (see the
API 2000 - Source Exhaust Pump figure).

Figure 2-5. API 2000 - Source Exhaust Pump

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TurboIonSpray and Ion Source

This figure shows the gas flows through the venturi system. The solenoid
valve is operated by a 230 VAC connection directly from the AC
Distribution. A switch on the AC Distribution controlled by the System
Controller switches power to the solenoid valve whenever a valid Ion
Source is installed. When the power is switched to the solenoid valve, it
opens, enabling the gas flow through the venturi tube.
A pressure switch attached to the Source Exhaust Line is monitored by the
System Controller. The switch status indicates the operational status of the
Source Exhaust System. Should the pressure in the line rise above the trip
point (0.1 in. water), the System Controller assumes that the Source
Exhaust System is ‘OFF’. If this occurs when either the TurboIonSpray or
the Heated Nebulizer gas is installed, the System Controller interrupts the
Power Supply Enable signal causing the instrument’s electronics to shut
down.

Note When the pressure in the exhaust line falls below the set point of
the instrument’s electronics, the System Controller automatically
restores the Power Supply Enable signal, and the instrument’s
electronics are activated.

With the TurboIonSpray source attached, a rise in pressure that trips the
pressure switch does not disrupt the Power Supply Enable signal. Instead,
a warning appears on the Application’s Computer stating that the pump is
not operating.

WARNING With the TurboIonSpray Source attached, the instrument will

operate if the pressure in the Source Exhaust Line exceeds
the trip point. However it is strongly recommended that the
Source Exhaust System be left on at all times.

Whenever an instrument is switched on and an Ion Source is installed,

power to the Source Exhaust solenoid is switched ‘ON’ initiating the venturi
gas flow. The solenoid valve has no manual or software control. The
adjustable flow control valve at the Source Panel provides a means to
control the draw on the Ion Source. Opening the valve increases the gas
flow to the venturi and the draw on the Ion Source, but lowers the pressure
in the exhaust line. Conversely, closing the valve decreases the gas flow in
the venturi and increases the pressure in the Source Exhaust Line.

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 TurboIonSpray and Ion Source

Note The TUNE software must be running before the Source Exhaust
Pump will turn on. The pump will remain on after the TUNE
software stops running. An overnight quit function shuts off the
Source Exhaust Pump. Windows NT and MAC users should
choose Standby from the Acquire menu. This command is
equivalent to the overnight quit command.

Note Closing the valve causes pressure to rise and can trip the pressure
switch. Depending on the Ion Source attached, this can disable
the system’s electronics and interrupt any ongoing data
acquisitions. Ensure that you open the valve when the pump is
operating normally.

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TurboIonSpray and Ion Source

2.5 TurboIonSpray Inlet

The TurboIonSpray Inlet (see the next figure) consists of one unit: the
TurboIonSpray Source. The Analyst software controls the flow of the Turbo
Heater Gas (Gas 2).
The TurboIonSpray has a fixed angle adjustable TurboIonSpray probe and
a fixed position TurboProbe. All electrical and gas connections are made
through the interface. The Turbo Heater temperature is set at the
Applications Computer using the TUNE software by modifying the TEM
parameter in the State Window. The correlation between the parameter
value of TEM and the actual heater temperature is direct (for example TEM
350 is equal to 350°C at the heater). The TurboIonSpray gas is connected
to Gas 2 through the interface and is UHP nitrogen (99.999%) or zero air
(99.999% purity) at flow rates of up to 8 L/min.
The TurboProbe temperature, which is set at the Applications Computer, is
maintained by the Temperature Control Board (TCB) mounted behind the
Front panel (below the IonSource housing). The TCB adjusts the flow of
power to the heater element as a function of the difference between the
actual heater temperature and the temperature setting at the Applications
Computer. The probe temperature is monitored by a thermocouple
connected directly to the heater element that maintains the temperature
within +15 degrees of the Applications Computer setting. The operating
range for the probe is from 100°C to approximately 500°C.

Note The temperature is controlled by monitoring the output of the

thermocouple connected to the heater surrounding the metal tube.
The thermocouple output is compared with the temperature
setting at the TCB. The difference determines the power flow to
the heater.

The operating temperature should be adjusted relative to the LC mobile

phase composition and flow rate. In general, a combination of heat and gas
flow that allows the liquid spray to reach dryness before reaching the
Curtain Plate will provide optimum performance.
The TurboIonSpray probe is adjustable in two directions: towards the orifice
from a scale of 0 to 15 (adjustable by the X-Y mechanism mounted on the
TurboIonSpray probe, and side-to-side across the orifice from +5 to 0 by the
Lateral Adjustment control on the X-Y mechanism.
Turbo gas flows of approximately 5 L/min can be considered optimum for
conditions where heat is required. Ionization efficiency is improved with the
input of heat for all liquid flow rates. However, at lower flow rates
(<20 µL/min), the gains are small. Heat inputs may be desirable under low
flow conditions for the additional reason of enhancing in-source

40
 TurboIonSpray and Ion Source

(orifice-skimmer) fragmentation. Temperatures as low as 80° - 100° C have

proven useful for enhancing the capability (for example, phosphopeptide
mapping) when operating at low flow rates.

Figure 2-6. TurboIonSpray Unit

For more information, see the TurboIonSpray Ion Source Manual.

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TurboIonSpray and Ion Source

2.6 Service Procedures

Assembling the TurboIon Spray

Figure 2-7. TurboIon Spray Schematic

1. Install the gasket, the two windows and spring into the source housing
assembly. Using a spring tool, compress the spring, then rotate it 90°
clockwise to the lock position.
2. Place the O-ring into the vent fitting and insert this assembly into the
opening of the source housing.
3. Place the spring against the vent fitting and mount the Top Cover on
the housing using the screws and lock washers.
4. Connect the two gas fittings to the housing, then using the screws,
attach the connector strip. Loosely insert the set screw.
5. Slide the latch bushing onto the handle rod noting the orientation of the
flange. Slide the spring onto the handle.
6. Using the spring pin, attach the handle to the handle rod. Ensure that
the handle points in the same direction as the pin on the handle rod.
7. Carefully insert the handle assembly into the source housing. Support
the handle to ensure that the handle spring compresses.

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 TurboIonSpray and Ion Source

8. Using external retaining ring pliers, install the retaining ring in the
handle rod ensuring that it straddled the rod pin. Slide the clip past the
pin. While compressing the spring, carefully insert the retaining ring
into the groove of the handle rod. Be careful not to stretch the retaining
ring.
9. Using the two screws and the lock washers, attach the cable assembly
to the housing, then using a lock washer and nut, attach the ground
wire from the cable assembly to the mounting screw.
10. Connect the remaining wires from the cable assembly to the connector
strip.
11. Install the heater assembly on the housing and rotate the heater so
that the RTD is closest to the front face of the housing. Gently tighten
the set screw.
12. Slide the teflon sleeving over the two heater leads and connect the
RTD and heater leads from the heater assembly to the connector strip.
13. Measure the resistance of the RTD and heater across the connector
strip using a DVM. The values should be as follows:

Red to Black20 Ω
White to Blue110 + 10 Ω
White to Yellow110 + 10 Ω
Blue to Yellow5 + 2 Ω
14. Measure the resistance from each terminal on the connector strip to
the ground. All terminals should read >10M Ω to ground.
15. Place the O-ring into the X-Y mechanism and secure the X-Y
mechanism to the housing using the O-rings and screws.
16. Using a screw and lock washer, attach the tee to the handle. The tee
hole should face away from the housing.
17. Cut the tubing to the required length. Using the appropriate fitting and
ferrule, attach the tube to the probe assembly, then route the tubing
through the housing and attach it to the barb fitting.
18. From the outside, attach the HV cable to the housing by threading the
fitting on the cable into the housing.
19. Slide the clamp to the end of the probe, making sure that the threaded
hole is correctly oriented.
20. Gently screw the terminal end of the HV cable to the clamp to prevent
the clamp from distorting.
21. Route the gas tubing from the probe assembly through the slot in the
handle and attach the handle to the housing using the screws and lock

43
TurboIonSpray and Ion Source

washers.
22. Using retaining ring pliers, attach the retaining ring to the HV
connector on the HV cable. Place the ring into the groove at the wire
end of the connector. Insert the HV connector into the housing and
attach it to the housing using the two retaining rings.
23. Using the screws and lock washers, reattach the bottom cover.
24. Install the union fitting into the tee. Attach the other end of the tubing
to the probe assembly.
25. Attach the appropriate labels.
Assembling the TurboIonSpray X-Y Mechanism

Figure 2-8. TurboIonSpray X-Y Mechanism

1. Remove the nut from the micrometer head and unscrew the head to
the 12mm position. Place the nut in the guide slot in the top of the

44
 TurboIonSpray and Ion Source

guide and thread the micrometer head into the nut. Align the microme-
ter scale with the set screw hole in the top guide (keeping the nut
snug), install the set screw and tighten the micrometer jam nut.
2. Loosely install the four remaining set screws into the top guide.
3. Install two bearings into each side of the bottom guide. Ensure that the
bearings are fully seated in the guide.
4. Place the bottom guide into the top guide making sure that the bottom
guide ball is facing the micrometer head. Install the shafts into the top
guide until the ends of the shafts protrude through the bottom guide.
Slide the springs on the shafts and tighten the four set screws.
5. Attach the guide assembly to the housing plate using the four screws.
6. Attach the appropriate label on the shaft holder.
7. Install the O-ring and its bearing in the shaft holder.
8. Trim the other bearing and insert it in the shaft holder making sure that
you align the gap in the bearing with the shaft holder’s hole.
9. Attach the shaft holder assembly to the guide assembly (with the label
facing the micrometer head) using the four screws.
10. Install the O-rings in the bottom plate, twisting (to prevent damage to
the O-ring) the plate assembly (with the O-ring facing the plate) on the
end of the shaft holder and up to the bottom plate.
11. Place the spring on the end of the shaft holder and screw on the
bottom nut.
12. Place the spring in the notch left of the slot (90° counterclockwise) over
the long end of the T-shaft.
13. Push the spring and the T-shaft into the shaft holder making sure that
the other end of the spring goes into the hole in the shaft.
14. Compress the spring, rotate the shaft slightly counterclockwise, and
install and tighten the locking pin through the hole on the top guide.
15. Attach the outside nut to the inside nut using the two screws making
sure that the screws are in the center of the slots before tightening
them.
16. Install the washer on the T-shaft and place the nut assembly over the
end of the shaft. Compress the shaft spring and thread the nut
assembly on the T-shaft until “0” is reached on the scale.
17. Place two O-rings in the probe insulator, then lubricate the O-rings with
water and insert the insulator into the T-shaft.

45
TurboIonSpray and Ion Source

Note When the first O-ring passes the hole in the shaft, carefully
compress the O-ring to prevent it from tearing as the insulator is
fully inserted.

18. Rotate the probe so that the probe’s holes line up with the holes on the
T-shaft.
19. Place the O-ring on the probe’s tip and thread the tip into the probe
tube.

Note Carefully screw the tip into the probe to prevent the O-ring from
pinching. The O-ring must be completely inside the tube.

20. Place the O-rings on the probe tube, then carefully insert the probe
tube into the probe insulator making sure not to catch the O-rings. To
minimize catching the O-rings, rotate the probe as it is inserted.
21. Install the O-ring on the tube nut. Using tweezers, drop the nut on the
end of the tube assembly and tighten the nut until it bottoms. Blow out
the end of the probe with compressed air to remove any particles.
22. Install the O-rings in the fitting nut, and then place the ferrule into the
fitting. Insert the electrode into the fitting, slide the nut assembly over
the electrode and tighten it into the fitting.
23. Place the spring into the end of the T-shaft and carefully insert the
electrode assembly into the probe tube.
24. Thread the jam nut into the end of the T-shaft.
25. Insert the O-ring into the probe nut and thread the nut assembly into
the end of the T-shaft to hold the electrode assembly in place, making
sure that the electrode nut fits properly into the slots of the T-shaft.
26. Insert the O-ring into the probe insulator and install the plug fitting into
the T-shaft making sure that the hole in the T-shaft lines up with the
hole in the probe insulator prior to assembly.
Removing the Ion Source
1. Finish or abort any ongoing scans.
2. Shut down the sample flow to the Ion Source.
3. Loosen the two latches attaching the Ion Source to the Vacuum
Interface Housing. Turn the latches outwards until the Ion Source
Housing is loose.
4. Pull the Ion Source away from the Vacuum Chamber so that the
latches clear the connections in the Vacuum Interface Housing.

46
 TurboIonSpray and Ion Source

Opening the TurboIonSpray Ion Source

1. Finish or abort any ongoing scans.
2. Shut down the sample flow to the Ion Source.
3. Turn the latches on the front plate of the source. See the
TurboIonSpray Inlet and Ion Source figure.

Note Loosen the latches completely, but be aware that they cannot be
removed.

4. Remove the TurboIonSpray source from the front of the API 2000
instrument.
Removing the Peek Tubing
1. Unscrew the Peek tubing fittings from the probe inlet and grounded
union/splitter fitting and discard the old tubing (the
fittings may be re-used if they have not been over-tightened and
damaged). (see the TurboIonSpray Assembly figure).

Figure 2-9. TurboIonSpray Assembly

WARNING Peek tubing (or Fused Silica) with Peek fittings must be used
as the transfer line. Metal tubings or fittings must not be
used. The use of metal may expose the user to High Voltage.

47
TurboIonSpray and Ion Source

2. Obtain a new piece of 0.0025” Peek tubing (it must be at least 30 cm

long) and place Peek connection fittings on each end.
3. Connect the Peek tubing to the probe inlet and grounded union/splitter
fitting.

Changing The Stainless Steel Sprayer Tube

The standard TurboIonSpray set-up uses a 0.004” (100 µm) ID metal
sprayer tube. The procedure outlined below should be used to exchange
the metal tube in the TurboIonSpray in the event of blockage or degradation
of the sprayer tip.
1. Remove the TurboIonSpray and set on its side.
2. Disconnect the Peek transfer line from the probe inlet.
3. Unscrew and remove the black inlet probe fitting. A Peek union, metal
spring and the metal sprayer tube can now be removed from the
probe.
4. Unscrew the fitting holding the metal tube to the Peek union. Remove
the tube from the fitting and discard. Do not discard the fittings.

Note If you prefer, the procedure can be performed by removing the Ion
Source to a work table to perform the maintenance procedures on
the Ion Source.

5. Place a new sprayer tube and ferrule in the fitting and screw into the
Peek union. Ensure that the sprayer tube is placed as far as it can go
into the Peek union to guarantee a leak-proof seal (two wrenches
should also be used to tighten the fittings).
6. Place the metal spring and metal tube/Peek union back into the probe.
7. Place the black inlet probe fitting over the Peek union and tighten. This
fitting is used to adjust the protrusion of the metal sprayer tube tip at
the end of the probe. The metal tube should protrude approximately
0.75 mm, although a protrusion between 0.5 to 1.25 mm is also
acceptable.

Changing The Grounded Union/Splitter Fitting

A Peek tubing transfer line connects the sprayer probe inlet to a grounded
fitting that can be used either as a union or splitter. Since the liquid being
sprayed from the source is in contact with high voltages, the transfer line
must be connected to the grounded fitting.

48
 TurboIonSpray and Ion Source

WARNING The use of the Peek tubing transfer line connected to the
grounded fitting is mandatory since it prevents any exposed
peripherals connected to the source from floating at high
voltage.

The procedure outlined below should be used to change between the union
and splitter insert fittings.
1. Remove the TurboIonSpray and set on its side.
2. Disconnect the Peek transfer line from the ground fitting.
3. Disconnect any other fittings or tubing that may be connected to the
grounded fitting.
4. The insert within the grounded fitting should now move freely and can
be removed by tilting the source and allowing it to fall out.
5. Place the new insert into the fitting and align it such that all the
openings match.
6. Connect the Peek transfer line to the grounded fitting and any other
fittings or tubing that may be used.

WARNING Peek tubing (or fused silica) with Peek fittings must be used
as the transfer line. Metal tubing or fittings must not be used.
The use of metal may result in the exposure of high voltage
to the user.

49
TurboIonSpray and Ion Source

Removing the Electrode Tube

The electrode tube sticks out past the nebulizer tip. When installed, the
sprayer electrode becomes the end of the sprayer and carries the Ion
Source high voltage. The silica tubing slides through the electrode tubing.
1. Remove the TurboIonSpray source.

Note If you prefer the procedure can be performed by removing the Ion
Source to a work table to perform the maintenance procedures on
the Ion Source.

2. Using a 4" adjustable wrench, loosen the nozzle nut at the end by
turning it counterclockwise.
3. Remove the nozzle nut.
4. Using a pair of tweezers, carefully remove the electrode tube.
Replacing the Electrode Tube
1. Slide the electrode tube between the lips of the Nebulizer tube.
2. Thread the Nebulizer tube into the teflon sleeve.
3. Using an adjustable 4" adjustable wrench, give the teflon sleeve a 1/4
turn.
Cleaning the Sprayer Electrode Tube
This electropolishing procedure is used to clean the TurboIonSpray
electrode tube. It should be cleaned, as required.
The cleaning process requires the following equipment:
• One DC power supply (0 to 24V and 0 to 1A variable)
• One microscope
• Three copper or stainless steel crocodile clips
• Two stainless steel rods or tubing for use as cathodes
• One polypropylene (nalgene) container for electrolyte
• A solution of 60% phosphoric acid (H3PO4), 20% sulfuric acid (H2SO4)
and 20% water for use as electrolyte
1. Use crocodile clips to connect the two cathodes to the negative pole
of the power supply and the sprayer nozzle to the positive pole of the
power supply, as shown below.

50
 TurboIonSpray and Ion Source

Stainless Steel
Needle

Cathode Cathode

Electrolyte
DC Power
Supply
+
–

Figure 2-10. Electropolishing Apparatus

2. Immerse 5 mm (3/16") of the electrode tube tip into the electrolyte

bath.
3. Adjust the current on the power supply to 100 mA.
4. Slowly move the nozzle back and forth in the electrolyte for
approximately two seconds. Moving the electrode tube minimizes
bubble buildup around the area to be electropolished.
5. Rinse the electrode tube in water and examine the electropolished
area under a microscope to verify that the area is smooth and
undamaged.
6. If necessary, repeat steps 2 to 5.

51
TurboIonSpray and Ion Source

2.7 Source Exhaust System Service

2.7.1 Venturi Gas Supply
Maintenance procedures on the gas supply source exhaust system are few
as the potential failure points are small and easy to isolate. However, the
source exhaust system is an important safety feature and if it is not
functioning, it may prevent the instrument from operating.
There are three main console components that could cause the Source
Exhaust System to fail. They are:
• Solenoid valve
• Pressure switch
• AC Distribution
If these systems are functioning and the system fails to operate, a plumbing
problem, such as a substantial leak in the venturi line or a blocked gas line,
may be the cause of the problem.
The assembly schematic shows the system plumbing connections.
If the source exhaust system is failing, complete the following diagnostic
procedures with the instrument on, pumped down, the Source Cover
closed, and an Ion Source installed:
1. Ensure that the venturi gas supply is properly connected and supply-
ing the instrument.
2. Open the flow control valve on the Source Panel.
3. Check the pressure switch. Jump the switch connectors with a paper
clip. If that causes the system to work, replace the switch (see the API
2000 - Source Exhaust Pump figure).
4. Confirm that AC power is reaching the solenoid valve. Check that Pin
3 on the connector to the solenoid valve is live. If not, replace the AC
Distribution Board. For procedures on replacing the AC Distribution,
refer to the Power and Electronics section in this manual.

52
200 I'M INVISIBLE

3 Vacuum Interface
3.1 Overview
The Vacuum Interface separates the low pressure Vacuum Chamber from
the atmospheric pressure in the Ion Source. The purpose of the Vacuum
Interface is to allow the transfer of ions from the Ion Source to the Mass
Spectrometer while restricting sample, solvent and ambient air from
entering the Vacuum Chamber. This is accomplished using a “gas curtain”
of dry nitrogen.
The Vacuum Interface (see the figure below) comprises two distinct
pressure chambers: the Gas Curtain Interface and the Differentially
Pumped Interface. The two interface regions are separated by the Orifice
Plate that contains a 0.10” orifice through which the ions and a small
volume of Curtain Gas must pass before entering the Vacuum Chamber.

Figure 3-1. Vacuum Interface - Side View

53
Vacuum Interface

Ions are transferred from the Ion Source through the Vacuum Interface into
the Vacuum Chamber by the potential gradient across the Vacuum
Interface. The operator can adjust the ion flow by varying the voltages
applied to the Orifice Plate and the Focusing Ring. The Curtain plate
voltage is fixed and varies only in polarity depending on the polarity of ions
to be analyzed.
The Vacuum Interface is bolted to the main body of the Vacuum Chamber
for easy access to the interface and to the front bulkhead of the Mass Filter
Rail. For more information on the Mass Filter Rail, refer to the Vacuum
Chamber section in this manual.

3.1.1 Gas Curtain Interface

The Gas Curtain Interface is a small volume chamber at atmospheric
pressure that is flushed with a pure, inert Curtain Gas (nitrogen is
recommended). Curtain Gas is pumped into the interface at a rate ranging
from 0.6 to 2.0 L/min. Approximately 600mL/min of Curtain Gas flows
through the Orifice into the Differentially Pumped Interface, while the
remaining flows back into the Ion Source through the aperture in the Curtain
Plate.
The Gas Curtain Interface provides a region for ion declustering. In the
interface, sample ions collide with the gas molecules. The collisional energy
assists in breaking ion clusters and separating the sample ions from solvent
molecules. The controlled inert atmosphere in the interface helps to retain
the stable ion-molecule products from the Ion Source.
The Curtain Gas’ flow rate is set from the Applications Computer and is
physically controlled by a variable orifice valve controller. A detailed
description of the Organ Pipe and the Curtain Gas Control is contained in
the Vacuum Control System section in this manual. The gas line is
connected to the Gas Curtain Interface through a connection on the bottom
of the Vacuum Interface, as shown in the next figure.
To protect the sensitive components of the instrument, the Curtain Gas flow
is interlocked to the Pumping System and Ion Optics. If the Curtain Gas
pressure is more than 5 psig from the required pressure, the System
Controller disables the high-voltage supplies, sets the ion optic voltage to
zero, and turns off the Turbomolecular Pumps. When the gas flow is
restored, the System Controller automatically restarts the Turbomolecular
Pumps and attempts to recover the operating conditions. For more
information on the Curtain Gas control and safety locks, refer to the
Vacuum Control System section in this manual.

54
 Vacuum Interface

Figure 3-2. Vacuum Interface - Front View

3.1.2 Differentially Pumped Interface

The Differentially Pumped Interface is the first low-pressure stage in the
transition from the atmospheric pressure Ion Source to the low pressure
Vacuum Chamber. The pressure in the interface in maintained below 1.4
torr by the D16 Rotary Vane Interface Pump that is located outside the Main
Console. This pumping system is explained further in the Vacuum Control
System section in this manual.
Curtain Gas and ions are drawn from the Curtain Gas Interface into the
Differentially Pumped Interface by the pressure differential across the
Orifice Plate. The ions are further drawn through the Differentially Pumped
Interface by the voltage difference (for example, declustering voltage)
between the Orifice Plate and the Focusing Ring. The ions enter the
Vacuum Chamber through the aperture in the Skimmer.

55
Vacuum Interface

Vacuum lines connect the Interface Pump to the port underneath the
Differentially Pumped Interface (see the previous figure). The pump is
interlocked to the ion optics and the Pumping System by a pressure switch
connected to the vacuum port. If the pressure in the interface rises sharply,
the switch trips, notifying the System Controller of an Interface Pump fault.
The System Controller, upon receiving the indication of a pump fault,
disables the high-voltage power supplies, sets the ion optic voltages to
zero, and turns off the Turbomolecular Pumps until the pressure in the
Differentially Pumped Interface is restored.
Pure nitrogen is fed as CAD Gas to the Collision Cell in the Vacuum
Chamber. For more information, refer to the Collision Cell section in this
manual.

3.1.3 Entrance Optics

The Entrance Optics consist of the Curtain Plate, the Orifice Plate, and the
Focusing Ring. Voltage potentials applied to these elements help guide the
sample ions thorough the Vacuum Interface. The voltages applied to the
Orifice Plate and the Focusing Ring are controlled by the operator from the
Applications Computer. The Curtain Plate voltage is fixed. Depending on
the ions’ polarity (as determined by the operator), the Curtain Plate’s
polarity is automatically set. It is also heated up to 80°C to help with
desolvation.

Table 3-1. Entrance Optics Functions

Optic Element Function

Curtain Plate - separates the sample flow from the curtain gas flow
- is electrically isolated from the vacuum housing so
that the ions are not constrained to pass through
ground potential at this point
- ensures that the voltage is the computer-controlled
Orifice Plate - provides a division between atmosphere and the
approximately 1.4 torr pressure of the Differentially
Pumped Interface
- contains the 0.010" orifice
- is electrically isolated*
Focusing Ring - focuses the ions through the Skimmer into the
Vacuum Chamber
- is electrically isolated*
*The Orifice Plate and the Focusing Ring are electrically isolated such that a variable
declustering voltage of 0 to +350V can be obtained between them.

The power supplies used to generate the voltages applied to these

elements are located on the Lens Power Supply Board inside the System
Electronics Box (refer to the System Electronics Box Circuit Descriptions

56
 Vacuum Interface

section in this manual). For a list of standard voltage settings, see the table
below.

Table 3-2. Entrance Optics Standard Voltage Settings

Component ID *MS *MS/MS *Range

Curtain Plate ** +1 kV +1 kV +1 kV
Orifice Plate OR +35V +35V ± 200V
Focusing Ring RNG +300V +300V ± 400V
*Values are for positive ion mode. For negative ion mode, the voltages are
the same, but the polarity is reversed.
**The curtain plate voltage is not controlled by the software.

57
Vacuum Interface

3.2 Hook-up Schematic

Figure 3-3. Vacuum Interface Hook-up Schematic

The Vacuum Interface is bolted to the Vacuum Chamber, and can be

opened to expose both ends of the Interface and the front region of the
Vacuum Chamber. All external connections, including the Curtain Gas,
voltage connections, and vacuum line to the Interface Pump, are made
through the Vacuum Interface Housing (see the figure above).

58
 Vacuum Interface

3.3 Vacuum Interface Maintenance

Assembling the Vacuum Interface

Figure 3-4. Vacuum Interface Schematic

To assemble the Skimmer and Orifice:

1. Using the lock washers and the nut, install the contact on the skimmer.
2. Install the O-rings on the skimmer.
3. Using your hand, press the skimmer and the orifice plate assembly
together. Observe the orientation of the connector pins.
4. Using a soldering iron and an electronic grade solder, solder the pins
together, making sure the pins are straight and tight against each other
after soldering. Thread the completed assembly into the curtain plate.
5. Assemble the curtain plate on the skimmer/orifice assembly. Observe
the orientation of the curtain plate. The connector assembly should
line up with the through hole on the skimmer/orifice assembly. Press

59
Vacuum Interface

the assembly together by hand.

To assemble the Vacuum Housing:
1. Place the O-ring into the vacuum fitting. Using the two screws, flat
washers, and the lock washers, attach the vacuum flange to the hous-
ing.
2. Attach the gas supply fitting to the housing.

Note This fitting comes with a nylon gasket. Do not over tighten.

3. Attach the warning label.

4. Place the two strips of Kapton tape over the solder side of the heater
harness.
5. Using screws, lock washers, eyelets, flat washers, and nuts, attach the
interface heater harness to the housing. Do not over tighten because
the eyelets can be crushed.
6. Using the screw, flat washers, lock washers, and nuts, install the probe
heater cable assembly to the interface housing.
7. Install the ground wire under one of the mounting screws.
8. Remove the nut, O-ring, heat shrink, and circlip from the cable
assembly Ion Source HV#2.
9. Slide the HV cable through the housing and attach it to the housing
using the circlip.
10. Slide the heat-shrink tubing back into the HV cable. With the
heat-shrink tubing pressed tightly against the housing, shrink the
tubing against the wire and connector.
11. Re-install the nut and the O-ring on the cable assembly.
12. Cut three pieces of tubing, each 65 cm. long. Push the tubing into the
glass fittings.
13. Install the O-rings into the gas fittings and place the springs into the
back of the gas fitting. Install the gas fittings through the front of the
housing and secure it in place with retaining rings.
14. Attach the O-ring to the end of the interface drain and thread the drain
into the housing. Gently tighten the drain because over tightening will
cause the teflon ring to become distorted in the housing.
15. Install the O-ring in the fitting, and slide the assembly over the end of
the source drain fitting.
16. Install the skimmer/orifice assembly, making sure that the PCB is

60
 Vacuum Interface

properly seated. Install the three mounting screws and gently tighten
them.
17. Label the gas line (Gas 1, Gas 2, and Gas 3). Place the labels on the
appropriate tubes approximately 5 cm from the loose end of the tubes.
Opening the Vacuum Interface
1. Safely shut down the instrument.
2. Remove the Ion Source.

Note It is necessary to remove the Ion Source to open the Interface.

Removing it makes it easy to maintain the interface and reduce the
risk of damaging the Ion Source.

Note Ensure that the Interface’s ion optic voltage leads do not catch on
the Source Panel as the Interface opens.

Cleaning the Vacuum Interface

The Interface components (Skimmer, Curtain Plate, Orifice and Focusing
Ring) should be cleaned periodically to ensure optimal instrument
performance. Cleaning will keep the orifice clear, reduce electrical noise
and prevent samples from adhering to the Interface components and
altering the electrical performance of the Interface.
Both the Curtain Plate and the Skimmer can be removed and cleaned with
methanol and a clean lint free wiper (Kim Wipe™). You can clean the Orifice
and Focusing Ring without removing them. Because they do have fragile
components, extra care must be taken when cleaning them.

WARNING If hazardous, biohazardous, or radioactive materials have

been analyzed in the instrument, take all necessary
precautions as outlined on the material MSDS when cleaning
the Interface, Ion Source, and Vacuum Chamber components.

Caution Do not spray solvent or water through the orifice or into the
Vacuum Chamber.

Caution Take extreme care when cleaning the Orifice. Do not use a
cleaning wipe or a wire. The Orifice is very thin and can easily
be damaged. Do not sonicate.

61
Vacuum Interface

Note Always wear powder free latex gloves when cleaning the
Interface. Keep the components and Vacuum Chamber free of
dust and lint.

To clean the Interface:

1. Shut down the instrument.
2. Remove the Curtain Plate.
3. Remove the Skimmer.

Caution The tip of the skimmer is fragile. Handle it very carefully.

4. Clean both the Curtain Plate and Skimmer with methanol and a clean
lint free wipe. Spray the plates with dry gas to evaporate the residual
methanol or allow them sufficient time to dry before reinstalling them.
5. From the Skimmer (Vacuum Chamber) side of the interface, gently
clean the Focusing Ring and Orifice with a swab damp with methanol.
Take care not to damage the Orifice.
6. Allow the methanol on the Orifice and the Focusing Ring to dry.
7. Replace the cleaned Skimmer and Curtain Plate. Follow the
appropriate procedures.

62
 Vacuum Interface

3.4 Vacuum Interface Service Procedures

The Vacuum Interface is available as a Field Replaceable Unit (FRU) and
can be replaced in the field as a complete unit. However, for most Interface
field service repairs, the Interface can be disassembled and assembled
with replacement parts. The Curtain Plate and the Skimmer can be
replaced without disassembling the Interface.
Removing and Replacing the Vacuum Interface Assembly
Follow this procedure to remove and replace the complete Vacuum
Interface Assembly with a replacement assembly. The procedure
essentially involves disconnecting and removing the Interface, and then
installing the replacement.
To remove the Vacuum Interface:
1. Shut down the instrument.
2. Shut off all gas supplies.
3. Remove the Ion Source.
4. Disconnect the Curtain Gas’ connection. See the Vacuum Interface
Hook-up Schematic figure.
5. Disconnect the high voltage, interlocks coupling and gas connections
(using C-spring pliers), the source exhaust, and the vacuum hose.
6. Disconnect the vacuum line from the vacuum flange.
7. While supporting the Interface, using a 5 mm Allen key, unscrew and
remove the four screws that connect the Interface housing to Vacuum
Chamber.
8. Remove the Interface.
To replace the Vacuum Interface:

Caution Keep the replacement Interface clean and free of dust and
lint. Do not open the assembly until just prior to installation.
Wear powder-free latex gloves to prevent getting fingerprints
on the exposed Curtain Plate and Skimmer.

1. Before installing the new Interface assembly, use a multimeter to con-

firm that:
• There is electrical continuity between the Curtain Plate and the connec-
tor. See the Vacuum Interface Assembly figure.
• There is electrical continuity between the Orifice Plate and the connector.

63
Vacuum Interface

• There is electrical continuity between the Focusing Ring and the connec-
tor.
• The Focusing Ring and the Orifice Plate are electrically isolated. There
should be no electrical leakage between the Ring and the Orifice Plate.
• The Skimmer is grounded.
2. Hold the replacement Interface in position aligning it with the mounting
holes of the Vacuum Chamber. Insert the four screws that secure the
Interface housing.

Caution The Q0 rods protrude into the Skimmer. Be careful not to

damage the Q0 rods or the Skimmer when fitting the
Interface.

3. Adjust the Interface position so that the Interface housing fits flush with
the Vacuum Chamber housing and then completely tighten the
mounting screws.
4. Connect the high voltage, interlocks coupling and gas connections
(using a C-spring pliers), source exhaust, and vacuum hose.
5. Connect the Curtain Gas to the Interface.
6. Re-clamp the vacuum line from the Interface Pump to the vacuum
flange. See the Vacuum Interface Assembly figure.
Cleaning the Orifice/Skimmer Module
The Vacuum Interface components should be cleaned periodically to
ensure optimal instrument performance. Cleaning keeps the orifice clear,
reduces electrical noise, and prevents sample and solvents from
accumulating on the Interface components that can alter the electrical
performance of the Interface.

WARNING If hazardous, biohazardous, or radioactive materials have

been analyzed in the instrument, take all necessary
precautions as outlined on the MDS material when cleaning
the Vacuum Interface, Ion Source, and the Vacuum Chamber
components.

Caution Do not spray solvent or water through the orifice into the
Vacuum Chamber.

The front of the orifice can be cleaned without venting the instrument.

64
 Vacuum Interface

WARNING Using the overnight quit command before performing this

procedure allows you to remove the Ion Source. To fully
ensure that the high voltages are not applied, a full shutdown
(without venting) should be used. Windows NT and MAC
users should choose Standby from the Acquire Menu.

Caution When cleaning the orifice, take care not to damage it. The
orifice is thin and fragile.

To clean the front of the orifice:

1. Remove the Ion Source.

WARNING The Interface region is heated and the Curtain Plate can be
hot to the touch. Once the Ion Source is removed, the
Interface heater is automatically shut off and the Curtain
Plate will begin to cool down.

2. Remove the Curtain Plate.

Note When cleaning the Interface components, always wear powder-

free latex gloves, and keep the components and Vacuum
Chamber free of dust.

3. Slightly dampen a poly swab with 2-propanol or methanol and gently

wipe the Orifice Plate around and over the orifice. You may need to
use a small amount of water to remove any contaminants that are not
soluble in organic solvents. Ensure that the poly swab is not too damp.
Any excessive solvent can enter the Vacuum Chamber and cause the
pressure to rise above the instrument reset set point. If this does occur,
allow the instrument to pump down to the operating pressure before
proceeding with further cleaning or instrument use.
4. Remount the Curtain Plate.
5. Replace the Ion Source.
The back of the Orifice, Ring Electrode, and Skimmer can be cleaned by
shutting down and venting the instrument, then removing the
Orifice/Skimmer module from the Vacuum Interface.

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Vacuum Interface

Removing and Replacing the Orifice/Skimmer Module

Caution Keep the replacement Skimmer clean. Dust, dirt, even

fingerprints will contribute to chemical background noise. Do
not open the replacement Skimmer until just prior to
installation. Always wear latex gloves when handling the
Skimmer.

Caution Handle the Skimmer tip with care. The tip is fragile. Damage
to the tip will affect the instrument’s operation.

To remove the Orifice/Skimmer module:

1. Shut down the instrument.
2. Shut off all gas supplies.
3. With a 3.0 mm Allen key, remove the three hex-head screws that
attach the Curtain Plate and the Orifice/Skimmer module to the
Vacuum Interface.
4. Disconnect the clamp connecting the interface vacuum line to the
vacuum flange (see the Vacuum Hook-up Schematic figure).
5. Unhook the latch that closes the Interface housing to the Vacuum
Chamber, and swing open the Vacuum Interface.
6. To remove Curtain Plate and Orifice/Skimmer module, pull it
perpendicularly from the Interface. (see the Vacuum Interface
Assembly figure).

Note If the Curtain Plate/Orifice/Skimmer module stick to the Interface

collar, gently pull on the components.

To clean the back of the Orifice, Focusing Ring, and Skimmer:

1. Gently separate the Orifice Plate from the Skimmer.

Note If the Orifice/Skimmer module is tight and cannot be separated

manually, insert a small screwdriver between the two plates and
gently pry the Skimmer to loosen it.

2. Clean the Skimmer with methanol and a clean dust-free wipe. Spray
the Skimmer and Skimmer Plate with dry gas to evaporate the residual
methanol and allow them to dry completely before reinstalling them.

66
 Vacuum Interface

Note Do not use cotton swabs in any of the cleaning procedures

because they leave cotton fibres behind. Only use the poly swabs
that are provided with instrument.

3. From the Skimmer (Vacuum Chamber) side of the Interface, gently

clean the Focusing Ring and Orifice with a poly swab damped with
methanol. Take care not to damage the Orifice; it is very fragile.
4. Allow the methanol on the Orifice and the Focusing Ring to dry
completely before re-assembling them.
5. Re-assemble the Orifice/Skimmer module by aligning the two plates
such that the voltage connectors on the Orifice Plate pass through the
corresponding holes in the Skimmer Plate. Press together.
6. Replace the cleaned Orifice/Skimmer module according to the next
procedure.
To replace the Skimmer:
1. Place the Orifice/Skimmer module within the Interface Assembly align-
ing the voltage connectors on the module with the feedthroughs on the
Vacuum Interface. (See the Vacuum Interface Assembly figure).
2. Replace and tighten the three hex-head screws.
3. Power up the instrument.
Cleaning Q0
The high pressure entrance quadrupole (Q0) can become contaminated if
the instrument is operated with a curtain gas setting that is too low or if the
Ion Source sprays directly towards the Orifice. Symptoms of a
contaminated Q0 include a dramatic loss in sensitivity (typically a
factor of 5) and a decrease in ion peaks widths. For more information, refer
to the API 2000 Qualified Service Operator’s Manual.
To clean Q0:
1. Remove the Orifice/Skimmer module (see the procedure earlier in this
chapter) to expose the front of Q0.
2. Gently clean Q0 from the front to the end with the provided poly swab
dampened with methanol by carefully sliding it through the center of
the four quadrupoles. Do not use excessive force when inserting the
swab.

Note Do not use cotton swabs in any if the cleaning procedures

because the may leave cotton fibres behind. Only use the poly
swabs that are provided with the instrument.

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Vacuum Interface

3. Allow the methanol on Q0 to dry.

4. Replace the Orifice/Skimmer module, and then power up the
instrument.
Removing and Replacing the Curtain Plate

WARNING Using the overnight quit command before performing this

procedure will allow you to remove the Ion Source. To ensure
that high voltages are not applied, you will have to shut down
the instrument completely. Windows NT and MAC users
should choose Standby from the Acquire Menu.

To remove the Curtain Plate:

1. Remove the Ion Source.
2. With a 3.0 mm Allen key, unscrew the three hex-head screws that
attach the Curtain Plate to the Vacuum Interface.
3. To remove the Curtain Plate, pull it perpendicularly from the Vacuum
Interface.

Note In some cases, the Curtain Plate may stick to the Teflon mounting
collar. If this occurs, gently pull on the Curtain Plate.

68
 Vacuum Interface

Figure 3-5. Vacuum Interface Assembly

To replace the Curtain Plate:

1. Place the Curtain Plate in position against the Teflon portion of the
Vacuum Interface.
2. Replace and tighten the three hex-head screws.
3. Replace the Ion Source.
Disassembling the Vacuum Interface Assembly

Caution Dust, dirt, even fingerprints will contribute to electrical

background noise. Always wear powder-free latex gloves
when handling the Interface components. Take the necessary
precautions to keep them free of dust and dirt.

The Vacuum Interface Assembly comes as a Field Replacement Unit (FRU)

and can be replaced in the field as a complete unit.

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Vacuum Interface

To remove the Vacuum Interface Assembly:

Note Before performing this procedure, you should wait 15 - 20 minutes

to allow the Interface time to cool down.

1. Shut down the instrument.

2. Using a 2.5 mm Allen key, unscrew the three hex-head screws that
secure it in place. See the figure below.

Figure 3-6. Skimmer Plate/Curtain Assembly

3. Using a small screwdriver, remove the Curtain Plate by prying

between the Teflon piece. Gently remove the Curtain Plate from the
Interface Assembly.

Caution When removing the Curtain Plate, never insert the

screwdriver in the region of the PCB interlock. This can
damage the Vacuum Interface.

Re-Assembling the Vacuum Interface

If the rear Retaining Ring and Skimmer Plate remain intact, skip this portion
of the assembly procedure.
1. Ensure that the O-ring is in position around the Skimmer plate. See the
Vacuum Interface Assembly figure.

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 Vacuum Interface

2. Position the Skimmer in the Skimmer plate, making sure that the O-
ring is in place around the Skimmer flange.
3. Ensure that the gas feedthroughs and the Interlock feedthroughs are
aligned with the connections on the bottom of the Interface housing.

Caution Be careful not to damage the tip of the Skimmer. It is fragile.

4. Ensure that the Skimmer does not touch Q0.

5. Rock the Skimmer back and forth until it is in place. Push down firmly
to ensure that it is seated flush with the O-ring.

Figure 3-7. Interface Plate - Rear View

6. Align the Curtain Plate with the holes for the high power voltage, the
feedthroughs, and the three connectors. See the figure above.
7. Push the connectors until they are flush.
8. Using a 3.0 mm Allen key, slightly tighten all three screws first, then

71
Vacuum Interface

tighten one at a time.

9. With a multimeter, confirm the following using the Vacuum Interface
Hook-up Schematic figure as a reference:
• That there is electrical continuity between the Curtain Plate and the con-
nector.
• That there is electrical continuity between the Focusing Ring and the con-
nector.
• That there is electrical continuity between the Orifice and the connector.
• That the Focusing Ring and the Orifice Plate are electrically isolated.
There should be no electrical leakage between the Ring and the Orifice
Plate.

72
300 I'M INVISIBLE

4 Vacuum Chamber
4.1 Overview
The Vacuum Chamber is a single aluminum extrusion that houses the four
quadrupole rod sets, most of the ion optics, the Collision Cell, and the Ion
Detector (ETP). The quadrupoles, Collision Cell, and associated ion optics
are assembled on the Mass Filter Rail and inserted into the Vacuum
Chamber as a single unit (See the API 2000 Mass Filter Rail figure). The
Ion Detector, which is housed in the ETP module, is installed inside the
Vacuum Chamber after the Mass Filter is in position.
A seal formed by the Front Bulkhead on the Mass Filter Rail divides the
Vacuum Chamber into two distinct regions. The Q0 Region contains the Q0
rod set. It is located between the Vacuum Interface and the Front Bulkhead
on the Mass Filter Rail. This region is maintained at 8 x 10-3 torr by the split
DI220 LPS Turbo Pump.
The High Vacuum Region contains the three remaining rod sets and the
associated ion optics. It is maintained at about 1x 10-5 torr by the split DI220
LPS Turbo Pump. The Q2 quadrupole rod set is contained in the Collision
Cell that forms part of the High Vacuum Region (see the Collision Cell
section in this chapter). The Q1 and Q3 mass filter quadrupoles are located
on either side of the Collision Cell and are open for free pumping by the split
DI220 LPS Turbo Pump.

Note The Vacuum Chamber is safely interlocked such that if the

pressure inside the High Vacuum Region reaches 1 x10 -4 torr or
greater, all ion path voltages will be set to zero.

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Vacuum Chamber

Figure 4-1. API 2000 Mass Filter Rail

74
 Vacuum Chamber

4.1.1 Mass Filter Rail

The quadrupole rod sets and ion optics are installed, aligned, and wired on
the Mass Filter Rail before the rail is inserted into the Vacuum Chamber.
The front end of the Mass FIlter Rail is supported by the Front Bulkhead.
The other end of the Mass Filter Rail is bolted to the rear flange that seals
the detector end of the Vacuum Chamber. The Front Bulkhead can be
accessed through the Vacuum Interface to easily remove the Mass Filter
Rail.
All gas lines and internal wires are routed along the Mass Filter Rail. The
external ion optic and the gas connections are made through vacuum
connectors on the rear flange.
Vacuum Feedthroughs are used to connect the RF and DC voltages for the
Q1 and Q3 mass filter quadrupoles through the bottom of the Vacuum
Chamber. The leads are connected after the Mass Filter Rail has been
installed.

Caution The Mass Filter Rail cannot be removed unless the Vacuum
Feedthrough leads are disconnected.

For more information on vacuum feedthroughs, refer to the Vacuum

Feedthroughs section in this chapter.

4.1.2 Quadrupoles
The four quadrupoles are mounted on the Mass Filter Rail inside the
Vacuum Chamber. Q1 and Q3 are mass filters that selectively filter ions
based on their mass-to-charge ratio (m/z). Q0 and Q2 are RF-only
quadrupoles that have no filtering effect.

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Vacuum Chamber

4.1.3 Mass Filters (Q1 and Q3)

In the API 2000 instrument, both Q1 and Q3 are quadrupole mass filters. A
quadrupole mass filter consists of four cylindrical electrodes (rods) to which
precise DC and RF voltages are applied. The Q1 and Q3 rods are enclosed
by ceramic collars and positioned accurately on the Mass Filter Rail using
the locating pins.
In a paper entitled, “Energetic Ion Mass Analysis Using a Radio-Frequency
Quadrupole Filter”, published in Rev. Sci. Instrum. 49(6), June 1978, S.S.
Medley presents an excellent and concise review of the more salient
features of quadrupole mass filters. The following excerpt has been taken
from this article:
A quadrupole mass filter is constructed ideally of four
electrically conducting parallel hyperbolic cylindrical
surfaces. For convenient fabrication, most mass filters
are constructed with poles of circular cross section (see
the Mechanical and Electrical Configuration of a
Quadrupole Mass Filter figure). The best approximation
to a hyperbolic field using cylindrical poles is to space
them so that r = 1.16r0, where r is the pole radius and r0
is the radius of the inscribed circle which is tangent to the
four pole edges. Opposite electrodes of the filter are
electrically connected. To one pair is applied a potential of
U + V coswt, where U is a DC voltage and V is the peak
amplitude of an RF voltage at frequency w = 2πf . To the
other pair is applied a potential of the same amplitude, but
the DC voltage is of opposite polarity and the RF voltage
is shifted in phase by 180°.
Optimum performance of the quadrupole filter depends
on precise DC and RF fields along the entire length (L) of
the rod assembly which requires both high mechanical
and electrical stability of the applied voltages. The
fractional dimensional accuracy needed is given by
1/4 ( ∆M ⁄ M ) and required electrical stability is 1/2 ( ∆M ⁄ M ) ,
where M ⁄ ∆M is the mass resolution of the filter. The mass
resolution is controlled by the ratio U/V of the DC to RF
potentials according to the equation:

0.126
M ⁄ ∆M = --------------------------------
0.168 – 〈U|V〉

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 Vacuum Chamber

Figure 4-2. Mechanical and Electrical Configuration of a Quadrupole Mass Filter

Local radial variations in the pole’s dimensions are not as

detrimental to quadrupole performance as extended axial
errors, since these errors conceivably may have a
cumulative effect. Ions injected parallel to the Z axis of the
quadrupole undergo transverse oscillations caused by
the perpendicular DC and RF voltages applied to the
electrodes. The ion trajectories are described by Mathieu
equations, the solutions of which contain either an
exponential or an oscillatory factor, depending on the
charge to mass ratio (e/M) of the ion.
With proper selection of U and V, ions of a given e/M will
have stable trajectories, that is, they will oscillate about
the Z-axis and ultimately emerge from the opposite end of
the mass filter. Ion with other values of e/M will have
unstable oscillations which increase in amplitude until
they collide with the electrodes, thus being neutralized
and removed from the injected ion beam.

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Vacuum Chamber

Q1 and Q3 have very high mechanical precision necessary for achieving

high transmission and high resolution. The normal trade-off between high
ion transmission and narrow peak width must be optimized for each
particular application. Q1 and Q3 normally operate at a constant mass
width ( ∆M ) that is independent of the ion mass (M). Hence, the resolution
( M ⁄ ∆M ) in this mode of operation is directly proportional to the mass
being observed.
Q3 is also capable of being operated in “total ion mode” in which only RF
voltage is applied to the quadrupole rods (other terms are “RF-only mode”
and AC-only mode”). This essentially allows ions of all masses present in
Q3 to be transmitted to the Ion Detector.

4.1.4 RF-Only Quadrupole (Q0 and Q2) and Stubbies

An RF-only quadrupole is similar in construction to a quadrupole mass filter,
but is only capable of being operated in total ion mode (only RF voltage is
applied to the rods). In the API system, both Q0 and Q2 are RF-only
quadrupoles.
Q0 is mounted in the Front Bulkhead of the Mass Filter Rail. The Q0 rod set
focuses and transfers ions from the Vacuum Interface through the interquad
lens Q1 into the Stubbies and in the High Vacuum Region. The Stubbies
prefilter and transfer the ions into the Q1 mass filter. To optimize ion
transfer, both Q0 and the Stubbies are electrically connected to the Q1 RF
voltage. The RF voltage applied to Q0 and the Stubbies is a consistent
fraction of the RF voltage applied to Q1.
Q2 is housed inside the Collision Cell that is mounted between Q1 and Q3
on the Mass Filter Rail. It transmits ions through the Collision Cell into Q3.
Similar to Q0, the Q2 RF voltage is capacitively coupled to the Q3 RF
voltage. The Q3 RF voltage is capacitively coupled to the Q2 voltage so that
the Q2 RF voltage is ramped in a constant ratio with respect to that of Q3.
Q2 is an integral part of the Collision Cell. For more information on the
Collision Cell, refer to the Collision Cell section in this chapter.

4.1.5 Vacuum Feedthroughs

The amplified RF and DC voltages for Q1 and Q3 are connected through
the bottom of the Vacuum Chamber via the Vacuum Feedthroughs (see the
Vacuum Feedthrough figure). There are four feedthroughs: two for Q1 and
two for Q3. Each feedthrough carries the combined RF and DC voltages for
one pair of opposing quadrupole rods.
The feedthroughs are installed through punch-outs in the tops of the Q1 and
Q3 Coil Boxes into designated holes in the bottom of the Vacuum Chamber.
One end of each feedthrough lead is connected to the respective

78
 Vacuum Chamber

Interconnect Circuit Board inside the Vacuum Chamber; the other end to a
sleeve in the respective Coil Box.

Figure 4-3. Vacuum Feedthrough

4.1.6 Collision Cell

The Collision Cell is a ceramic housing pressurized with Curtain Gas. The
housing contains Q2 and is closed at either end by interquad lenses IQ1
and IQ2.
Ions enter Q2 through IQ2 and collide with the Curtain Gas molecules in the
cell. The collisions provide the energy needed to dissociate precursor ions
into fragment ions. All ions in the Collision Cell are transferred to Q3 where
the precursor or fragment ions can be selectively filtered and transferred to
the ETP for counting.
Curtain Gas is fed through a vacuum fitting on the end of the flange of the
Vacuum Chamber. The Curtain Gas line is then routed along the Mass Filter
Rail and fed through a hollow locating pin in the top of the Collision Cell.
Since the degree of fragmentation is a function of Curtain Gas thickness
(CGT), the CGT must be controlled. This is accomplished by controlling the
flow of Curtain Gas that has been re-directed from the Differentially
Pumped Interface and fed through a gas flow controller to the Collision Cell.
The gas flow is set by the operator from the Applications Computer. For
more information on Gas Flow Control, refer to the Vacuum Control System
section in this manual.

4.1.7 Ion Optics

The API 2000 ion optics are designed to help guide and focus the sample
ions through the mass filters and deliver these selected ions to the Ion
Detector. Voltage potentials are applied to the ion optics by the operator at

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Vacuum Chamber

the Applications Computer and can be varied for different sample and
application requirements.
The ion optics are illustrated in the API 2000 Ion Optics Path figure and
consist of the following:
• Curtain Plate
• Orifice Plate (OR)
• Focusing Ring (RNG)
• Stubbies (ST)
• Interquad Lenses (IQ1, IQ2, IQ3)
• Exit Lens (EX)
• Deflector (DF)
A list of ion optics standard voltage settings is provided in the following
table.
The Curtain Plate, Orifice Plate, and Focusing Ring are part of the Vacuum
Interface and have been discussed previously in the Vacuum Interface
section in this manual.
The Stubbies, Interquad Lenses, and the Exit Lens are mounted on the
Mass FIlter Rail. The Stubbies help transfer the ions from the Q0 region to
the Q1 mass filter in the High Vacuum Region. This lens is actually a
shortened version of an RF-only quadrupole (see the RF-Only Quadrupole
(Q0 and Q2) and Stubbies section described earlier in this chapter). The
Interquad Lenses help the transmission of ions into the respective
quadrupoles, the Deflector helps to improve the collection efficiency of the
Ion Detector.
The Deflector, Ion Detector (ETP), and support electronics are contained in
a separate module that attaches to the front of the Vacuum Chamber at the
detector end of the instrument. For more information, refer to the Ion
Detector (ETP) and Signal Handling section in this chapter.

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 Vacuum Chamber

Table 4-1. Ion Optics Standard Voltage Settings

Component ID *MS *MS/MS *Range

Ion Source IS +5 kV +5 kV 0 to 8 kV
Curtain Plate ** +1 kV +1 kV +1 kV
Orifice Plate OR +35 kV +35 kV +0 to +200V
Focusing Ring RNG +300 kV +300 kV +0 to +400V
Quadrupole 0 Q0 -10V 10V +0 to -17V
Interquad Lens 1 IQ1 -12.0V +12V +0 to -40V
Stubbies ST -15V -15V +0 to -40V
Quadrupole 1 Q1 -12V -12V +0 to -20V
Interquad Lens 2 IQ2 -25V -25V +0 to -200V
Quadrupole 2 Q2 -25V -25V +0 to -200V
Interquad Lens 3 IQ3 -100V -50V +0 to -200V
Quadrupole 3 Q3 -100V -26 to -28V +0 to -200V
Exit Lens EX +0V -0V +0V
Deflector DF 0V 0V -400 to 0V
Ion Detector ETP as optimized as optimized +0 to -
3200V
*Values are for positive ion mode. For negative ion mode, the voltages are the same,
but the polarity is reversed.
**The Curtain Plate’s voltage is not controlled by the software.

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Vacuum Chamber

Figure 4-4. API 2000 Ion Optics Path

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 Vacuum Chamber

4.1.8 Ion Detector (ETP) and Signal Handling

The figure below shows the makeup of the ETP Unit.

Figure 4-5. ETP Unit

The table below shows ETP voltage and its limits.

Table 4-2. ETP Voltage and Limitations

Mode DET Voltage Limits for DET- Voltage Limits for Bias Voltage
Positive 500V -6800 to -5500V < +1000V
Positive 2000V -6800 to -5500V +1600V to +2500V
Positive 3000V -6800 to -5500V +2600V to +3600V
Negative 500V +3600 to +4400V < +1000V
Negative 2000V +3600 to +4400V +1600V to +2500V
Negative 3000V +3600 to +4400V +2600V to +3600V

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Vacuum Chamber

ETP and the Deflector

ETP- Voltage
The ETP- voltage is fixed depending on the polarity of the ions that you are
analyzing. For positive ions, the voltage ranges from -6800V to -5500V; for
negative ions, the voltage ranges from +4000V to +3600V. This voltage
comes from the High Voltage Power Supply Board. The network divider is
used to supply the low voltage test point for the ETP- voltage. By using
1000 M Ω (R7) and 1.1M Ω (R6), the divider ratio is set to 1000:1
approximately. This enables an accurate test point when you are running
diagnostics. You can also reduce the noise by over 35db on the signal due
to rippling on the ETP+ terminal by adding a RC filter (R3//C3) in series.
ETP+ Voltage
The potential gradient is created with a second ETP voltage and the bias
voltage. The bias voltage applied to the end of ETP is typically set between
2000 to 3000 volts. Therefore, the actual voltage applied to the end of the
ETP is the combined ETP- voltage and bias voltage. The bias detector
voltages are also supplied from the HV Power Supply board. The network
divider is used to supply the low voltage test point for the ETP+ voltage. By
using 1000 M Ω (R4) and 1.1M Ω (R1), the divider ratio is set to 1000:1
approximately. This enables an accurate test point when you are running
diagnostics.
Deflector Voltage
The Deflector voltage is supplied by the Lens Power Supply Board. Its
varies from -400 to +400 volts and can be set by the operator at the
Applications Computer. The gas resistor (DS1) acts as a Surge Voltage
Protector for this circuit.
Signal Handling Board
The Signal Handling Board serves two distinct functions:
• Converts low-level Ion Detector output pulses to digital levels that can be
transmitted to the System Controller.
• Acts as a conduit for the ETP’s high voltages (power).
In pulse-counting-mode, the ETP responds to each strike by producing a
current pulse that flows through the connector socket (J1). This current
pulse then flows through a 511 ohm resistor (R1) producing a negative, bell-
shaped pulse (see the next figure).

84
 Vacuum Chamber

Figure 4-6. Response of the Signal Handling Circuit to Pulse Input

The amplitude of the pulse can vary up to about 200mV depending on the
ETP’s condition, bias voltage setting and other normal statistical variations.
The operational amplifier U1 is a precision voltage-feedback amplifier that
has a fast settling time, excellent differential gain and differential phase
performance. The non-inverting gain of U1 is set to 21 V/V via resistors R5
and R9. Resistor R7 and diodes D1 and D2 are only used to protect U1 from
potential transient conditions. The low-frequency gain of U1 is unity to
reduce the effect of DC level shift due to AC coupling of the input signal.
R15 and C5 are used for the +5V power supply filtering, whereas R12 and
C4 are used for the -5V power supply filtering.
The amplified pulse is conducted to the positive input of a high-speed
comparator (U2), where it is compared to a discriminator voltage applied to
the negative input of the comparator. The discriminator voltage (threshold)
is the minimum pulse strength for which the signal handling circuitry will
register an ion [Link] combination of the potentiometer R2, resistors
R3, R4, and capacitor C1 gives a stable negative DC discriminator voltage.
Using R2, this voltage can be adjusted between 0 and -200mV and can be
measured between TP2 (ground) and TP1. Resistors R13, R11 and
capacitor C3 are specifically used to introduce hysteresis at U2 by
temporarily injecting some positive feedback each time a pulse crosses the
discriminator level. This ensures a minimum output pulse width for the
counting circuit.
The non-inverted TTL output of the comparator U2 is passed to the System
Controller via a driver in U5. This driver converts its TTL input to balance
pseudo ECL levels. Pseudo ECL levels are the ECL levels shifted by 5V to
run on a single +5V power supply.
The “test signal” function helps verify the ion counting circuitry. The test
signal is a pseudo ETP output signal that originates at the System
Controller. When it is enabled, it transmits a pulse-like test signal to the
Signal Handling Board. This signal input is received and converted to TTL
levels by a receiver in U5. It is then fed to the positive input of the
comparator U2 via R8 and C13. If the signal handling circuitry is functioning
properly, the Applications Computer produces scan results with an ion
intensity equal to the frequency of the test signal.

85
Vacuum Chamber

4.2 ETP Service Procedures

Removing the ETP Module

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

1. Shut down and vent the Instrument.

2. Remove the console power cord from the right-hand side of the
bulkhead behind the instrument.

WARNING HIGH VOLTAGE. Follow the shut down procedure to ensure

that the voltage is disconnected.

Caution The ETP is fragile. Use care when installing the new ETP
assembly. Do not allow dust or dirt on the ETP assembly or
the vacuum feedthroughs. Contamination can cause
electrical noise.

3. Open the ETP Cover.

4. Disconnect the ETP Signal and Control Panel Cable from the Signal
Handling Board.

Caution Do not disconnect the ETP cable while voltage is applied to

ETP because it can damage the Signal Handling Board and
the System Controller.

5. Remove the two hex-head screws that connect the ETP housing to the
Vacuum Chamber.
6. Slide the ETP housing straight out of the Vacuum Chamber until the
guide arm clears the rear flange.
7. Place the ETP assembly carefully on a flat work space with the Signal
Handling Guard flat on the table.
Replacing the ETP Module
1. Remove the ETP Module and place it on a clean work surface.

86
 Vacuum Chamber

2. With a 3 mm Allen Key, remove the hex-head screw and associated

lock washer connecting the ETP mounting board to the stand off on
the vacuum flange. See the ETP Replacement figure.
3. Pull the ETP mounting board to release it from the four feedthroughs.
4. Without touching the ETP, attach a new ETP assembly to the
feedthroughs. Firmly push the ETP mounting board against the
feedthroughs to ensure a sound connection. Gently push the ETP
PCB back towards the Guide Arm.
5. Replace the hex-head screws that secure the ETP mounting board to
the vacuum flange.
6. Install the ETP module by sliding the ETP housing straight into the
Vacuum Chamber.
7. Replace the two hex-head screws that connect the ETP housing to the
Vacuum Chamber.
8. Connect the ETP signal and the Control Panel Cable to the Signal
Handling Board.

87
Vacuum Chamber

Figure 4-7. ETP Replacement

88
 Vacuum Chamber

Replacing the Signal Handling Board

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

The Signal Handling Board can be replaced with the ETP Module installed
in the Vacuum Chamber.

WARNING To prevent exposure to high voltage ensure that the

instrument is off and the power is disconnected before
opening the ETP Cover.

Caution Do not disconnect the ETP cable while the voltage is applied
to ETP because it can damage the Signal Handling Board.

Figure 4-8. ETP Module Assembly

Installing the ETP Module

89
Vacuum Chamber

1. Slide the ETP assembly into position. Make certain that the O-ring is
properly installed around the vacuum flange.
2. Re-connect the ETP Signal and Control Panel Cable to the Signal
Handling Board.
3. Secure the assembly by replacing the two hex-head screws with the
flat washers that connect the ETP vacuum flange to the Vacuum
Chamber.

90
 Vacuum Chamber

4.3Mass Filter Rail Service Procedures

When servicing the instrument, removing the Mass Filter Rail is always a
last resort. It is a rare occurrence for the ion optics to be the cause of a
malfunction in an operational instrument. Remove the Mass Filter Rail only
on advice from technical support personnel after exhausting all other
possible causes of instrument malfunction.
The Mass Filter Rail slides from the rear of the Vacuum Chamber as a
complete assembly. The Q1 and Q3 feedthroughs and the ETP Module
must be removed before the Rail can slide from the Vacuum Chamber.

Caution The Mass Filter Rail houses the fragile and sensitively
aligned ion optics. Handle the rail with care. Keep the rail
clean and wear powder-free latex gloves when handling it.

Note If ions can be detected there is no reason to remove the mass rail.

Removing the Mass Filter Rail

The Mass Filter Rail, the Q2 and the Q0 AC rod assembly are designed to
be Field Replaceable Units (FRUs). Do not attempt to repair them in the
field. Return the replaced assemblies to the factory for repair.
The Mass Filter Rail is dimensionally critical. The quadrupole support pins,
and locating pins are factory aligned. Do not attempt to re-position them.
1. Shut down the instrument.
2. Remove all instrument covers.
3. Remove the Ion Source and set it aside.
4. Disconnect all gas connections and the ion optic connection, and allow
the Vacuum Chamber to vent.
5. Remove Q1 and the Q3 Coil Box covers.
In both Q1 and Q3 Coil Boxes, there are two vacuum feedthroughs that must
be removed before the Mass Filter Rail can slide from the Vacuum Chamber.
6. The procedure to disconnect the feedthroughs is the same for both the
Q1 and Q3 coil boxes. For more information on the Coil Boxes, refer
to the Quadrupole Power Supply (QPS) section in this manual.
7. Unlatch the feedthrough latch locking mechanism to the feedthrough
housing. See the next figure.
8. Slide out the silver plate.

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Vacuum Chamber

9. Gently pull the front feedthrough out of the Vacuum Chamber, and
maneuver them out of the coil box.
10. Repeat steps 8 and 9 to remove the second feedthrough which is
directly behind the first.

Caution The vacuum feedthroughs are sensitive to contamination.

Always wear powder-free latex gloves when handling the
feedthroughs and place them in a plastic bag immediately
after removal to ensure they remain clean.

FEEDTHROUGH
HOUSING

SLEEVES

FEEDTHROUGH
LOCKING
MECHANISM

COIL BOX

COIL BOX
WIREFORMS

FEEDTHROUGH

Figure 4-9. Feedthrough Installation Schematic

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 Vacuum Chamber

11. Repeat steps 7 to 10 to remove the two feedthroughs in the other Coil
Box.
12. Remove the ETP Module.
13. Place the ETP Module on a clean surface and cover the ETP with a
dust-free covering.

Vacuum Chamber
Housing

O-Ring

Q0 Rod Set

Bulkhead
Flange

Lock Nut &

Flat Washer

Figure 4-10. Front Bulkhead

14. Loosen, but do not remove, the three lock nuts on the front face of the
bulkhead. See the figure above.

Note The nuts sandwich the O-ring between the Bulkhead Flange and
the Bulkhead forcing it against the Vacuum Chamber housing to
provide a vacuum seal. When the nuts are loosened the seal is
released allowing the Front Bulkhead to slide through the Vacuum
Chamber.

15. Disconnect the ion optics harness from the rear flange.

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Vacuum Chamber

16. Using a 6.0 mm Allen key, remove the four lock nuts securing the rear
flange to the studs mounted in the Vacuum Chamber housing.
17. Firmly and evenly, pull on the flange handle and slide the Mass Filter
Rail from the Vacuum Chamber. As the rear flange clears the mounting
studs, twist the handle 180° while pulling. If the Mass Filter Rail does
not slide, loosen the nuts on the Front Bulkhead until it slides through
the Vacuum Chamber.

Caution While removing the rail, ensure it does not scrape against the
side of the Vacuum Chamber. Keep the rail level as you slide
it clear of the Vacuum Chamber.

Caution The Q0 RF-only quadrupoles are attached to the Mass Filter

Rail on the front of the Vacuum Chamber Bulkhead. Care
should be taken to ensure that the quadrupoles are not
damaged.

Removing the Collision Cell

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

The Collision Cell is a standard quadrupole enclosed with two ceramic caps
to provide a localized high pressure region for MS/MS collisional
dissociation.
The ceramic caps that enclose the ends of the RF-only Q2 Quadrupole set
contain the interquad lenses IQ2 and IQ3.
The Collision Cell is supported on eight support pins, and located by one
locator pin, all of which are mounted on the Mass Filter Rail. It is held in
position by two springs that stretch around the Collision Cell and hook to
the Mass Filter Rail on either side. The springs also connect the voltages
for the IQ2 and IQ3 interquad lenses.
1. Shut down the instrument.
2. Remove the Mass Filter Rail.

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 Vacuum Chamber

Caution Care should be taken to ensure the Mass Filter Rail and the
ETP are kept clean and free of chemical or dust
contamination. Cover Vacuum Chamber openings with foil if
they are to be left open for any length of time. Always wear
powder-free latex gloves when handling the Mass Filter Rail
and Ion Optics to prevent contamination.

3. Undo all connections to the quadrupoles, the top and bottom of the
PCB, and disconnect all electrical wires to the unit.
4. Remove the PCB and the protective bar.

Figure 4-11. Collision Cell Installation

5. Undo the two screws at the bottom of the Mass Filter Rail and lift out
the collision cell. See the figure above.
Replacing the Collision Cell
1. Attach the two wireforms to the replacement Q2 rod set, as shown in
the figure above. Make certain that Q2 is aligned so that the Q2 locator
is positioned closest to the IQ2 Cup, and the wireforms oriented as
drawn.

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Vacuum Chamber

2. Set the collision cell on the Mass Filter Rail. It rests on eight support
pins and is located by one locator pin that fits inside the locator on the
underside of the Q2 collar.
3. Use a pair of needle nose pliers to stretch the two springs across the
collision cell. Hook the spring catches into the cut outs on both sides
of the rail.
4. If not already connected, connect the black and orange wires to the
springs; orange to the IQ2, black to the IQ3.
5. Place an M3 SS flat washer over each of the connecting posts on the
top of Q2 on top of the wireforms.
6. Reconnect the Q3 RF interconnect leads to the connecting posts as
shown in the previous figure.
Replacing Q1 an Q3 Mass Filters
Q1 and Q3 are made from identical rod sets. What distinguishes the
quadrupoles is the orientation of the rod set on the rail and the installation
of the wireforms.
1. Remove the Mass Filter Rail.

Caution Care should be taken to ensure the Mass Filter Rail and the
ETP are kept clean and free of chemical or dust
contamination. Cover Vacuum Chamber openings with foil if
they are to be left open for any length of time. Always wear
powder-free latex gloves when handling the Mass Filter Rail
and Ion Optics to prevent contamination.

2. Remove the Collision Cell.

3. With a 2.5 mm Allen key, remove the four screws connecting the four
Q1 RF interconnect leads to the interconnect PC board.
4. With a 2.5 mm Allen key, unscrew the two hex-head screws
connecting the Q1 wireforms to the underside of the Q1 Interconnect
PC board. See the Collision Cell figure.
5. Disconnect all wires from the underside of the Q1 interconnect PC
board.
6. Remove the two screws connecting the Q1 interconnect PC board to
the spacers mounted on the Mass Filter Rail, and remove the Q1
interconnect PC board.

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 Vacuum Chamber

Figure 4-12. Collision Cell

7. Slide the interconnect PC board into the space vacated by the collision
cell and remove it clear of the Mass Filter Rail.
8. Lift Q1 from the rail.
9. Unscrew the four screws that connect the two Q1 wireforms to the Q1
rod set. Remove and save the wireforms, the screws, washers and
lock washers. See the Collision Cell figure.
Replacing Q1 and the Interconnect PC Board

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

1. Connect the two Quadrupole wireforms to the replacement Quadru-

pole as shown in the next figure.

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Vacuum Chamber

Note For Q1, the wireforms are attached to the rod set at the end
opposite the locator on the bottom of the ceramic collar. Torque
the screws to 60 inch ounces.

2. Place the rod set into position on the Mass Filter Rail. The locator in
the Q1 collar fits over the locating pin on the rail. The lip of the collar
rests on four quad support pins.
3. Position the Q1 interconnect PC board on the Mass Filter Rail spacers
and screw the interconnect PC Board to the spacers. Make certain the
spring clip fixed to the interconnect PCB aligns with the indents on the
ceramic collar.

Note The interconnect PCB spring clip sits in the two indents on the
quadrupole ceramic collar. The clip along with the two screws
attaching the interconnect PCB to the spacers on the Mass Filter
Rail hold the mass filter in position.

Figure 4-13. Q1 Mass Filter and Interconnect PC Board

4. Screw the quadrupole wireforms to the underside of the Interconnect

PC board as shown in the Collision Cell figure.
5. Connect the RF interconnect leads to the Q1 interconnect PC board
as shown in the figure above.

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 Vacuum Chamber

Note It is essential that the leads are connected as shown so that the A
and B rods of Q1, Stubbies and Q0 are electrically aligned.

6. Connect all wires to the bottom of the Interconnect PC board.

7. Replace the collision cell.

Figure 4-14. Q1 - Q0 RF Connections

8. Install the Mass Filter Rail.

Removing Q3 and the Interconnect Board

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

1. Remove the Mass Filter Rail.

Caution Care should be taken to ensure the Mass Filter Rail and the
ETP are kept clean and free of chemical or dust
contamination. Cover Vacuum Chamber openings with foil if
they are to be left open for any length of time. Always wear
powder-free latex gloves when handling the Mass Filter Rail
and Ion Optics to prevent contamination.

2. Remove the Collision Cell.

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Vacuum Chamber

3. With a 2.5 mm Allen key, remove the two screws connecting the
Quadrupoles, all lens voltage wires, and the top and bottom of the
PCB. See the figure above.
4. With a 2.5 mm Allen key, remove the two hex-head screws connecting
the Q3 wireforms to the underside of the Q3 interconnect PC board.
5. Disconnect the white wire from the underside of the interconnect PC
board. Remove all connections to the spring mounts for the PCB’s
U-shaped filter.
6. Remove the two screws connecting the Q3 interconnect PC board to
the spacers on the Mass Filter Rail.
7. Remove the Interconnect PC board.
8. Lift the Q3 rod set from the rail.
9. Unscrew the four hex-head screws that connect the two wireforms to
the Q3 Rods. Remove and save the wireforms, the screws, washers
and lock washers.
Replacing Q3 and the Interconnect Board
1. Connect the two Q3 wireforms to the replacement Q3 ceramic collar
as shown in the previous figure.

Note For the Q3 rod set the wireforms are connect to the rod set collar
above the locator.

2. Position the Q3 rod set on the Mass Filter Rail. The locator on the
bottom of the Q3 collar fits over the locating pin on the rail. The lip of
the Q3 collar rests on the four support pins.
3. Position the Q3 interconnect PC board onto the spacers on the Mass
Filter Rail, and screw the interconnect PC Board to the spacers.
Ensure that the spring clip fixed to the interconnect PC board aligns
with the indents on the ceramic collar.

Note The interconnect PCB spring clip sits in the two indents on the
quadrupole ceramic collar. The clip along with the two screws
attaching the interconnect PCB to the spacers on the mass filter
rail hold the mass filter in position.

4. Screw the two Q3 wireforms to the interconnect PC board. (See the

previous figure).
5. Connect the Q3 RF interconnect leads to the interconnect PC board
as pictured in the Q1 Mass Filter and Interconnect PC Board figure.

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 Vacuum Chamber

Note It is essential that the leads are connected as shown so that the A
and B rods of Q2 and Q3 are electrically aligned.

6. Connect the white wire to the connector on the bottom of the

Interconnect PC board.
7. Replace the Collision Cell.
8. Install the Mass Filter Rail.

Figure 4-15. Q3 - Q2 Connection Schematic

Installing the Mass Filter Rail

The Mass Filter Rail is installed upside down in the Vacuum Chamber with
the quadrupoles actually hanging from the rail. This orientation aligns the
Interconnect PC boards with the coil boxes so the vacuum feedthroughs
connect with the Interconnect PC boards.
1. Before installing the Mass Filter Rail, wipe the inside of the Vacuum
Chamber with a dust-free wipe. Perform the following tests to confirm
the electrical connections:
• Check that there is continuity between the connector pins and the individ-
ual ion optics elements according to the following table:

Table 4-3. Continuity Check Pins

Pin Ion Optic Element

A Q3 Interconnect PC Board
Q2ROB
B IQ3
C IQ2
D Q2ROA

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Vacuum Chamber

E
F Stubbies
Q1 Interconnect PC Board
G IQ1
H Q0 Rod Offset

• Confirm that each pin on the connector has a path to the ground.
• Measure the resistance between the following points.
(The resistances should measure 20 mΩ ).
- Pin A to each connecting post on the collision cell
- Pin F to each of the Stubbies rods
- Red wire and each of the Q0 rods

Note Q0, Stubbies and Q2 rod offset voltages (Q0 STRO,Q2RO)

should be connected through a 20 mΩ resistor.

• Confirm that the resistance of the two RF chokes is less than 1 kΩ .

• Check that the Q0 shield is grounded.
• Check that the exit lens is grounded.
• Confirm visually that the Q1 and Q3 RF leads are connected to the Inter-
connect PC board.
2. Carefully insert the Q0 end of the Mass Filter Rail into the Vacuum
Chamber from the detector end of the instrument.

3. Slide the rail into the chamber, and turn the rail 180° so the rail is
oriented with the ion optics facing down, hanging from the rail.
4. Fit the rail so the four studs in the Vacuum Chamber housing fit
through the corresponding holes in the Mass Filter Rail’s rear flange.
Place a flat washer over each of the studs and tighten the four M6 hex
bolts.

Note Always tighten the Mass Filter Rail’s rear flange before sealing the
front bulkhead. This ensures that the rail remains straight inside
the Vacuum Chamber.

5. Through the front end of the Vacuum Chamber, tighten the six lock
nuts that connect the bulkhead flange to the Mass Filter Rail’s front
bulkhead.

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 Vacuum Chamber

Note To ensure the Mass Filter Rail remains straight, snug the bolts in
the order they are numbered in the Front Bulkhead figure. After
they are snugged, tighten them to the specified torque in the same
sequence.

6. Connect the Curtain Gas Fitting and ion optics cable to the rear flange.
7. Close and latch the Vacuum Interface.
8. Clamp the Interface Pump line to the Interface vacuum flange.
Installing the Vacuum Feedthrough Connections
9. Hold the first feedthrough by its ceramic collar, and insert it
perpendicular to the Vacuum Chamber through the right rear punch
out in the roof of the Q1 Coil Box.

Note Firmly and smoothly, push the feedthrough into position in the
Vacuum Chamber. Ensure that the feedthrough is inserted
straight up and down so that it connects with the collar on the
Interconnect PC board.

10. While holding the feedthrough in place, slip the connecting sleeve over
the end of the feedthrough.
11. Repeat steps 9 and 10 to install the second Q1 feedthrough directly in
front of the first.
12. Push the locking mechanism tight against the feedthrough housing
and tighten the thumb screw which holds the locking mechanism
closed.
13. Repeat steps 9 through 12 to connect the Q3 feedthroughs.

Note The procedure to install the Q3 feedthroughs is the same, with the
minor difference that the feedthroughs are installed through the
punch outs on the top left side of the Q3 Coil Box.

14. Check the following before closing the coil boxes:

• That the wireform sleeve connectors are seated securely over the two RF
detector connectors at the back of the coil box.
• That the wireform sleeve connectors are seated securely over both vac-
uum feedthrough connectors.
• That the soldered connections joining the tuning capacitors to the wire-
forms is secure, and that the lead from the capacitors is not broken.

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Vacuum Chamber

• That the fly leads from the top and bottom of each coil are soldered
securely to the wireforms. Each of the fly leads must not be closer to the
walls of the coil box than the wireforms.

Caution Failure to connect the coil boxes properly can damage the RF
detectors.

15. Replace the Q1 and Q3 coil box covers and tighten the 16 hex-head
screws with the associated washers.
16. Replace the ETP Module.
17. Connect the interface backing pump to the gas flange below the
interface.
18. Connect the three interface voltage connections: Curtain Plate, Orifice
and Focusing Ring.
Assembling the Ion Optics
1. Mount the Mass Filter Rail in the base and clamp fixture. Slide the AC
rods assembly in the Front Bulkhead, making sure that there is no
clearance between the face of the AC rod collar and the face of the
bulkhead.
2. Place the washers, spacers, and shield on the studs. Ensure that the
tabs on the shield are perpendicular before installation.
3. Install the shield nuts. Tighten the top nut first, then the other two
bottom ones. All nuts should be snug before the final tightening.
4. Check the AC rods assembly alignment by placing the Q1 mass filter
on the rail and visually check the vertical alignment between the
Stubbies and the mass filter. If the alignment is poor, replace the
required components.
5. Attach the purple wire to the AC rods assembly using the washer and
nut.
6. Fit the O-ring into the Front Bulkhead Flange and slide it over the
mounting studs to the bulkhead. Loosely install the flat washers, lock
washers and nuts. Tighten the nuts enough to hold the flanges
together, but not enough to compress the ring.
7. Assemble the wireform to the AC rods assembly. Torque the screws to
the required value.
8. Place the Q1 mass filter on the rail so that the locating pin engages the
hole in the rear collar of the Mass Filter Rail. Verify that the ground
surface of the collar is in contact with the four support pins by using a
0.05 mm feeler gauge.

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 Vacuum Chamber

9. Install the retaining spring clamp screw, the three flat washers, and the
lock washer into location on both sides of the Mass Filter Rail. Only
insert the screw two to three turns.
10. Install the clamps by pushing them down until the ends of the clamp
latches on to the rail. Tighten the screws.
11. Using the screw, flat washers, and lock washers, install the
interconnect PCB. Mount the PCB. Install the center screws first, then
install the remaining screws. Tighten the center screws first, then
tighten the remaining screws.
12. Using the screws and washers, connect the AC rod wireforms to the
interconnect board.
13. Using the screws, lock washers, and flat washers, connect Q1, Q2,
and Q3 wireforms to the interconnect PCB.
14. Install the protective bar and spring. Slide the spring over the end of
the bar, and then slide the spring and bar over the pin on the rear
flange. Line up the front of the protective bar with the pin on the Front
Bulkhead and release.
15. Connect the electrical harness wires to the bottom of the interconnect
PCB.

105
Vacuum Chamber

106
5 Vacuum Control System
5.1 Overview
The Vacuum Control System is elemental to the safe and reliable operation
of the instrument. A stable Vacuum Chamber pressure below 1 x 10-4 torr
must be maintained to perform spectrographic analyses. This is
accomplished using a Staged Pumping System.
The Vacuum System is controlled transparently by the System Controller.
When the instrument is switched on, the System Controller automatically
attempts to pump down the Vacuum Chamber. Only after reaching a stable
operating pressure will the System Controller enable the instrument’s
analytical components.
The pressure inside the Vacuum Chamber is monitored using a hot cathode
Vacuum Gauge. The System Controller continually monitors the Vacuum
Gauge output and several physical interlocks to determine the vacuum
status. If the vacuum integrity is breached, the System Controller will shut
down the instrument’s high voltages until the vacuum operating conditions
are regained.

5.1.2 Pumping System

The Pumping System uses a staged combination of Turbomolecular (turbo)
and Rotary Vane pumps to maintain the high vacuum pressure in the
Vacuum Chamber. The Q0 region of the Vacuum Chamber is maintained at
8 x 10-3 torr by a TW 220 LPS Turbo Pump. The high vacuum Q1 region is
maintained at about 1 x 10-5 torr by a TW 220 Turbo Pump. A D16E Rotary
Vane Pump, referred to as the roughing pump, maintains the Differentially
Pumped Interface at a pressure below 1.4 torr.

5.1.3 Turbo Pump

The TW 220 Turbo Pump is clamped horizontally to the side flanges at the
back of the Vacuum Chamber. The Turbo Pump is not connected directly to
the system electronics, but is controlled by a separate controller that is
powered from the AC Distribution Board. The Turbo Pump and its controller
are maintenance-free.
The TW 220 Turbo Pump has a cooling fan that is attached directly to the
back of the pump. The 24 VDC cooling fan is connected to the System
Controller through the motherboard, and runs continuously while the
instrument is switched on.

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Vacuum Control System

5.1.4 Turbo Pump Controllers and Gas Control Assembly

The Turbo Pump Controllers, (as well as the Gas Flow Controller assembly
for the gas control), are mounted on the chassis on the bracket at the inlet
end of the Main Console as shown below.

Figure 5-1. Turbo Pump Controller and Gas Control Assembly

The controller is a frequency converter that converts the single-phase AC

power from the AC Distribution Board into the three-phase, variable
frequency power required by the Turbo Pump’s induction motors. The
converter is controlled remotely by the System Controller as part of the
Vacuum Control System.

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 Vacuum Control System

The Turbo Pump Controller has four LEDs, labelled POWER,

ACCELERATION, NORMAL and FAILURE, that indicate the pump’s
operational status.
Upon receiving a signal from the System Controller, the Turbo Pump
Controller initiates a start-up procedure for the TW 220 Turbo Pump. This
includes a self-diagnostic routine during which the controller outputs are
turned off and the four indicator lights on the controller’s front panel are
illuminated. If the diagnostics routine completes successfully, the indicator
lights, with the exception of the POWER indicator, are shut off. The Turbo
Pump is then started and the ACCELERATION light illuminates as the
turbomolecular fans accelerate. The pump is in normal operating mode
when it reaches its rated rotational speeds. In normal operating mode, the
POWER and NORMAL indicators are illuminated.
During normal operation, the controllers monitor the Turbo Pump for
significant changes in turbo speed, operating parameter temperature, and
load faults. Should a fault occur, the controller shuts off the respective
pumps, and the controller’s FAILURE indicators are illuminated.
The instrument’s firmware detects the change in the Turbo Pump’s status
and attempts to re-establish operating vacuum conditions. If the Turbo
Pump fails to stabilize after three attempts within a set time-out period, a
hard fault is registered and the operator must restart the instrument. The
next figure shows a flow diagram of the Vacuum Pump-Down Sequence.

109
Vacuum Control System

Figure 5-2. Vacuum Pump-Down Sequence

110
 Vacuum Control System

5.1.5 Rotary Vane Pump

The second stage of the Pumping System entails a Rotary Vane Pump. The
Roughing Pump is connected to the exhaust ports of the Turbo Pump, and
acts as a backing pump in support of the Turbo Pump.
The Roughing Pump is housed outside the instrument’s main console and
is not controlled by the system firmware or the Applications Computer. It
also requires its own external 230 VAC, 50/60 HZ power supply, and is
operated manually using switches mounted on the pumps.
The operational status of the pumps is monitored using pressure switch
interlocks (see the Safety Interlocks section described later in this chapter).
The pump must maintain a pressure low enough to satisfy the Interlocks
before the System Controller will initiate the Turbo Pump. If the pressure in
either pump’s intake lines rises sufficiently to trip the Interlocks, the System
Controller shuts down the Turbo Pump and the ion optic voltages.
The Rotary Vane Pump features an Anti-Suck Back Valve and a Gas Ballast
Valve, which are described below. An optional smoke eliminator is strongly
recommended if the pump is operated in a closed environment. The pump
requires periodic maintenance that includes changing the pump fluid and,
if the mist eliminator is installed, replacing the mist eliminator’s coalescing
element.

WARNING If biohazardous or hazardous material is injected into the

instrument, all appropriate safety precautions should be
taken when handling the pump’s fluid and coalescing filter.
The fluid will be contaminated and should be handled
according to hazardous material safety regulations in the
country of use. (For example, WHMIS, in Canada).

5.1.6 Roughing Pump

The Roughing Pump is a Leybold D16E Rotary Vane Pump (see the next
figure). It eases the initial start-up load on the Turbo Pump by reducing the
pressure in the Vacuum Chamber to about 0.300 torr. It also creates a
pressure differential across each Turbo Pump’s exhaust ports, ensuring
that a back pressure does not overload the pumps.
The intake port of the Roughing Pump is linked to a vacuum line connecting
the Turbo Pump exhaust ports via the Vacuum Pump Bulkhead.

111
Vacuum Control System

Figure 5-3. Roughing Pump

112
 Vacuum Control System

5.1.7 Anti-Suck Back Valve

The Rotary Vane Pumps has a built-in Anti-Suck Back Valve that prevents
any pump oil vapors to pump exhaust back into the Vacuum Chamber. The
valve is triggered automatically when the pump is either shut off or there is
a power failure. As the main shaft rotation slows, a valve opens. This
causes the pumping chamber to vent and the Anti-Suck Back Valve to
close. When closed, the valve seals the pump intake isolating the pump
chamber from the instrument.

5.1.8 Gas Ballast Valve

The pump also comes with a manually controlled Gas Ballast Valve that can
prevent water vapor and other condensable gases from condensing in the
pump. Condensation degrades the pump’s fluid, limiting the pump’s
performance and life expectancy.
When opened, the Gas Ballast Valve permits a controlled volume of air into
the pump chamber. This lowers the partial pressure of condensable vapor
in the pump and causes the pump temperature to rise. These two factors
hinder condensation.

Note Operating the roughing pump with the Gas Ballast Valve open,
raises the pumps’ ultimate pressure, increases the pumps’ oil
consumption, and increases the amount of oil in the exhaust.

Given the controlled, dry atmosphere in the Vacuum Interface and the
Vacuum Chamber, condensation is not a problem. Therefore, under normal
instrument operating conditions, both Rotary Vane Pumps should be
operated with the Gas Ballast Valve closed.
The Gas Ballast Valve on the roughing pump is controlled by the lever on
the front of the oil casing (See the Roughing Pump figure). The Roughing
Pump Gas Ballast Valve is controlled from the black knob on the top of the
pump. To open the valve, turn the knob until one of the two holes on
opposite sides of the knob aligns with the opening in the valve below.

5.1.9 Smoke Eliminator

If the instrument is operated in a closed environment, it is highly
recommended that a Smoke Eliminator be installed on the exhaust ports on
the Roughing Pump to prevent the emission of oil vapors into the
environment, unless there is an oil exhaust system available.

5.1.10 Vacuum Gauge

A hot cathode Vacuum Gauge (see the figure below) is used to monitor the
pressure inside the Vacuum Chamber. The gauge is connected directly to

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Vacuum Control System

a port on the rear of the Vacuum Chamber between the Turbo Pump (refer
to the API 2000 System - Rear figure). It is controlled via the Vacuum
Gauge Controller.

Figure 5-4. Vacuum Gauge

The Vacuum Gauge produces and measures an ion current that is

proportional to the pressure inside the Vacuum Chamber. Electrons
produced by a controlled current flowing through the filament inside the
Vacuum Gauge accelerate towards the grid electrode that is held at a
potential of +150V. The electrons collide with gas molecules inside the
Vacuum Gauge tube creating positive ions. These ions are attracted to the
collector electrode that is held at -13V.
The ion current measured at the collector is directly proportional to the
vacuum pressure, the electron emission current flowing between the
filament and the grid, and the gauge sensitivity factor. By regulating the
electron emission current, the pressure inside the Vacuum Chamber can be
directly determined from the ion current measured at the collector.
The power supply for the filament is +6.5 VDC from the DC Power Supply.
The high voltage bias for the grid electrode (+150V) is generated by a
power supply on the Ion Path DACs and the Vacuum Gauge Control Board
inside the System Electronics Box. For description of the DC Power Supply

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 Vacuum Control System

and the System Electronics Box, refer to the Power and Electronics section
in this manual.

5.1.11 Vacuum Gauge Controller

The Vacuum Gauge Controller is located on the Ion Path DACs and the
Vacuum Gauge Control Board inside the System Electronics Box. It
performs the following functions (see the next figure):
1. Enables power to the Vacuum Gauge filament in response to the
‘Gauge Enable’ signal from the System Controller. This occurs after
the Turbo Pump Controllers reach normal operating condition (usually
below 10-3 torr.
2. Regulates the voltage applied to the Vacuum Gauge filament to
ensure a consistent electron emission current of 0.1 mA.
3. Provides the ‘Vacuum Ready’ signal to the System Controller to
enable the ion path voltages once the pressure reaches 10-4 torr.
4. Monitors the ion current signal at the Vacuum Gauge collector to
ensure that the pressure inside the Vacuum Chamber remains below
5.0 x 10-5 torr.

Figure 5-5. Vacuum Gauge Controller Block Diagram

If the pressure inside the Vacuum Chamber rises above 10-4 torr, the
Vacuum Gauge Controller sends a digital signal to the System Controller.
The System Controller then initiates the ‘Vacuum Off’ sequence, disables

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Vacuum Control System

power to the high voltage power supplies and the Turbo Pumps, and sets
the ion path voltages to zero. The System Controller also instructs the
Vacuum Gauge Controller to turn off the Vacuum Gauge to protect the
filament. The System Controller attempts to recover the vacuum integrity
automatically without operator intervention.
The low-level ion current signal measured at the collector is converted to a
high-level voltage signal. The signal is scaled such that one volt is
equivalent to 1 x 10-4 torr.

5.1.12 Gas Control System

Three gas flows are required for the instrument. They are:
• Nebulizer Gas (Gas 1)
• Heater Gas (Gas 2)
• Curtain Gas
Gas Flow Controllers
The controller circuit works by sensing the pressure in the volume of gas
between a variable inlet and a fixed orifice outlet. It continually adjusts the
pressure by varying the inlet to match the sensed pressure with the set
point pressure. If the pressure is too high, the inlet closes, allowing the
pressure to drop. If the pressure is too low, the inlet opens to raise the
pressure. As the measured pressure reaches the required set point, the
analog valve starts to close to a point where it is opened enough to keep
the flow through the controller the same as the flow through the orifice,
therefore keeping the pressure constant at the outlet.
When a lower pressure set-point is required, the valve closes completely
until the pressure at the outlet reaches the lower set-point (the pressure
drops because the higher-pressured gas is flowing through the orifice
without being replaced). At that time, the valve opens just enough to keep
the pressure constant. Reaching a lower pressure set point from a higher
one takes longer because lowering the pressure is achieved by letting the
pressurized gas out through the small orifice while increasing is achieved
by opening the inlet.
A temperature-compensated, pressure sensor is used to measure the
pressure volume of gas between the valve and the orifice. This type of
sensor gives an output that is linearly related to the gauge pressure and
only needs to be amplified when used in the controller. No calibration
trimports or temperature compensation networks are required. The gauge
sensor output is amplified with an integrated circuit instrumentation
amplifier.
The control actuator is a variable orifice valve (voltage sensitive orifice or
VSO) that responds to current input. The current drives a solenoid that

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opens the orifice against a spring (the VSO is closed with no applied
current). The drive current is controlled through a power transistor.
The control loop has proportional integral differential (PID) compensation.
The set-point inputs are differential analog voltage inputs with a 0 - 10 volt
input controlling the pressure from 0 - 100 psig. Analog pressure monitor
outputs are provided for system diagnostics. These outputs are buffered
and sealed from the amplified pressure sensor output.
The readback of the Curtain Gas pressure monitor outputs allows the
Curtain Gas pressure switches to be eliminated from the system. If the
supply pressure drops below the set-point pressure, then the pressure
drops and this is detected.
Nebulizer Gas (Gas 1) Flow
Nebulizer Gas is used to optimize the signal’s stability and sensitivity.
Typically, a value of 10 to 45 psi is used as applied by the Applications
Computer.
Heater Gas (Gas 2) Flow
Heater Gas aids in the evaporation of the solvent that aids in increasing the
ionization of the sample. The higher the liquid flow or the higher the
aqueous composition of the solvent, the higher the Heater Gas temperature
and gas flow required. However, a temperature that is too high, can cause
premature vaporization of the solvent, and result in a high chemical
background noise. A Heater Gas flow that is too high, can produce a noisy,
or unstable signal. For more information, refer to the API 2000
TurboIonSpray Ion Source Manual.

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Vacuum Control System

Figure 5-6. Gas 1/Gas 2 Control Connection Schematic

Curtain Gas Flow

The Curtain Gas is used to isolate the Ion Source from the Vacuum
Chamber. The gas acts, as its name suggests, like a curtain restricting the
flow of air, sample and solvent into the Vacuum Chamber. For more
information on the Curtain Gas, refer to the Vacuum Interface section in this
manual.
The Curtain Gas is connected through the Gas Connection Panel on the
chassis to the Gas Flow Controller assembly. For the Gas Flow Controller,
the Curtain Gas is connected to the Gas Curtain Interface through the

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Vacuum Interface housing. The flow is interlocked to the Vacuum Control

System and the ion optics by a pressure switch connected to the Gas Flow
Controller’s intake manifold. This is further described in the next section,
Safety Interlocks.
Gas Control Sequence
When the Vacuum Chamber pressure is stable below the Vacuum Ready
setpoint of 1 X 10-4 torr, the three gas flows are controlled by the operator
at the Applications Computer. However, when the instrument is either
pumping-down or venting, the Curtain Gas flow rates are set by the System
Controller independent of the software setting at the Applications
Computer. By overriding the software Gas Flow Controller settings, the
System Controller ensures the consistent, predictable behavior of the
instrument during pumping-down or venting.
During the pumping-down or venting, the Curtain Gas is set to its maximum
flow (that is, all three Gas Flow Controllers’ valves are open), and the
Curtain Gas is set to approximately half its maximum flow. In the Pump-
Down sequence (described later in this chapter), the Vacuum Gauge
Controller informs the System Controller that the vacuum is ready when the
vacuum pressure surpasses the setpoint (1 x 10-4 torr). Upon receiving the
Vacuum Ready signal, the System Controller releases the gas control to the
software.
After the Curtain Gas flow is returned to software control, the vacuum
pressure typically drops rapidly from the Vacuum Ready setpoint at
1 x 10-4 torr to the operating pressure specification at 1 x 10-5 torr. This
rapid decrease in vacuum pressure occurs because the Curtain Gas
software setting is generally considerably lower than the maximum flow set
by the System Controller.

5.1.13 Safety Interlocks

The Vacuum Control System has safety interlocks to protect the
instrument’s sensitive electronic components. These interlocks prevent the
normal operation of the instrument in the event that certain operating
parameters outside the direct control of the system circuitry are not
maintained.
The two interlocks that directly affect the pumping sequence are:
• Curtain Gas Flow
• Roughing Pump Pressure
When an interlock is triggered, the Vacuum Off Sequence is initiated (see
the Vacuum Control Sequence section in this chapter). The Turbo Pumps
are disabled and the ion optic voltages are set to zero. When the interlocks

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Vacuum Control System

are recovered, the system will automatically attempt the Pump-Down

Sequence.
A set of interlocks prevents the instrument from switching to ‘Analysis
Mode’ if a valid Ion Source is not properly installed. These interlocks do not,
however, affect the Pumping System. For more information, refer to the
Pumping System section at the beginning of this chapter.
Curtain Gas Interlocks
Curtain Gas flow is essential to the consistent and safe operation of the
instrument. Without a significant flow of Curtain Gas, the Vacuum Chamber
draws ambient air from the Ion Source, the moisture and composition of
which can negatively affect the operation of the instrument. Even though
small amounts of Curtain Gas enter the Vacuum Chamber with the sample,
the operation of the instrument is not detrimentally affected because the
quantity and the composition is controlled. For more information, refer to
the Vacuum Interface section in this manual.
A pressure switch connected to the Curtain Gas flow between the gas
cylinder and the Gas Flow Controller is triggered if the pressure drops
below a setpoint that corresponds to a flow rate of 0.7 L/min. If the interlock
is tripped, the Vacuum Off Sequence is initiated (see the Vacuum Control
Sequence section below) and the Turbo Pumps and the ion optic voltages
are disabled. The instrument automatically attempts to pump down when
the Curtain Gas Flow interlock is satisfied.
Roughing Pump Interlock
A pressure switch attached to the vacuum line that connects the exhaust
port of the Turbo Pumps to the Rotary Vane Roughing Pump acts as the
indicator of the Roughing Pump’s operational status. If the pressure in the
vacuum line rises significantly and triggers the interlock switch, the Vacuum
Off Sequence is initiated. The Turbo Pump shuts down and the ion optics
are disabled.
The instrument automatically attempts to pump-down when the vacuum
pressure in the Roughing Pump line is regained and the pressure switch
interlock closes.

5.1.14 Vacuum Control Sequence

On power-up, the instrument goes directly into Pump-Down Mode (see the
Operating Modes figure). The Pump-Down Sequence is controlled by the
firmware independent of the Applications Computer. This means that the
Pump-Down Sequence, once initiated, is transparent to the user.
When a stable operating vacuum pressure is established and the required
safety interlocks are satisfied, the instrument switches directly to ‘Analysis
Mode’. In ‘Analysis Mode’, the instrument is ready for spectrographic

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analysis; the ion path voltages, gas flows, and the other operating
parameters are controlled by the operator at the Applications Computer.

POWER ON

Pump-Down
Mode
Pump-Down
Sequence
(see Figure 5.x)
IF:
Interlock Fault
IF: Turbo Pump Fault
Gas Mode "Pump-down" Pressure Fault
Turbo Pumps "Normal"
Operational Vacuum
Interlocks Satisfied Vacuum Off
Sequence
Disable Turbo Pumps
Disable Vacuum Gauge
Gas Mode "Venting"
Analysis
Mode

Figure 5-7. Operating Modes

Pump-Down Sequence
The Pump-Down Sequence is initiated when the instrument’s power is
switched on. Before attempting to initiate the Turbo Pump, the status of the
system interlocks and fault conditions, including the Vacuum Gauge and
Turbo Pump status, are evaluated. The proper setting of the Curtain Gas is
verified, and when the initial conditions are correct, the control sequence
initiates the Turbo Pump.
The status of the Turbo Pump is monitored by the firmware control circuitry
(see the Turbo Pump and Turbo Pump Controller sections described earlier
in this chapter). If the Turbo Pump does not reach the normal operating
mode within a specified time-out period, the sequence triggers a ‘turbo
transition fault’. The system attempts to start the pumps three times. If the
pump fails to stabilize after the three attempts, the firmware controller
registers a hard fault and aborts the Pump-Down Sequence.
The Turbo Pump switches to the normal operating mode when its
turboblades reach its rated rotational speeds. Power to the Vacuum Gauge
filament is enabled 55 seconds after the Turbo Pump has reached its
normal status. The Vacuum Gauge output is not monitored until 10 seconds

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Vacuum Control System

after the gauge has been enabled. This delay allows the gauge output to
stabilize before it is used as a variable in the Pump-Down Sequence.
There is a two-stage pump-down sequence. When the Vacuum Chamber
pressure reaches 10-4 torr, the gases are put under the control of the
Analyst software. Before the electrons are enabled, the vacuum must reach
2 x 10-5 torr.
Vacuum Off Sequence
When the Vacuum Off Sequence is initiated, the Turbo Pump, ion optics
and Vacuum Gauge are disabled, and the gas flows are set to the values in
the Pump-Down state. The sequence then recycles to the beginning of the
Pump-Down Sequence. If the sequence fails in three attempts to regain a
stable operating pressure, a hard fault results and the system exits the
Pump-Down Sequence.

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5.2 Gas Control Service Procedures

The orifices for the three Gas Flow Controllers have a maximum pressure
rating of 100 psig, well within the recommended setting for the Curtain and
Nebulizer gas source pressure of100 psig. The orifices fit firmly into the
intake manifold and cannot be replaced individually in the field. Should one
of the orifices prove to be defective, the entire intake manifold assembly
must be replaced.
Removing the Gas Flow Controller

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

Note You can use the following procedure to all three Gas Flow
Controllers.

1. Shut down the instrument.

2. Remove all covers.
3. Disconnect the three gas connections from the control block.
4. Disconnect the input gas leads.
5. Remove the entire Gas Flow Controller.
Replacing the Gas Flow Controller
1. Position the Gas Flow Controller against the bracket and thread the
two hex-head screws with flat washers through the outlet manifold to
the bracket.
2. Connect the Curtain Gas supply cable, Gas 1 and Gas 2 cable
connectors to the solenoid valves.
3. Connect the gas lines to the fittings as shown in the Gas 1 / Gas 2
Control Connection Schematic and TW 220 Turbo Pump Mount
figures respectively.

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Vacuum Control System

Assembling the Gas Controller Module

1. Clean the block and fittings as per standard cleaning procedures.
2. Press the flow orifice into the Swagelok fitting. Using the stamping
fixture to hold the fitting, stamp the side of the fitting: F36.
3. Install the 1/8" Swagelok fitting into the control block.
4. Install the two 1/4" Swagelok fittings into the bottom of the control
block.
5. Install the two 10-32 plugs into the end of the control block.
6. Install the three tube barbs into the face of the control block.
7. Place the control block on a flat surface so that the valve-mounting
surface is facing up. Install the six O-rings in the counterbores.
8. Using the screws and washers, mount the first valve on the control
block, making sure that the valve ports are facing the control block.
9. Mount the remaining two valves on the control block.
10. Remove the protective plastic covering the Turbo Pump inlet ports.
Using isopropanol and a clean wiper, remove any glue residue.
11. Remove the two Turbo Pump centering rings from their packages and
discard the outer metal ring from both. Insert the centering rings into
the Turbo Pump ports on the Vacuum Chamber.
12. Mount the Turbo Pump to the rear of the Vacuum Chamber by sliding
the mounting plate on the two dowels in the rear of the Vacuum
Chamber, making sure that the pump fits snugly on the dowel pins.
13. Using mounting bolts, lock washers, and flat washers, fasten the
Turbo Pump to the Vacuum Chamber.
14. Install the vacuum gauge to the rear of the Vacuum Chamber using the
KF16 centering ring, the quick connect clamp, and the mounting
screws. Ensure that the gauge is pointed straight down.

Note The mounting screws should be tightened evenly by hand. DO

NOT use a wrench.

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5.3 Turbo Pump Maintenance

The Splitter Assembly unit is part of the Turbo Pump, and is an FRU that
can be replaced in the field. To replace the Turbo Pump, you must replace
the entire Splitter Assembly unit.
Replacing the TW 220 Turbo Pump
The TW 220 is part of the Splitter Assembly.
1. Shut down the instrument.

Figure 5-8. TW 220 Turbo Pump Mount

2. Open the Source Cover.

3. Remove the vacuum hose from the Interface.
4. Remove the Front Cover.
5. Unscrew the three screws and remove the T-connection from the
TW 220 Turbo Pump.
6. Unscrew the two screws that connect the controller connection to the
Turbo Pump.
7. Unscrew the four bolts that attach the Splitter Assembly to the Vacuum
Chamber. Using a wrench, remove the Splitter Assembly unit.
8. Ensure that the two centering rings are in place and slide the Splitter
Assembly unit back into position.

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Vacuum Control System

9. Slide the Turbo Pump into the Splitter Assembly.

10. Tighten the four bolts diagonally to center the unit.
11. Using the two screws, replace the controller connection.
12. Attach the T-connection to the TW 220 Turbo Pump by using the three
screws you removed in step 5.
13. Reattach the vacuum hose to the Vacuum Interface.
Replacing the D1220 Turbo Pump Controller

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

The Turbo Pump Controller is secured by a bracket that is hinged to the

chassis. The hinge allows the controller to be removed with minimal
disassembly.
1. Shut down the instrument.
2. Remove all covers.
3. From the back of the controller, remove the electrical connections, the
ground strap and disconnect the AC power cable and the TW 220
cable connecting the controller to the turbo pump. Also disconnect the
ground bracket from the back of the controller.
4. Using an 8 mm nut driver, remove the four nuts that secure the
controller box to the back plate.
5. Disconnect the remote control wires from the back of the controller.
The wires are part of the Turbo and Gas Flow Controller harness.
6. From the front of the instrument, remove the two Philips head screws
that attach the controller to the bracket.
7. Remove the two hex-head screws that secure the front of the bracket
to the chassis.
8. The bracket is hinged at the back. With the front bolts removed, you
can lift the chassis and remove the controller from the front.
9. Raise the controller bracket and slide the controller over the lowered
front panel clear of the controller bracket.

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 Vacuum Control System

Note You may need two hands to remove the controller. If this happens,
raise the bracket high enough so that the controller can be easily
removed. Place shims under the bracket support legs.

Figure 5-9. Turbo Pump Controller Connections

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Vacuum Control System

Replacing the D1220 Controller

10. Check that the voltage setting is set at the 220V setting as shown in
the figure above. If the indicator does not appear in the 220V window,
open the box, remove the circuit board and reinsert it so the 220V
value is readable.
11. Reverse the steps from 3 to 10 to replace the D1220 Controller.

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 Vacuum Control System

5.4 Rotary Vane Pump Maintenance

The routine maintenance for the rotary vane pump involves maintaining the
level and quality of the pump oil. If the pump oil level drops, or the oil
becomes contaminated, the pump performance will deteriorate and the
pump will suffer increased wear and may ultimately seize.
The pump oil level for both pumps should be maintained between the marks
on the oil sight glass when the pump is operating at close to its ultimate
pressure. If the pump oil falls outside these boundaries oil should be added
or drained.
The pump manufacturer recommends that the pump oil be changed under
the following conditions:
• When the oil is contaminated or every six months
• Before and after the pump is stored for a lengthy period
The condition of the pump oil can be determined by observing when the
pumps are operating. When in good operating condition, the oil will appear
light in color and be relatively clear. If the pump oil becomes dark, appears
dirty, or excessively turbid, the oil should be changed.
The D16E Roughing Pump has a separate sight gauge on the side of the
oil casing for observing the pump oil condition (see Roughing Pump figure).
Replacing the Rotary Vane Pump Oil

Note The pump oil should be changed when the pumps are warm. Use
the replacement oil as specified on the pump identification tag.
Use HE 200 for the D16E Roughing Pump.

WARNING If biohazardous or hazardous materials are injected into the

instrument, all appropriate precautions should be taken when
handling the pump fluid and the mist filter. Deposit
biohazardous material in appropriately labelled containers.
Potential risk of severe personal injury if proper procedures
for handling and disposing of biohazardous materials are not
followed.

1. Shut off and vent the instrument.

2. While the Rotary Vane Pump is still warm, remove the drain plug with
an 8 mm Allen key and drain the pump oil into a suitable container.
3. When the flow slows, replace the drain plug and switch the pump on
for not more than 10 seconds.

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Vacuum Control System

4. Remove the drain plug once more and allow the remaining oil to drain.
5. Replace the drain plug. Be certain the flat gasket is in good condition
and properly in place.
6. Open the oil-fill plug with an 8 mm Allen key wrench and fill the pump
with 1 quart (app. 950 ml) of the specified pump oil.
7. Replace the oil-fill plug.
Cleaning the Filter Trap
The Roughing D16E Rotary Vane Pump has a filter trap inside its intake
tubes. If the traps become clogged, the pump performance will deteriorate.
Given the controlled atmosphere in the Vacuum Interface and Vacuum
Chamber, it is unlikely that the filter trap will become clogged under normal
operating conditions. However, if the pump performance deteriorates, the
trap should be examined and cleaned, if necessary.
1. Shut down and vent the instrument.
2. Remove the vacuum intake line from the pump.
3. Lift the filter trap from inside the intake.
4. If necessary, remove any material in the trap.
5. Replace the trap and reconnect the pump.
Replacing the Mist Eliminator Filter
If the pump has the optional mist eliminator installed on the pump exhaust,
the mist eliminator filter should be replaced periodically.

WARNING If biohazardous or hazardous materials are injected into the

instrument, all appropriate precautions should be taken when
handling the pump fluid and the mist filter. Deposit
biohazardous material in appropriately labelled containers.
Potential risk of severe personal injury if proper procedures
for handling and disposing of biohazardous materials are not
followed..

1. Shut off and vent the instrument.

2. Unscrew the thumb screw on top of the mist eliminator and lift away
the top section of the eliminator to expose the coalescing filter.
3. Lift the filter out of the top of the Mist Eliminator housing.
4. Drop in a new filter.
5. Close the Eliminator and replace the thumb screw.

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 Vacuum Control System

5.5 Vacuum Gauge Service Procedures

The vacuum gauge must be replaced when the filament voltage required to
maintain the 0.1mA electron emission current surpasses 3.5V. Normally the
filament requires 1.5V to 3.5V to maintain the required electron emission
current.
The filament voltage can be read from test point TP1 on the Ion Path DACs
and Vacuum Gauge Controller Board. Normally the green LED D21 on the
Ion Path DACs and Vacuum Gauge Controller illuminates when the vacuum
gauge is enabled. However, if the filament voltage reaches the 3.5V ceiling,
the LED will not illuminate when the gauge is enabled.

Figure 5-10. Vacuum Gauge Assembly

Removing and Replacing the Ion Vacuum Gauge

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Vacuum Control System

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

1. Shut down and vent the instrument.

2. Open the Top Cover.
3. Disconnect the connector from the vacuum gauge.
4. Remove the Vacuum Gauge assembly by unscrewing the clamp that
connects the gauge to the Vacuum Chamber.
To replacing the Ion Vacuum Gauge:
5. With a clean lint-free wipe, clean the vacuum fitting on the new gauge
and the sealing surface of the Vacuum Chamber.
6. Re-clamp the Vacuum Gauge assembly to the Vacuum Chamber.
7. Reconnect the connector to the gauge.

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500 I'M INVISIBLE

6 Power and Electronics

6.1 Introduction
The most important part of the API 2000 is the System Controller and
on-board computer that controls and co-ordinates the operation of the
instrument. The System Controller controls all aspects of the API 2000,
including the ion optics and mass filter settings, scanning parameters, data
accumulations and preliminary data processing, without relying on the
Applications Computer.
Data acquisition experiments are designed by the operator at the
Applications Computer and uploaded to the System Controller. The System
Controller then initiates the acquisition and relays the data back to the
Applications Computer in the form requested. At the Applications
Computer, the data can be analyzed using the specific data processing
software: MassQuan, Multiview, or BioToolBox.
The computer power embedded in the System Controller frees the
Applications Computer to perform other independent tasks, including post-
data acquisition analysis or other user-specific applications.
This chapter outlines the instrument’s power requirements and the power
distribution module that distributes the power in the necessary form to the
system’s electronics and the main module equipment. It then describes the
System Controller and the other modules in the System Electronics Box
that control the instrument’s spectrographic functions.

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Power and Electronics

6.2 Power Distribution Module

The Power Distribution Module is the interface between the external 230
VAC power supply and the instrument’s electronics. The module supplies
all required power for operating the mass spectrometer.
Operating the instrument requires two separate 230 VAC power sources at
50 or 60 Hz. One single phase 230 VAC power source is required for the
instrument’s Main Console. The second is required for the two externally
mounted Rotary Vane Pumps. The Applications Computer, printer and
other accessories (including LC equipment) are powered separately from
standard wall outlets. An optional Line Adjustment Transformer can be
purchased to provide accurate, consistent power for the instrument and the
two Rotary Vane Pumps.
The instrument operates within design specification with line voltage
variations of 230 VAC +5% VAC. The OEM equipment including the Rotary
Van Pumps specify that line variations also be minimized to 230 VAC +5%
VAC.
All operating voltages for the instrument are generated from the 230 VAC.
The power is sub-divided at the AC Distribution Board and distributed by
detachable cables to the Main Console equipment. A DC Power Supply
converts the AC power into three distinct DC voltages.

6.2.1 AC Power Distribution

The AC Distribution Board is the instrument’s main power distribution
center. The 230 VAC power enters the Main Console by a detachable cable
and is fed through a filter to the main power switch on the Power Distribution
Panel. The switch doubles as a circuit breaker that trips and disables power
to the instrument, if there is a power surge. When the Power switch is “ON”,
power is directed straight to the AC Distribution Board where it is divided
and connected by detachable cables to the following equipment on the
Main Console (see the next figure):
• Main DC Power Supply
• Card Cage Cooling Blower
• Heated Nebulizer Inlet (optional)

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 Power and Electronics

Figure 6-1. DC Power Supply Connections

6.2.2 DC Power Distribution

The DC Power Supply converts the 230 VAC input power from the AC
Distribution Board into four DC voltages: +5.0V, -18V, +24V A and +24V B.
The DC voltages are supplied to the motherboard where they are available
to the modules that include the System Electronics Box and the main
module equipment. The DC Power Supply has a feedback sensing circuit
that ensures the consistency of the DC voltages across the motherboard.

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Power and Electronics

6.3 System Electronics Box

The System Electronics Box houses the following seven printed circuit
boards:
• System Controller
• Ion Path DACs and Vacuum Gauge Controller
• Lens Power Supply
• HV Power Supply
• QPS Exciter
• Q1 Amplifier
• Q3 Amplifier
These boards are contained in individual modules (see System Electronics
Box - Layout figure) to reduce potential electro-magnetic radiation and
susceptibility problems. Each module plugs into the common Motherboard
which forms the back of the System Electronics Box. Together, the modules
control the instrument and convert the input power into the precise RF and
DC voltages. These voltages drive the mass filters and supporting ion
optics.
The QPS Exciter Board and the Q1 and Q3 Amplifiers form part of the
Quadrupole Power Supply which provides the precise AC and DC voltages
to the Q1 and Q3 Mass Filters. Refer to the Quadrupole Power Supply
(QPS) section described later in this chapter.

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 Power and Electronics

Figure 6-2. System Electronics Box - Layout

6.3.1 Motherboard
The motherboard is the interface between the API 2000 equipment and the
System Electronics. Conceptually, the motherboard is the instrument's
electronic hub, supporting the necessary electrical interconnections
between the system’s printed circuit boards and the API 2000 main module
equipment.
The four DC voltages are connected through the motherboard to the
System Electronics Box modules and by detachable cables to the main
module equipment.

6.3.2 System Controller Module

The System Controller is the focal point for the instrument’s high-speed
data acquisition and control functions. It uses two highly integrated
microprocessors and associated memory chips with embedded software
(firmware) to control the operation of the instrument.
The instrument’s firmware essentially controls and coordinates all
instrument’s components and functions, including the ion optics, mass

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Power and Electronics

filters, collision cells, ion detector, gas flows and vacuum system. In
addition, the firmware facilitates the IEEE communication link with the
Applications Computer and the RS232 link with external sample
introduction devices. The following is a list of the major functions controlled
by the instrument’s firmware:
• Instrument control
• Scanning and data acquisition
• Preliminary data processing
• Communications to the host computer
• Mass calibration
• Instrument tuning
• Interface to sample introduction devices
• Maintaining configuration tables
• Error handling and reporting
System Controller Design
The next figure is a block diagram of the System Controller showing the
internal and external connections to and from the System Controller. The
different digital inputs and outputs, both external and internal, are listed in
the System Controller Digital I/O table.

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 Power and Electronics

Figure 6-3. System Controller Interconnect

Both System Controller microprocessors can be reset via common local

LEDs on the Power Module Cover. Resetting the microprocessors is similar
to rebooting a computer. It interrupts any ongoing procedures and discards
any data in the RAM memory. The System Controller’s microprocessors
also reset automatically when the +5V Power Supply on the motherboard
drops below ~4.6V.

Note Care should be taken when resetting the System Controller to

prevent the loss of unsaved data.

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Power and Electronics

The two on-board indicators, a red and a green LED are each driven by one
of the microprocessors. The red and green LED reset switches on the
Power Module Cover are external representations of the on-board LEDs.
While in reset mode, both LEDs are illuminated; otherwise they revert to
firmware control and definition. For more information on LED indicators,
refer to the Vacuum Control System section in this manual.

Table 6-1. System Controller Digital I/O

Internal External
Ion Detector Signal(s) IEEE-488
Synchronous Serial Link (SSL) RS-232
Scan Timing and Control (STC) Auxiliary I/O
Miscellaneous Parallel I/O Injection Manifold (optional)

Table 6-2. Miscellaneous Parallel I/O

Input Output
Curtain Gas Status Vacuum Gauge On/Off
Vacuum Ready Vacuum Voltages On/Off (includes
Interface High Voltages)
Interface Pump Status CAD Gas Pressure Control Organ Pipe
Backing Pump Status Curtain Gas Flow Control Organ Pipe
DI220 LPS Turbo Pump Status - Normal Turbo Vent Valve
Sample Interface High Voltage Interlock DI220 LPS Turbo Pump On/Off
Source Exhaust Pump Status (optional) Solvent Exhaust Pump On/Off (optional)
Injection Manifold Valve Position (optional)

6.3.3 Internal Functions

The System Controller’s main console functions can be divided into two
separate, but interrelated functions:
• Data Acquisition
• Instrument Control, Vacuum system and gas flows
Data Acquisition
Data acquisition experiments are designed by the operator at the
Applications Computer using the TUNE, or Sample Control software (see
the API 2000 Operator’s Manual). When an experiment is designed and
initiated, the necessary information is uploaded to the System Controller.
From that point, the data acquisition is controlled from the System
Controller’s firmware. The scan parameters are set and the data is acquired
in the format requested. The data is then relayed back to the Applications
Computer where it can be displayed as it is acquired, or saved to a specified
file to be analyzed later.

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The firmware is designed so that once a data acquisition method is defined,

it can be performed by the firmware without relying on the Applications
Computer. As a result, the firmware stores the necessary mass to DAC
calibration tables for both the Q1 and Q3 Mass Filters and the defined state
files that specify instrument settings.
The firmware not only stores calibration tables, but actually supports an
automatic calibration routine. For more information on calibration
procedures, refer to the TUNE chapter in the API 2000 Operator’s Manual.
The interactive routine requires the operator to specify the known mass
peaks for the sample to be injected. Given that information, the firmware
scans for the specified peaks and develops the mass to DAC value tables
necessary to interpolate subsequent DAC values and converts them to
mass units.
The firmware actually stores two calibration tables: a default table (stored
in the non-volatile memory) and an active table (stored in the RAM
memory). Either of these calibration tables can be transferred from the
System Controller to the Applications Computer where they can be
examined and saved.

Note It is recommended that you save the calibration files in a common

file on the Applications Computer disk so that they can be
uploaded to the System Controller’s memory when required.

Ion Optics Control

The System Controller firmware transfers the digital ion path parameter
data set at the Applications Computer to the appropriate DACs on either the
Exciter board, the Ion Path DAC, or the Vacuum Gauge Controller board.
The DACs, in turn, convert the digital signal into a low-level analog signal
that is transferred to the Lens Power Supply board, the High Voltage Supply
board, or the QPS Amplifier boards for amplification.
The ion path parameters are relayed using the SSL (Synchronous Serial
Link), a full duplex serial interface that provides a high-speed data
communication link. The SSL signals are not connected directly from the
System Controller to each DAC. Instead, each data transfer from the
System Controller specifically addresses a particular DAC and is sent to a
device on the Exciter board, the Ion Path DACs, or the Vacuum Gauge
Controller board. The device decodes the address and relays the data to
the preload register on the appropriate DAC.
When prompted by the Time Processing Signal, (refer to the next section
on the Time Processing Unit), the data in the preload register is loaded to
the DAC. This initiates the change in the ion optic voltages.

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Ion Counting
The System Controller receives a digital signal from the Signal Handling
Board, where each digital switch marks the boundary of a single ion pulse
(count). For more information on the Signal Handling Board, refer to the
Vacuum Chamber section in this manual. The System Controller has a
counter; in actual fact, two 32-bit counters. One counter is ‘active’; the other
is ‘inactive’. While the active counter counts, the inactive counter is re-
transmitting the previous count to the Applications Computer. After
successfully transmitting the count data, the inactive counter is cleared,
making it ready to become the active counter.
The configuration means that one counter is always available to count. The
counters alternate or toggle between active and inactive, leaving no dead
time between data measurements.
TPU (Time Processing Unit)
Both the Ion Counting and the Ion Optics Control functions depend on the
Time Processor unit or TPU signal initiated from the System Controller. The
TPU consists of five signals that control the sequencing of ion counting and
the uploading of ion path DACs. The table below lists the signals and
describes how the instrument responds to each signal.

Table 6-3. Scan Timing and Control (STC) Signals

STC Signal Description

Settling Gates on the ion counting/measurement process at a meaningful time,
such as after a large jump in mass once the mass filter has settled
down. When active high (1), it disables ion counting. When inactive
low (0), it enables ion counting. Also, its rising edge sets the QPS
Mass DAC (s) to whatever value is in the Mass DAC’s preload register.
Capture Point Its rising edge represents the end of one measurement period (dwell)
and the start of the next.
AMU Simultaneously updates all Ion Path DACs with the value currently in
their respective preload registers. This signal pulses low about once
per amu in ramp scan mode.
Increment Q1 Each rising edge increments the Q1 Mass DAC by one LSB. Used in
Mass ramp scan mode only.
Increment Q3 Each rising edge increments the Q3 Mass DAC by one LSB. Used in
Mass ramp scan mode only.

Instrument Control
The System Controller monitors the status of the vacuum system and the
related main console equipment using the Miscellaneous Parallel I/O
signals listed in the Miscellaneous Parallel table. As prescribed in the
System Controller firmware, the appropriate miscellaneous output signals
are triggered depending on the vacuum conditions. The firmware and the
miscellaneous I/O signals ensure consistent and predictable vacuum
system and gas flow behavior as outlined in the Vacuum Control System
section in this manual.

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6.3.4 Windows NT and Mac Users

Because Analyst runs on Windows NT, you can operate it in a network
environment. This means that you can perform some functions remotely,
which can save you time and effort. Analyst functions are divided into five
modes: Configure, Tune, Acquire, Explore and Quantitate. You can switch
from one mode to another without closing the current mode in which you
are working. For more information, see the Analyst Operator’s Guide.
The Tune mode allows you to:
• Perform mass calibration
• Set auto-tuning on or off
• Perform manual tuning
• Optimize resolution
• Set auto optimize quantitation
• Build a tuning method
• Build a quick single period, single experiment acquisition method
If you are a Mac user, you will notice that in Tune mode you no longer adjust
individual lens voltage. YOu now have to specify ion energies that
correspond to potential differences between the lenses. For differences
between Mac and Windows NT, refer to the Analyst Operator’s Guide.
To use this function, you must first log into Windows NT. The Navigation bar
that appears on the left-side of the Analyst window allows you to use the
various modes common to the Analyst software and allows you to quickly
access specific functions. When you double-click the icon for a particular
mode, the tree expands or collapses to show or hide icons for common
functionality within the mode you selected. These icons are shortcuts to
options or actions that components can perform.
Tune Software
The Tune software allows you calibrate and optimize your instrument. The
functions includes the following:
• Resolution optimization
• Mass calibration
• Quantitation optimization
• Manual tuning

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Mass Calibration
Before you begin mass calibration, you must set the tuning options.
1. From the Tool menu, click Settings, then click Tuning Options. The
Tuning Options dialog box appears.
2. On the Calibration tab, select the calibration standard, PPGs Pos.
3. Select the appropriate polarity, the reference and the appropriate
method
4. Click OK.
5. Ensure that the Manual Tune icon is active on the Navigation bar.
6. Acquire the data and select the spectrum.
7. On the Navigation bar, click Calibrate from Current Spectrum. The
Mass Calibration Option dialog box appears.
8. Type the search range, peak width and threshold you want and click
the Reference button. The Reference Table Edit dialog box appears.
9. Click the appropriate Use check boxes to select the masses you want
to calibrate and click Start. When the mass calibration ends, three
graphs are displayed in the Calibration window. The graph and mass
shift, shows the difference between the measured masses from the
current calibration and the true masses. The peak width graph shows
the peak width for each mass. For unit resolution this should be 0.7
amu at half height. The intensity difference graph shows the intensity
difference between the previous calibration and the current calibration.
10. In the Calibration Report window, you can:
• Click the Update button to update the calibration table with the new val-
ues. No changes will be made for masses in the existing calibration table
that were not calibrated during this operation.
• Click the Replace button to replace all values in the calibration table with
new values from the mass calibration.
Optimizing the Resolution
Before you begin, set the tuning options for the resolution optimization.
1. Ensure that the Resolution Optimization icon is active in the Naviga-
tion bar.
2. Click Resolution Optimization. The Auto Resolution Option dialog
box appears.
3. Select the calibration standard, PPGs Pos.

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4. To select the quadrupole or quadrupoles on which to perform the

resolution optimization, select the Q1 or Q3 check box, or both check
boxes.
5. To select the resolution or resolutions you want optimized, select the
Unit or High check box, or both check boxes.
6. Click Start. The automatic resolution optimization operation starts and
the Automatic Resolution Report begins to appear. When the function
is completed, a real-time display of the results of the operation is
displayed.
7. To save the resolution table, click Yes in the Save Resolution Table
message box.
8. To complete the operation, click OK in the Auto Resolution message
box.
Optimizing the Quantitation
Quantitation optimization allows you to automatically optimize the
instrument for best performance for both the infusion and the flow-injection
types of sample inlet. Analyst provides a wizard to aid you in setting up
quantitation optimization.
1. Ensure that the Quantitation Optimization icon on the Navigation bar
is active.
2. From the Tools menu, choose Quantitation Optimization. The
Instrument Setting dialog box appears.
3. Select Infusion as the inlet type; click MS Analysis and then click
Next. The Ions to use in MS Analysis dialog box appear.
4. Select the polarity. If you select Both, Analyst optimizes using both
polarities and selects the best polarity for each target compound.
5. Select the resolution from the list.
6. Select the target ion.
• If you select Base Peak Ion, Analyst optimizes one compound only. You
can name the compound and edit the search range. The label on the Next
button changes to Finish. Go to step 9.
• If you select MW Ion, Analyst can optimize more than one compound.
Go to the next step.
7. Click Next. The Target Components dialog box appears.
8. Type or edit the list of compounds, molecular weights and the number
of charges.
9. Click Finish. Quantitation starts and the Quantitation Optimization
Report is displayed.

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6.3.5 External Connections

The System Controller supports the external links to either the Applications
Computer, the injector manifold, or other LC sample introduction
equipment. The System Controller Digital I/O table lists the external
connections to and from the System Controller.
The IEEE-488 connection from the instrument to the Applications
Computer and the RS-232 and Auxiliary I/O port connections on the I/O
panel are primarily used to coordinate real-time activities between the
instrument and other LC sample introduction and detection devices. The
Injection Manifold is optional.

6.3.6 Ion Path DACs and Vacuum Gauge Controller Module

The Ion Path DACs and the Vacuum Gauge Controller board have two
distinct functions:
1. To provide reference voltages for control of the Ion Path, Ion Source
and ETP Power Supplies.
2. To provide power and control for the Vacuum Gauge.
If your system has the Heated Nebulizer option, this board performs a third
function, which is to provide control of the Heated Nebulizer Temperature
Controller.
Ion Path DACs
The Ion Path DACs convert the digital signals containing the ion path
voltage data into low-voltage analog control signals. The analog signals are
sent to the Ion Path Power Supplies on the Lens Power Supply board, the
Ion Source and the ETP Power Supplies on the HV Power Supply Board
where they are amplified to their target voltage.
Seven dual-output DACs with 12-bit resolution produce the output analog
voltages. Five of the DACs are configured for bipolar operation (-5V to
+5V), while the other two are configured for unipolar operation (0V to
+10V). An internal +5V reference is used for all DACs and is also passed
off-board to provide a fixed reference voltage for the ETP Power Supply. A
relay is used to disconnect the +5V reference voltage that zeros the outputs
of the DACs in response to the Reference Enable signal. Zeroing the DAC
outputs sets the ion optic voltages to zero.

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Figure 6-4. Ion Path/HV System Interconnect

Vacuum Gauge Controller

The Vacuum Gauge Controller enables power to the filament inside the
Vacuum Gauge in response to a signal from the System Controller. The
Vacuum Gauge is enabled when both Turbo Pump Controllers reach
normal operating conditions (usually below 10-3 torr). The operation of the

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Vacuum Gauge is described in the Vacuum Control System section in this

manual.
The power supply for the filament is +6.5 VDC from the Main DC Power
Supply. The actual voltage applied to the filament is regulated to ensure that
an electron emission current of 0.1 mA is maintained. The voltage required
to maintain the electron emission current increases as the vacuum gauge
ages. When the voltages reach 6.0V, the gauge should be replaced. For
information on replacing the Vacuum Gauge, refer to the Vacuum Control
System section in this manual.

6.3.7 Lens Power Supply Module

This board supplies all the DC voltages required by the ion optics, excluding
the ion path voltages that are part of the QPS (for example, Q1 and Q3 Rod
Offsets).
Eleven power supplies are required in total (see the Scan Timing and
Control (STC) Signals table), all of which are computer adjustable with the
exception of the Curtain Plate Power Supply that has a fixed output. There
is also sequencing logic to control polarity reversals that occur when the
polarity of the ion to be analyzed is switched.
The adjustable power supplies are actually configured as amplifiers whose
inputs are the low-level analog voltages from the appropriate DAC on the
Ion Path DACs and the Vacuum Gauge Controller board. The amplifiers are
powered by rail voltages of +530V and +270V generated by a switching
DC-to-DC converter. The DC-to-DC converter also produces a polarity-
reversible 1100V output for the Curtain Plate Power Supply.
Test points are provided on the front panel of the module for all adjustable
lens voltages.

Table 6-4. Lens Power Supply Ranges

Component S/W Mnemonic Power Supply Name Power Supply Range

Curtain Plate +1K VDC, fixed
Orifice Plate OR 200VPS1 +200 VDC
Focusing Ring RNG 400VPS3 +400 VDC
Q0 Rod Offset Q0 22VPS1 -22 to +22 VDC
Interquad Lens IQ1 22VPS2 -22 to +22 VDC
1
Stubbies ST 200VPS1 +200 VDC
Interquad Lens IQ2 200VPS1 +200 VDC
2
Q2 Rod Offset Q2 200VPS1 +200 VDC
Interquad Lens IQ3 200VPS1 +200 VDC
3
Deflector (DF) DF 200VPS1 +400 VDC

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The lens power supply sequencing logic is programmed to disable the

switching converter and zero the amplifier reference voltages from the ion
path DACs on initial power-up and during ion polarity reversal. In addition,
the ion path DAC output reference voltages are disconnected under the
following conditions:
a. In response to the Power Supply Enable signal (Vacuum and Safety Inter-
lock Dependent)
b. For approximately two seconds allowing an ion polarity reversal
c. For approximately one second following power-up of the +24V supply

6.3.8 HV Power Supply Module

This module contains three distinct power supplies that provide two high
voltages for the ETP (bias and float) and the voltage Ion Source. The Ion
Source power supply provides the high voltage required by the IonSpray
Inlet and, if the Heated Nebulizer is installed, the high voltage for the corona
discharge needle. The ETP bias voltage and the Ion Source voltages are
set at the Applications Computer.
The HV Power Supplies use the +5V reference voltage derived from the Ion
Path DACs and Vacuum Gauge Control board as a base reference.
Each power supply uses a power amplifier and a step-up transformer to
generate a high voltage AC waveform from the low-level DAC output
voltage. The AC voltage is then converted to a DC output voltage by a
bipolar voltage multiplier.

WARNING Wait one minute after powering down before removing

modules from the card cage. Nonhazardous high voltage is
still present in the back plane of the module one minute after
powering down the instrument.

ETP Float Voltage Supply

The ETP Float Voltage Supply is fixed depending on the polarity of ions
being analyzed. For positive ions, the voltage is -6000V; for negative ions,
the voltage is fixed at +4000V. This voltage comes from the HV Power
Supply Module.
The divider network is used to provide a low voltage test point for the ETP
voltage. By using 1000 M Ω (R7) and 1.1 M Ω (R6), the divider ratio is set
approximately 1000:1. This ensures that the test point is adequately
accurate when running diagnostics.
The noise on the signal due to the ripple on the ETP+ terminal can be
reduced by adding a simple RC filter (R3//C3) in series.

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ETP Bias Voltage Supply

The ETP Bias Voltage Supply creates the potential gradient. The bias
voltage is applied to the end of the detector opposite the horn. It is set
between 2000 - 3000 V more positive than the horn voltage. Therefore,
ETP+ is equal to the sum of ETP- and bias voltage. The bias detector
voltages are supplied from the HV Power Supply Board. Similar as the
ETP-divider network, R4 and R1 are used to provide a divider
approximately 1000:1.
Ion Source Power Supply
The Ion Source Power Supply generates a variable DC output between 0kV
and 8kV in either polarity. It operates in voltage-regulated mode with the
IonSpray Inlet. With the Heated Nebulizer, the voltage is adjusted to control
the current flow between the corona discharge and the Curtain Plate.

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6.4 Quadrupole Power Supply (QPS)

The QPS generates the precise DC and RF voltages that drive the mass
filters Q1 and Q3. It is designed for high stability and accuracy and consists
of two coil boxes, two Amplifier Boards and a common Exciter Board (see
the figure below).

Figure 6-5. QPS System Interconnect

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6.4.1 Exciter Board

The Exciter Board generates the source DC and RF voltages that are
relayed to the appropriate Q1 and Q3 Amplifier Module for amplification.
The Exciter Board consists of two sections: digital and analog.
Digital
The principal function of the Exciter Board’s digital electronics is to relay the
QPS digital data received over the SSL to the on-board DACs for
conversion to a low-level analog signal. The following ion path parameters
are processed on the Exciter Board:
• Q1 and Q3 Mass DACs (16-bit)
• Q1 and Q3 Rod Offset DACs (dual, 12-bit)
• Q1 and Q3 Resolution DACs (dual, 12-bit)
• RF Mode Setting
• Power Supply Enable
The low level analog DAC output signals are then relayed to the Q1 and Q3
amplifier modules for amplification.
The QPS, RF and DC output voltages can be switched “ON” or “OFF” at the
Exciter Board by the Global Power Supply signal. Switching off the Global
Power Supply disables the RF and DC output voltages locally. The Global
Power Supply signal is under firmware control and will automatically switch
off the QPS voltages if operating vacuum conditions or safety interlocks are
breached.

Figure 6-6. Power Supply Enable Logic

As a result, the following physical conditions must be satisfied for the QPS
RF and DC voltages to be on:
1. System Controller Global Power Supply output bit/line set to ON (zero
volts).
2. Sample Inlet Housing installed to satisfy mechanical interlocks.
3. Power Supply Enable bit set (logic high/one) via the SSL.

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Analog Portion
The Exciter Board’s analog circuitry produces the precise low-level mass
filter RF voltages that are amplified at the Q1 and Q3 Amplifier modules and
coil box assemblies. It is the precision of the QPS voltages that is the basis
of the enhanced performance characteristics of the API 2000 mass
spectrometer.
The analog circuitry contains thermally sensitive elements and as a result
is enclosed in a thermally isolated, temperature stabilized oven. The oven
is heated by four power transistors that are bolted to the oven extrusions.
The temperature is monitored and a feedback circuit drives a power
transistor that maintains a constant temperature in the oven.
The analog circuitry is powered by four IC voltage regulators independent
of the DC Power Supply. This ensures that noise from the DC Power Supply
does not corrupt the sensitive QPS electronics. The voltage regulators
produce +12 VDC and +15 VDC outputs.
The RF signals are developed from a 816 kHz signal generated by a crystal
oscillator. The active element in the oscillator is a current mode amplifier
that produces a sine wave output. The signal is filtered and then split to
provide drive signals for both mass filters. The separate Q1 and Q3 RF
signals are then applied to a multiplier stage that sets the RF signal level
depending on the Q1 and Q3 mass DAC outputs.
The actual RF voltage applied to the mass filters after amplification is
detected and used in a negative feedback loop that nullifies the gain
variations of the RF amplifiers and coil assemblies. The RF voltage is
measured at the back of the coil boxes by the RF detector boxes and
compared with the output of the appropriate Q1 and Q3 mass DAC. The RF
signal adjusts to ensure the accuracy of the RF voltage applied to the mass
filters.

6.4.2 Amplifier Boards

The Amplifier Boards condition and amplify the RF and DC signals received
from the Exciter Board and pass them to the coil boxes. There are two
identical Amplifier Boards, one for Q1 and the other for Q3. Each contains
an RF stage and a DC stage.
The RF amplifier output stage consists of 4 amplifiers arranged as a parallel
push/pull circuit. The amplifiers are powered by two IC voltage regulators.
The maximum output RF voltage is 30V peak-to-peak. This is relayed to the
coil box for final amplification.
The DC output stage consists of two DC amplifiers that use six series-
connected FETs to produce the required output voltage. The gain of the DC
amplifiers is controlled by a precision voltage divider, with a low
temperature coefficient. The circuitry of the two DC amplifiers differ slightly.
One has a +200V offset capability and the other has a -200V offset

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capability. The amplifiers have an output swing of over 800V. The outputs
are short-circuit protected.

6.4.3 Coil Boxes

The coil boxes are the final stage in amplification. Each coil box is an EMI-
tight enclosure that contains resonating coils, tuning elements and RF
voltage sensing components. The resonating coils have an RF voltage gain
of 275 that increases the voltage up to the 8000V peak-to-peak required by
the mass filters.
The high-voltage RF leads from the coil boxes to the mass filters are
connected via feedthroughs that are mounted underneath the Vacuum
Chamber. The RF leads are connected after the Mass Filter Rail is installed
inside the Vacuum Chamber. For more information, refer to the Vacuum
Chamber section in this manual.

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6.5 System Electronics Box Circuit

Descriptions
The System Electronics Box houses the seven PC board modules. It is
assembled separately and mounted as a unit to the chassis. Each of the
board modules slides into the Systems Electronics Box and plugs into the
motherboard that forms the back wall of the box. The API system’s main
module equipment is linked to the system’s PC boards via detachable
cables that plug into the rear of the motherboard.
The Card Cage Blower is bolted to the bottom of the System Electronics
Box and connected to the AC Distribution Board via cable AC P3 through
the back of the box frame.
Each of the seven PC Boards are mounted in the System Electronics Box
in separate modules designed to minimize electro-magnetic radiation and
susceptibility hazards.
The modular design of the PC boards simplifies field service procedures.
Should one of the system PC boards require replacement, the complete
module can be replaced in minutes. The defective board should be returned
to the factory for repair.

Caution Do not remove any of the system modules with the

instrument switched on. Doing so will damage the system
electronics.

6.5.1 Motherboard
The motherboard is the interface between the LC2 equipment and the
System Electronics. Conceptually, the motherboard is the instrument's
electronic hub, supporting the necessary electrical interconnections
between the System’s PC boards and the LC2 main module equipment.
The motherboard receives +5.0V, -18V, +24V A and +24V B inputs from the
DC Power Supply. A fourth 5 VDC supply is produced on the motherboard,
from the 6.5V input. The four DC voltages are connected through the
motherboard to the System Electronics Box modules and by a detachable
cable to the main module equipment.
Motherboard Circuit Description
The regulator U1 provides a 5 VDC output from the 6.5V input from the DC
Power Supply. It is heat sinked to dissipate 3 amps of continuous current.
Capacitors C7 and C8 shunt to ground any voltage surges on the 6.5V input
and the 5V output from U1.

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TP 1

TP 2

TP 3

TP 4

TP 5

Figure 6-7. Motherboard

Resistors R1 and capacitors C1 and C2 reduce the 24V input to the +VIN
voltage that is relayed to regulator U4 on the Signal Handling Board.
Similarly, resistor R4 and capacitors C3 and C4 reduce the -18V input to -
VIN that is relayed to regulator U1 on the Signal Handling Board. The 24
and -18 DC voltages are reduced on the motherboard to limit the heat
dissipation demands on the confined Signal Handling Board, where the
+VIN and -VIN voltages are regulated to produce +5V and -5V supplies.
Test Points
The motherboard has five test points on the upper left back corner of the
board for confirming the 4 DC voltages. The test points and the outputs for
each are listed below. The voltages as measured on the motherboard

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should fall within 2% of the nominal voltage over the life of the machine in
varying operating environments and under different load conditions. Test
point five is grounded and is the reference against which the other voltages
are measured.
• TP1+5V
• TP2+24 V B
• TP3-18V
• TP4+24V A
• TP5ground

Note A list of motherboard external cable connections and pin

assignments is provided at the end of this chapter.

Replacing the Motherboard

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

1. Shut down the instrument.

2. Open the Source Cover.
3. Remove the Back Cover.
4. Open the Front Cover.
5. Disconnect the gas fitting from the rear flange and allow the Vacuum
Chamber to vent.
6. Remove all modules and all connections from the back of the
motherboard.
7. Remove the seven PC board modules from the System Electronics
Box.

Caution Ensure the main power supply is off. Disconnecting the

system PC boards with the power on will damage the
instrument's electronics.

8. Remove the clamp that connects the vacuum gauge elbow to the
Vacuum Flange.

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Power and Electronics

9. Disconnect the cable linking the DI220 controller to the DI220 turbo
pump.
10. Disconnect the two wires from the backing pump sensor.
11. Remove the clamp attaching the vacuum port to the exhaust port of
the DI220 turbo pump. Rest the vacuum line on the bench supporting
the instrument.
12. Carefully snip the two cable ties that secure the Curtain Gas tubing to
the top of the motherboard.
13. Snip the three cable ties clamping the following cables to the
motherboard:
• Interface and Ion Source Voltages
• Ion Source HV Extension Cable
• ETP @ Control Panel
• ETP Bias Voltage
14. Snip the two cable ties clamping the RF feedback cables (connectors
J29, J30, J31 and J32) to the motherboard.
15. Disconnect all the external connections to the back of the
motherboard.
16. Remove the 20 Phillips screws that attach the motherboard to the
Card Cage assembly and remove the motherboard.
17. Position the replacement motherboard against the Card Cage
assembly and replace the 20 screws.

Note Ensure that the five tie screw mounts #6 are in place as shown in
the System Electronics Box - Motherboard figure.

6.5.2 System Controller

The next figure is a block diagram of the System Controller.
Intercommunications between the 68332 and 68340 microprocessors
utilize a 4 kB dual port RAM (U29). Either microprocessor can
independently read or write to any location in this memory.
Both microprocessors can be reset via a common local switch (SW1) on the
System Controller or by activating the two LED reset switches on the Power
Module Cover. If the +5.0V power derived from the +6.5V power supply
drops below ~4.6V, both microprocessors will reset. All other reset
scenarios, such as firmware reset instruction, affect only the relevant
microprocessor.

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Figure 6-8. System Controller Block Diagram

Two on-board indicators, a red LED (DS1) and a green LED (DS2), are
driven from the 68340 and 68332 respectively. While in reset mode, both
LEDs are illuminated, otherwise they revert to firmware control and
definition. The read and green LED reset switches on the Power Module
Cover are an external representation of the DS1 and DS2 indicators.
The microprocessor system clock (SCK) is generated by an on-chip,
phase-locked loop circuit used to run the device up to 16.78 MHz from a
32.768 kHz crystal. To minimize potential noise, the 68340 microprocessor
contains the oscillator circuitry into which the 68332 taps for its 32.768 kHz
source.
The microprocessor’s RAM consists of 128 kB static devices organized into
banks of 256 kB. The 68340’s memory consists of two such banks, while
the 68322’s memory contains only one. All RAM operates with zero wait
states and is both byte and word addressable.
Non-volatile memory consists of 128kB flash EPROM devices organized
into a bank of 256kB. This memory operates with one wait state and is word

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addressable only. It is used to store firmware, Xilinx configuration data and

other miscellaneous configuration information. The Flash EPROMs require
12V for erasing and programming. This voltage is derived from +24V via a
linear regulator (U3) that can be switched on (+12V) or off (~1.35V) from
either microprocessor.
68332 Microprocessor
The 68332 processor is a 132-pin device used for:
1. Controlling the Vacuum System and Sample Introduction (that is, most
internal digital I/O, not including Ion Detector signals)
2. Controlling data acquisition.
In general terms, the 68332 contains:
• A 68020-like CPU operating at 16.78 Mhz
• A highly specialized micro-coded counter/timer, the Time Processor Unit
(TPU) and 2kB of RAM assigned to the TPU
• A high-speed synchronous serial port, Queued Serial Peripheral Interface
(QPSI)
• One conventional serial port, “C”
• Miscellaneous system integration logic
Digital I/O interfaces to the 68332’s bus via U23 and U24 form an 8-bit port
occupying four contiguous addresses. Thirty-two discrete digital outputs
are provided. The state of each output is controlled by the value written to
a flip-flop contained in one of ICs, U6, U16, U18, or U25 regulators that are
all forced to zero (logic low) by resetting. Twenty-two CMOS (5V) logic
inputs from the input portion of the digital I/O. Each input includes a
4.7kΩ pull-up to +5V, series 10kΩ input protection and a 0.1µF capacitor
for noise suppression.
Data acquisition control relies heavily on the TPU and QSPI. Five TPU
signals are used for Scan Timing and Control (see the Scan Timing and
Control (STC) Signals table), while the QSPI is a submodule used to control
the Synchronous Serial Link (SSL).
The SSL is a full duplex, serial interface that provides a simple, high speed,
communication link between the System Controller and the Ion Path
electronics. It is primarily used to transfer ion path-related data, such as Q1/
Q3 rod offsets, lens voltages and polarities. The SSL also monitors and
controls the following signals:
• QPS status
• IonSpray voltage setting
• Heated Nebulizer temperature setting (optional)

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• Heated Nebulizer temperature status (optional)

• Ion Source current setting (optional)
RS-422 differential drivers and receivers are used to condition these
signals where they exit or enter the System Controller board.
68340 Microprocessor
The 68340 processor is a 144-pin device responsible for:
1. Communications between the Main Console and the Applications
Computer via IEEE-488.
2. Processing data acquisitors measurements results (that is ion
counting).
The 68340 shares the same general architecture and CPU core as the
68332. In summary, it contains:
• A 68020-like CPU operating at 16.78 Mhz
• A two-channel Direct Memory Access (DMA) controller
• Two conventional serial ports, “A” and “B”
• Two general purpose 16-bit counter/timers
• Miscellaneous system integration logic
The two-channel DMA controller is used to minimize real-time demands
imposed by the IEEE-488 link and incoming ion pulses. One DMA channel
is committed to the IEEE-488 port and the other to the System Controller’s
Xilinx device that is set up for data acquisition.
The Xilinx device is a Field Programmable Gate Array (FPGA) that is a
high-density, application specific IC that does not require custom factory
configuration. It consists of many uncommitted, digital devices which, when
interconnected for a particular application, form a custom circuit. The
principal role of the System Controller’s Xilinx device is a conduit for
incoming measurement results for the Ion Detector. As a function of STC
signals “Capture Count” and “Settling” from the 68332, it transfers
measurement results via DMA or an interrupt request. Since Xilinx
technology is SRAM based and therefore volatile, it must be configured
upon each power-up. This Xilinx device is configured by the 68332
processor via its Port E, bits 4, 5 and 6, in accordance with the Xilinx Slave
Mode Bit Serial protocol.
The IEEE-448 interface is implemented using Texas instruments. National
Instruments 9914A controller (U49) and 488 Interface chips (U50 and U59)
are miscellaneous logic. The very slow (2-wait state) controller that
functions as a talker or listener can interrupt the 68340 and/or generate
DMA requests to one of the 68340 DMA channels.

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The two serial ports, A and B, connect from the 68340 to the board’s edge
via the RS-232 driver and receiver pairs within U39 and U52. Port A, which
includes CTS and RTs control lines, is routed to the outside of the Main
Console.
Unlike the 68332, the 68340 has very few chip select lines. To produce the
required number and type of chip select/control lines, two 16V8 PALs, U47
and U45 regulators are utilized. U46, a simple 8-bit comparator, is used to
derive the optional co-processor chip select.

6.5.3 Ion Path DACs and Vacuum Gauge Controller

Ion Path DACs
The Ion Path DACs send low voltage analog control signals to the Ion Path
Power Supplies on the Lens Power Supply Board and to the Ion Source and
ETP Power supplies on the HV Power Supply Board.
Seven dual-outputs DACs with 12-bit resolution provide the required
reference voltages. DACs U12-14, 17 and 20 are configured for unipolar
operation (0V to +10V). The internal +5V reference of U12 is used for all
DACs and is also passed off-board to provide a fixed reference voltage for
the ETP Power Supply. PhotoMOS relay U9 is used to disconnect the
reference, zeroing the outputs of all DACs in response to the Reference
Enable signal.
A Xilinx FPGA provides decoding of the address and data instructions sent
over the SSL to set the DAC values. DAC data and address codes are
received over the SSL from the System Controller. U1-3 are bus receiver/
transmitter devices used to interface with Xilinx U6. U6 decodes the
serialized address and provides parallel data, chip select and strobe to set
up the parallel loading DACs. U4 is a serial PROM that configures Xilinx U6
on power up. U6 also generates signals to enable the High Voltage and Ion
Path Power Supply to select current or voltage controlled mode in the Ion
Source Power Supply and to switch the polarity of the power supplies.
Vacuum Gauge Controller
The Vacuum Gauge Controller enables power to the filament inside the
Vacuum Gauge in response to a signal sent by the System Controller when
both Turbo Pump Controllers reach normal operating conditions. The
Vacuum Gauge Controller provides the signal to turn on the vacuum
electronics once the pressure reaches 10-4 torr. If, at any time, the pressure
exceeds 10-3 torr, the Vacuum Gauge Controller turns off the Vacuum
Gauge to protect the filament.
The power supply for the filament is 1.5 VDC to 3.5 VDC from the DC Power
Supply through the motherboard. The filament is regulated to provide an
electron emission current of 0.1 mA. The next figure is a schematic of the
Vacuum Gauge Control Circuit.

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 Power and Electronics

A Gauge Enable signal from the System Controller enables power to the
Vacuum Gauge filament by resetting flip-flop U19b and enabling gate U16b.
This turns off Q5, unclamping the Q1 gate and allowing the control loop to
regulate the filament current. R41 and C46 provide a soft-start, slowly
turning on Q1 to minimize the drop in the 3.5V power supply.
The electron emission current is measured at the grid electrode. With a
0.1 mA emission current flowing through R13, the grid voltage is +150V.
The emission current is regulated by the error amplifier U11b and the
integrator U11a.

Figure 6-9. Vacuum Gauge Controller Circuit Schematic

The ion current is collected at -15V, generating a voltage across R25. This
differential voltage is amplified by the instrumentation amplifier U10, whose
gain is set to 10 by R19. The overall gain of the amplifier is 107V/A yielding
an output signal of 104V/torr (1V = 10-4 torr).
U15a and U15b act as window comparators to verify that the control loop is
in regulation, as indicated by LED D21. If the control loop is in regulation
and the pressure is below the operating set point, U18a generates the
Vacuum Ready signal to enable the ion path voltages. U18b monitors for
the over-pressure fault condition and will set U19 if the pressure exceeds

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10-3 torr, turning off the filament power. The gauge can only be restarted by
toggling the Gauge Enable signal to reset U19.
The filament voltage required to operate at an emission current of 0.1 mA
varies considerably from gauge to gauge, but is normally in the range of
1.5V to 3.5V. As the Vacuum Gauge ages, or if the filament becomes
contaminated, the filament voltage will increase to compensate. Once the
voltage reaches about 3.5V, the circuit will no longer be able to regulate the
emission current. Under this condition, the indicator LED on the front panel
(D21) will not light when the gauge is enabled. At that point, the vacuum
gauge requires replacement.
A second power supply generates the high-voltage bias for the grid
electrode. U1a is configured as a square-wave oscillator at approximately
13 kHz. The AC output is stepped up to 215 VDC by 6 times the voltage
multiplier and then zener-regulated to 200V and filtered for the grid supply.
The oscillator is disabled by Q2 when the Vacuum Gauge is turned off. U7
and U9 provide regulated +15V to the board.

6.5.4 Lens Power Supply Board

Eleven power supplies are required for this board. All power supplies are
computer adjustable except for the Curtain Plate Power Supply that has a
fixed output. Sequencing logic to control polarity reversal for the power
supplies’ polarity reversal is also provided.
The adjustable power supplies are configured as amplifiers whose inputs
are low-level DAC reference voltages. These amplifiers are powered by rail
voltages of +530V and +270V generated by a switching DC-to-DC
converter. Test points are provided on the front panel of the module for all
adjustable lanes voltages. The switching converter also supplies rail
voltages to the DC amplifiers on the QPS Amplifier Boards.
The low voltage amplifiers are high voltage amps configured as non-
inverting amplifiers with a gain of 5. Short circuit protection is provided by a
10K current-limiting resistor. Front panel test points are made through
another 10K resistor.
The power supply sequencing logic is required to disable the switching
converter and zero the amplifier reference voltages on initial power-up and
during polarity reversal. U1 provides a local +5V supply for the sequencing
logic. Q1 disconnects the reference from the lens power supply DACs to set
all outputs to zero under the following conditions:
1. In response to the Power Supply Enable signal.
2. For approximately two seconds following an ion polarity reversal.
3. For approximately one second following power-up of the +24V supply.

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U2c enables the polarity switching relays on the HV Power Supply Board
approximately one second after the polarity control signal is switched.
There are five +200V amplifiers identical to 200VPS1. These are supplied
with +270V rails from the converter. U13 drives an opto-coupled, single-
ended, high voltage FET Q14 output stage. DC gain is set at 51 by R96 and
R100 with loop compensation provided by C73 and C66. Zener D26
protects the gate of Q14 against over-voltage stress. Filter R101 C82
prevents back-coupling of RF and also limits output short circuit current. A
100:1 voltage divider is provided for the front panel test point.
The design of the 400V amplifier is nearly identical to that of the 200V
amplifier except that the gain is increased to 101, the rail voltages are
+530V and the output voltage is shared across two FETs.
The DC-to-DC converter has an input of +24V and 7 outputs: +1100V,
+530V, +270V and a polarity-reversible 1100V output for the fixed Curtain
Plate Power Supply. The converter uses a number of clamped capacitor/
peak rectifier stages to generate the various output voltages from only two
secondary transformer windings. It operates partly as a flyback converter
and partly as a forward converter.
The circuit is controlled by pulse-width modulation controller IC U3. The
switching frequency set by C18 and R23 is 22Hz. U3 regulates the +1100V
output voltage by adjusting the duty cycle of switching transistor Q3 that
varies between 20% and 40% depending on the load. The switch current is
sensed by R6 and R7 and is filtered by R13 and C2. U3 monitors the current
and will limit the duty cycle on a pulse-by-pulse basis in the case of an
overload. Loop compensation is provided by C17, C25 and R26. C10, R14
and D2 form a snubber to clamp leakage inductance spikes and protect Q3
from damage. The +24V supply is filtered by L1, C34, C20 and C21. Q2 and
Q4 are used to disable U3 in response to the Power Supply Enable signal.
The Curtain Plate Power Supply includes relay K1 to switch the output
supply polarity. The DC current delivered to the Curtain Plate flows through
R15. The voltage developed is buffered by U4b and is used to regulate the
Ion Source Power Supply in regulated mode.

6.5.5 High-Voltage Supply Board

The output voltages of the HV Power Supply Board are controlled by
externally supplied reference voltages derived from the Ion Path DACs and
Vacuum Gauge Control Board.
A digital input signal controls the polarity of the Ion Source and ETP Float
Voltage Supplies. A second digital signal enables or disables the outputs.
Each power supply uses a power amplifier and a step-up transformer to
generate a high-voltage AC waveform. The high-voltage AC is converted to
DC output by voltage multiplier modules located inside the main module.

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ETP Float Voltage Supply

The ETP Float Voltage Supply is fixed depending on the polarity of ions
being analyzed. For positive ions, the voltage is -6000V; for negative ions,
the voltage is fixed at +4000V. This voltage comes from the HV Power
Supply Module.
The divider network is used to provide a low voltage test point for the ETP
voltage. By using 1000 M Ω (R7) and 1.1 M Ω (R6), the divider ratio is set
approximately 1000:1. This ensures that the test point is adequately
accurate when running diagnostics.
The noise on the signal due to the ripple on the ETP+ terminal can be
reduced by adding a simple RC filter (R3//C3) in series.
When there is an ion strike, the ETP generates a current pulse that flows
through the connector socket. This current pulse then flows through a
511 ohm resistor (R1) producing a negative, bell-shaped pulse. The
amplitude of the pulse can vary up to 200mV depending on the ETP’s
condition, ETP’s bias voltage setting and other normal statistical variations.
The operational amplifier U1 is a precision voltage-feedback amplifier
featuring fast settling time, excellent differential gain and differential phase
performance. The non-inverting gain of U1 is set to 21V/V via resistors R5
and R9. Resistor R7 and diodes D1 and D2 are used to protect U1 from
potential transcient conditions only.
The low frequency gain of U1 is unity to reduce the effect of DC level shifts
due to AC coupling of the input signal. R15 and C5 are used for the +5V
power supply filtering; whereas R12 and C4 are used for the -5V power
supply filtering.
The amplified pulse is conducted to the positive input of a high-speed
comparator (U2), where it is compared to a discriminator voltage applied to
the negative input of the comparator. Potentiometer R2, resistors R3, R4
and capacitor C1 combine to provide a stable negative DC discriminator
voltage. The discriminator voltage (threshold) is the minimum pulse
strength for which the signal handling circuitry will register a ion strike.
Resistors R13, R11 and capacitor C3 are used specifically to introduce
hysteresis at U2 by temporarily injecting some positive feedback each time
a pulse crosses the discriminator level. This is necessary to ensure that a
minimum output pulse width for the counting circuit.
The non-inverted TTL output of comparator U2 is passed to the System
Controller via a driver in U5. This driver converts its TTL input to balanced
pseudo ECL levels. Pseudo ECL levels are ECL levels shifted by 5V to run
on a single +5V power supply.
The Test Signal function helps to verify the ion counting circuitry. The test
signal is a pseudo ETP output signal that originates at the System

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Controller. When it is enabled, it transmits a pulse-like test signal to the

Signal Handling Board. This signal input is received and converted to TTL
levels by a receiver in U5. It is then fed to the positive input of the
comparator U2 via R8 and C13. If the signal handling circuitry is functioning
properly, the Applications Computer will produce scan results with an ion
intensity equal to the frequency of the test signal. R17, R18 and R19 are
required to approximately terminate the pseudo ECL side of U5.
ETP Bias Voltage Supply
The ETP Bias Voltage Supply creates the potential gradient. The bias
voltage is applied to the end of the detector opposite the horn. It is set
between 2000V - 3000V more positive than the horn voltage. Therefore,
ETP+ is equal to the sum of ETP- and bias voltage. The bias detector
voltages are supplied from the HV Power Supply Board. Similar to the ETP-
divider network, R4 and R1 are used to provide a divider approximately
1000:1.
Ion Source Power Supply
The Ion Source Power Supply generates a variable DC output between
0 kV and 8 kV in either polarity. It operates in voltage-regulated mode with
the IonSpray Inlet and current-regulated mode with corona discharge for
the Heated Nebulizer option. It is nearly identical to the ETP Float Voltage
Power Supply with the following exceptions:
1. JFET gain control stage has been replaced by an integrated gain con-
trol IC and U4. This allows for adjusting the output down to a voltage
below 100V.
2. It can be operated in current-controller mode. In this mode, the ion
source current is measured at the Curtain Plate on the Lens Power
Supply Board. The current is regulated by controlling the output of the
Ion Source Power Supply. U6 selects either voltage mode or current
mode control of the supply.

6.5.6 Exciter Board

The Exciter Board consists of two sections: digital and analog.
Digital
The principal function of the Exciter Board’s digital electronics is to control
various ion path parameters. The key parameters controlled are the:
• Q1 and Q3 Mass DACs (16-bit)
• Q1 and Q3 Rod Offset DACs (dual, 12-bit)
• Q1 and Q3 Resolution DACs (dual 12-bit)
• Q1 and Q3 RF Mode Setting
• Power Supply Enable

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The Exciter Board receives digital data (that is, DAC values and mode
settings) from the System Controller via the Synchronous Serial Link (SSL).
The SSL connects to the Exciter Board through the RS422 driver and
receiver chips U31 and U23 respectively.
The Exciter Board is connected to Xilinx chip U29 and U30, as well as to
12-bit ADC U34. Both U29 and U30 are configured from a common 1736
(U28) serial configuration PROM at power-up.
U29 has essentially been configured as the local SSL controller providing a
generalized assortment of capabilities. For more information, refer to the
Xilinx SSL Functional Details document and the Xilinx Configuration
schematic. Addresses transferred over the SSL are decoded within U29
and, if it is in the range of 0 to 31 inclusive, will enable the appropriate local
resource to accept or respond to subsequent data transfers until the next
address transfer. A local resource could be within U29 or external to it, such
as U30 or ADC U34.
Data destined to the Q1 (via U19) or Q3 (via U18) Rod Offset or Resolution
DACs are translated to the necessary format within U29 and then output to
the preload register of the appropriate DAC. When required, Scan Timing
and Control (STC) signal AMU will pulse low. This causes the contents in
the preload registers to simultaneously pass to the DAC outputs.
The Q1 and Q3 RF-Only mode bits and the Power Supply Enable control
bit (PS_EN) are transferred to a 16-bit parallel output register in U29 over
the SSL. Both RF-Only mode bits and a derivative of the Power Supply
Enable bit (Local Power Supply Enable) are passed to the analog circuitry
via buffer U33.
ADC U34 receives configuration data and returns conversion results
directly over the SSL. When addressed, U34 is enabled to use the SSL via
a chip select from U29. U29 also provides a constant, free-running 4 MHz
clock for U34’s internal use.
The Q1 (U14) and Q3 (U16) Mass DACs are driven by the Xilinx design in
U30. Mass DAC values are sent to U30 directly over the SSL provided that
U30 has been addressed and enabled from U29. Like the Rod Offset and
Resolution DACs, when there is an STC signal “settling” transitions high via
U2, the contents in the Q1 and Q3 Mass DAC preload registers within U30
are simultaneously passed to the DAC outputs. The STC Increment Q1and
Increment Q3 signals increase the relevant mass DAC by one LSB. These
signals are used with ramp mode scanning only.
The QPS RF and DC output voltages can be switched on or off by a Global
Power Supply signal that upon entering the Exciter, is buffered and inverted
by U25 on its way to Xilinx U29 (see the Power Supply Enable Logic figure).
Internal to U29, the Global Power Supply signal is NANDed with a parallel
output bit 15 (Power Supply Enable) resulting in an output signal (Local
Power Supply Enable).

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Analog Portion
The Analog circuitry is powered by four IC voltage regulators. This ensures
that noise from the DC Power Supply does not corrupt the sensitive QPS
electronics. The output voltages are +12V and +15V.
The analog circuitry contains the most thermally sensitive elements and is
therefore enclosed in a thermally isolated, temperature stabilized oven. The
oven is heated by four power transistors that are bolted to the oven
extrusions. The temperature is monitored and the output is applied to a
comparator that drives the power transistors to maintain a constant
temperature in the oven.
The DC signal generated by the Exciter Board is derived from the Mass,
Resolution and Rod Offset DACs. The Mass and Resolution DACs produce
balanced outputs from two amplifiers. The Rod Offset DAC generates a
common mode signal. A relay is used in RF-only mode to turn off the mass
and resolution signals.
An 816 kHz signal is generated by the crystal oscillator. The active element
is a current mode amplifier (U3a). The output of U3a is fed to a limiter that
DC bias current. This limits the amplitude of oscillation so that U3a operates
in its linear region producing a sine wave output rather than a square wave.
The output of the limiter is then applied to a resonant circuit that filters the
signal and applies it to the non-inverting input of U3a providing the positive
feedback required for oscillation.
The balanced detector signal is summed by the U6 instrumentation
amplifier. The output signal from the Mass DAC is applied to the inverting
input of an operational amplifier (U12a); the non-inverting input is
grounded. The RF level then adjusts itself so that the output of U6 applied
to U12a cancels the Mass DAC signal. U12a is wired as an integrator that
forces the static error of the RF feedback to zero. U12b inverts the polarity
of the control signal from U12a and reduces its amplitude to the 0 to 2V
range required for U5 (the multiplier stage). The circuitry for the other rod
set is identical.

6.5.7 Amplifier Boards

The Amplifier Boards condition and amplify the RF and DC signals received
from the Exciter Board and pass them on to the coil boxes. There are two
identical Amplifier Boards: one for Q1 and the other for Q3. Each contain
an RF stage and a DC stage.
The RF amplifier output stage consists of four amplifiers arranged as a
parallel push/pull circuit. The amplifiers are powered by two IC voltage
regulators. The maximum output RF voltage is 30V peak-to-peak.
The DC output stage consists of two DC amplifiers that use 6 series-
connected FETs to obtain the required output voltage capability. The gain
of the DC amplifiers is controlled by a precision voltage divider with a low

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temperature coefficient. The circuitry of the two DC amplifiers differs

slightly. One has a +200V offset capability and the other has a -200V offset
capability. The amplifiers have an output swing of over 800V. The outputs
are short-circuit protected.

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6.6 Temperature Controller

6.6.1 Temperature Control System
The temperature control system provides for the control of the heating of
the interface assembly and the TurboIonSpray or Heated Nebulizer inlets
where these are used. This requires two temperature controllers which are
mounted on one printed circuit assembly. The power for this system is
provided by a single mains transformer. This transformer provides 60 VAC
to the heaters and a 32 VAC center tapped winding used to generate power
for the control circuits.
The interface is heated to a temperature of about 100 DC by a Kaptan film
heater element rated at 200W when energized with 60 VAC. The
temperature of the interface is monitored by a Platinum Resistance
Temperature Detector (RTD) with a resistance of 100 Ohms at 0°C. The
temperature controller receives a nonadjustable set point command from
the DACS and Vacuum Gauge module.
The Heated Nebulizer or TurboIonSpray inlets are heated to a temperature
of about 500°C by a mineral filled heater element rated at 200W when
energized with 60 VAC. The temperature of the heater is monitored by a
Platinum Resistance Temperature Detector (RTD) with a resistance of 100
Ohms at 0°C. The temperature controller receives a set point command
from a Digital to Analog Converter under computer control.
The following Test Points are located on theTemperature Controller board:
• TP 1 Set value - Interface, Typically 1 volt
• TP 2 Read back value - Interface, Typically 1 volt
• TP 3 Set value for source heater (10 mV per degree)
• TP 4 Read back value for source heater (10 mV per degree)
• TP 5 Ground (GND)

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TP 1
TP 2
TP 3
TP 4

TP 5
(GND)

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6.7 Q1 and Q3 Coil Box

The Q1 and Q3 Coil Boxes are mounted against the pillars underneath the
Vacuum Chamber in line with the Q1 and Q3 Mass Filters. The Boxes
house the filter board assemblies that amplify the QPS voltages. The
voltages are relayed to the respective Q1 and Q3 quadrupoles by vacuum
feedthrough leads through the top of the respective coil box. The applied
RF Voltages are measured for a feedback loop by the RF Detector Boxes
that connect through the back of the pillar into the rear of the coil boxes.
The two coil box assemblies are similar. All parts that make up the
Assemblies are the same except for the wireforms that link the resonating
coil output to the respective RF Detector, tuning capacitor and RF
Feedthroughs. The Q1 and Q3 wireforms have different shapes that reflect
the different coil box orientations.
The procedure to replace the coil box, the filter board assemblies, or the
Tuning capacitors are the same for both coil boxes. The following
procedure can be used to repair or replace either coil box. Specific
instructions are provided where necessary to note the minor differences in
the Q1 and Q3 Coil Boxes.

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

WARNING Be careful of the high voltage. Ensure that the instrument is

shut off and that the main power line is disconnected before
opening the Coil Boxes.

Note This procedure is designed assuming the rear of the pillar is

accessible. In some cases, you may have to remove the source
exhaust pump housing to access to the Q1 pillar.

Removing the Filter Board Assembly

1. Shut down the instrument.
2. Open the Source Cover.
3. Open the Front Cover.
4. Remove the Back Cover.

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5. Remove the Coil Box Cover.

6. Separate the wireforms and the resonating coil output (LITZ) wires
from the tuning capacitors. The Q1 Filter Board Assembly
Connections figure shows the connections for Q1 Coil Box. The Q3
Feedthrough Installation Schematic figure shows the connections for
the Q3 Coil Box.

Note The coil wire is wrapped several times around the wireform lead or
capacitor wire and soldered. Disconnect the coil wire careful so
that it does not break.

Note Use a 60 watt soldering iron to burn off the coating on the coil wire
(LITZ). Use a good rosin core solder to make a good connection.

Figure 6-10. Q1 Filter Board Assembly Connections

7. Unlatch the feedthrough latch mechanism secures the feedthrough

locking mechanism to the feedthrough housing. Slide out the silver

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plate. See Coil Box Connections - Rear and Side View figure.

Caution The vacuum feedthroughs are sensitive to contamination.

Always wear powder-free latex gloves when handling the
feedthroughs and place them in a plastic bag immediately
after removal to ensure they remain clean.

8. Hold the ceramic collar of the front feedthrough and slide the wireform
sleeve connector off the bottom end of the feedthrough.

FEEDTHROUGH
HOUSING

SLEEVES

FEEDTHROUGH
LOCKING
MECHANISM

COIL BOX

COIL BOX
WIREFORMS

FEEDTHROUGH

Figure 6-11. Q3 Feedthrough Installation Schematic

9. Gently pull the feedthrough straight out of the Vacuum Chamber and
maneuver it out of the coil box.

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10. Repeat steps 7-9 for the second feedthrough that is directly behind the
first.
11. From the back of the instrument, disconnect the four cables that
connect to the filter board through the pillar. The next figure shows the
cable connections for the Q1 and Q3 Assemblies.

Figure 6-12. Coil Box Connections - Rear and Side View

12. With a 9/16 socket, remove the four hexagonal jam nuts and lock the
washers that secure the filter board connectors to the pillar.
13. From the back of the instrument unscrew the four hex-head screws
that thread into the standoffs on the filter board through the pillar.

Table 6-5. Coil Box Connections

MB Connector
DC1B J15
Coil Box RF1X J17
RF1Y J18
Q1 DC1A J16
FB1B J30
RF Detector FB1A J29
Heater J43

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DC3B J19
Coil Box RF3X J21
RF3Y J22
Q3 DC3A J20
FB3B J32
RF Detector FB3A J31
Heater J42

14. From the front of the machine, maneuver the filter board assembly
clear of the coil box.

Caution Do not displace the coil wrappings. The coil spacing is critical
to the coil box performance. The coil wraps are held in
position with a strip of silicon gel down the side of the coil.
Be careful not to damage the silicon.

Replacing the Filter Board Assembly

1. Maneuver the filter board assembly into the coil box so that the four
connectors on the filter board fit through the pillar.
2. From the back of the instrument, place the 1/2" lock washers over the
filter board connectors and hand tighten the 1/2" jam nuts to the
connectors.
3. From the back of the instrument, screw the four hex-head screws with
flat washers through the pillar into the standoffs on the filter board
assembly.
4. Tighten the four jam nuts (from step 3) to the connectors.
5. Wrap the resonating coil output (LITZ) wire several times around the
wireform at the top tuning capacitor leaving a minimum of slack. See
the Q1 Filter Board Assembly Connections figure for Q1 and the Q3
Feedthrough Installation Schematic figure for Q3.

Caution The LITZ wire from the coil should never be closer to the
sides of the coil box than the wireform leads. Do not leave any
sharp edges in the coil box connections or arcing may occur.

6. Solder the resonating coil output (LITZ) wire to the wireform. Trim the
excess wire and reflow the solder.
7. Wrap the resonating coil output (LITZ) wire several times around the
wireform at the join with the bottom tuning capacitor leaving a
minimum of slack. See the Q1 Filter Board Assembly Connections
figure for Q1 and the Q3 Feedthrough Installation Schematic figure for

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Q3.
8. Solder the resonating coil output (LITZ) wire to the wireform. Trim the
excess wire and reflow the solder.
9. With a multimeter, measure the resistance between the following
points. Each resistance should be less than 1.5 ohms:

Note The 1.5 ohm resistance value is the value after the lead resistance
has been subtracted.

• W1 on the filter board and the top wireform — LITZ wire connection
• W1 and the body of the top tuning capacitor
• W2 on the filter board and the bottom wireform — LITZ wire connection
• W2 and the body of the lower tuning capacitor
10. Before closing the coil boxes, check the following:
• That the wireform sleeve connectors are seated securely over the two RF
detector connectors at the back of the coil box
• That the wireform sleeve connectors are seated securely over both vac-
uum feedthrough connectors
• That the soldered connections joining the tuning capacitors to the wire-
forms is secure and that the lead from the capacitors is not broken
• That the fly leads from the top and bottom of each coil are soldered
securely to the wireforms. Each of the fly leads must not be closer to the
walls of the coil box than the wireforms

Caution Failure to connect the coil boxes properly may result in

damage to the RF detectors.

11. Replace the Q1 and Q3 Coil Box covers and tighten the 12 hex-head
screws with the associated washers.
Removing and Replacing the Tuning Capacitors
Each of the coil boxes has two tuning capacitors. The following procedure
can be followed to change any or all of the capacitors. The only differences
in the tuning capacitors result from the different orientations inside the coil
boxes. The differences are shown in the Q1 Filter Board Assembly
Connections figure and the Q3 Feedthrough Installation Schematic figure.
1. Shut down the instrument.
2. Open the Source Cover.

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3. Open the Front Cover.

4. Remove the Back Cover.
5. Remove the Coil Box Cover.
6. Separate the wireforms and the resonating coil output (LITZ) wires
from the tuning capacitors. The Q1 Filter Board Assembly
Connections figure shows the connections for Q1 Coil Box. The Q3
Feedthrough Installation Schematic figure shows the connections for
the Q3 Coil Box.

Note The coil wire is wrapped several times around the wireform lead or
capacitor wire and soldered. Carefully disconnect the coil wire so
that it does not break.

7. Unscrew the nut at the front of the coil box that secures the tuning
capacitor to the coil box.
8. Reach inside the coil box and maneuver the tuning capacitor through
the Coil Box cover and out of the coil box.
9. Position the new capacitor in the coil box and, from the front, tighten
the nut over the adjustable arm of the capacitor.
10. Solder the wireform to the wire lead wrapped around the capacitor.
See the Q1 Filter Board Assembly Connections figure and the Q3
Feedthrough Installation Schematic figure.
11. Wrap the resonating coil output (LITZ) wire several times around the
wireform at the tuning capacitor leaving a minimum of slack. See the
Q1 Filter Board Assembly Connections figure for Q1 and the Q3
Feedthrough Installation Schematic figure for Q3.

Caution The LITZ wire from the coil should never be closer to the
sides of the coil box than the wireform leads.

12. Solder the resonating coil output (LITZ) wire to the wireform, then trim
the excess wire and reflow the solder.
13. With a multimeter, measure the resistance between the following
points, each of which should be less than 1.5 ohms:

Note The 1.5 ohm resistance value is the value after the lead resistance
has been subtracted.

• W1 on the filter board and the top wireform — LITZ wire connection

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• W1 and the body of the top tuning capacitor

• W2 on the filter board and the bottom wireform — LITZ wire connection
• W2 and the body of the lower tuning capacitor
14. Before closing the coil boxes, check the following:
• That the wireform sleeve connectors are seated securely over the two RF
detector connectors at the back of the coil box
• That the wireform sleeve connectors are seated securely over both vac-
uum feedthrough connectors
• That the soldered connections joining the tuning capacitors to the wire-
forms is secure and that the leads from the capacitors are not broken
• That the fly leads form the top and bottom of each coil are soldered
securely to the wireforms. Each of the fly leads must not be closer to the
walls of the coil box than the wireforms

Caution Failure to connect the coil boxes properly may result in

damage to the RF detectors.

15. Replace the coil box cover and tighten the 12 hex-head screws with
the associated washers.
Removing the RF Detector Boxes
1. Shut down the instrument.
2. Open the Source Cover.
3. Open the Front Cover.
4. Remove the Back Cover.
5. Remove the Coil Box Cover.
6. Slide the wireform collars from both vacuum feedthroughs in the coil
box.
7. Slide the wireform collars off the RF Detector terminals at the inside
back of the coil box.
8. Disconnect the two RF Feedback connections from the back of the RF
Detector Box.
9. Disconnect the 6-pin connector attached to the Heater Board below
the RF Detector Box.
10. From the front of the instrument, while reaching over the instrument
and holding the Detector Box, unscrew and remove the two screws
securing the RF Detector to the pillar.

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11. Lift the RF Detector from the pillar.

12. Insert the replacement RF Detector Box through the back of the pillar
into the coil box. From inside the coil box, thread two hex-head screws
with flat washers into the RF Detector Boxes through the pillar.
13. Fit the wireform collar over the RF Detector terminals, as shown for the
respective coil boxes in the Q1 Filter Board Assembly Connections
figure for Q1 and the Q3 Feedthrough Installation Schematic figure.
14. Fit the wireform collar leads over the vacuum feedthroughs. See the
Q1 Filter Board Assembly Connections figure for Q1 or the Q3
Feedthrough Installation Schematic figure for Q3.
15. With a multimeter, measure the resistance between the following
points. Each resistance should be less than 1.5 ohms:

Note The 1.5 ohm resistance value is the value after the lead resistance
has been subtracted.

• W1 on the filter board and the top wireform — LITZ wire connection
• W1 and the body of the top tuning capacitor
• W2 on the filter board and the bottom wireform — LITZ wire connection
• W2 and the body of the lower tuning capacitor
16. Before closing the coil boxes, check the following:
• That the wireform sleeve connectors are seated securely over the two RF
detector connectors at the back of the coil box
• That the wireform sleeve connectors are seated securely over both vac-
uum feedthrough connectors
• That the soldered connections joining the tuning capacitors to the wire-
forms is secure and that the leads from the capacitors are not broken
• That the fly leads from the top and bottom of each coil are soldered
securely to the wireforms. Each of the fly leads must not be closer to the
walls of the coil box than the wireforms

Caution Failure to connect the coil boxes properly may result in

damage to the RF detectors.

17. Replace the coil box cover and tighten the 12 hex-head screws with
the associated washers.

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Removing the Coil Box

The coil box itself can be removed without removing the filter board
assembly because there is no complete back wall to the coil box. The pillar
forms the back of the box when the coil box is secured in position.
To remove the coil box itself, you must remove the RF Detector and
disconnect the vacuum feedthroughs and tuning capacitors. You can then
remove the coil box with the wireforms attached to the standoffs.

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

Note This procedure is designed assuming the back side of the pillar is
accessible. You may have to remove the source exhaust pump
housing or the transformer housing to access to the Q1 pillar.

1. Shut down the instrument.

2. Open the Source Cover.
3. Open the Front Cover.
4. Remove the Back Cover.
5. Remove the Coil Box Cover.
6. Unclip the clamp that secures the feedthrough locking mechanism to
the feedthrough housing.

Caution The vacuum feedthroughs are sensitive to contamination.

Always wear powder-free latex gloves when handling the
feedtroughs and place them in a plastic bag immediately after
removal to ensure they remain clean.

7. Remove the 18 screws from the coil box plate.

8. To remove the feedthroughs, unscrew the bolts on the top of the coil
box.
9. Disconnect the RF Connectors.
10. Remove the Filter Board Assembly.
11. Remove the two M-5 hex bolts on the bottom of the coil box.

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12. Remove the coil box.

13. With a multimeter, measure the resistance between the following
points. Each resistance should be less than 1.5 ohms:

Note The 1.5 ohm resistance value is the value after the lead resistance
has been subtracted.

• W1 on the filter board and the top wireform — LITZ wire connection
• One and the body of the top tuning capacitor
• Two on the filter board and the bottom wireform — LITZ wire connec-
tion
• W2 and the body of the lower tuning capacitor
14. Before closing the coil box, check the following:
• That the wireform sleeve connectors are seated securely over the two RF
detector connectors at the back of the coil box
• That the wireform sleeve connectors are seated securely over both vac-
uum feedthrough connectors
• That the soldered connections joining the tuning capacitors to the wire-
forms is secure and that the leads from the capacitors are not broken
• That the fly leads from the top and bottom of each coil are soldered
securely to the wireforms. Each of the fly leads must not be closer to the
walls of the coil box than the wireforms

Caution Failure to connect the coil box properly can damage the RF
detectors.

15. Replace the coil box cover and tighten the 18 hex-head screws.

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6.7 Card Cage Blower

The Card Cage fan is installed under the circuit board modules as part of
the System Electronics Box Assembly. The fan circulates air through the
circuit board modules and through both the Q1 and Q3 Coil Boxes. Vents
in the coil box assemblies allow the air from the fan to pass over the coils
and out the front vents in the Coil Box cover.
The fan is connected in parallel to the AC Distribution Board that supplies
them with 230 volts AC power. The fan operates continually when the main
circuit breaker switch is "ON".
Replacing the Card Cage Blower
1. Shut down the instrument.
2. Open the Front Cover.
3. Remove all the System boards from the Card Cage.
4. Remove the Filter covers.
5. Using a screwdriver, remove the four Phillips screws holding the fan
assembly in place.
6. Pull out the Card Cage Blower.
7. To replace the fan, reverse steps 4 to 6.
Assembling the Card Cage
1. Using four screws and lock washers, secure the four bars to the right-
hand card cage end plate. Do not tighten the screws.
2. Using one screw and lock washer, fasten the bar to the end plate,
noting the orientation. Do not tighten the screw.
3. Slide the bar into each of the four corner bars.
4. Using the four screws and lock washers, fasten the left-hand card
cage end plate to the ends of the bars.
5. Using the screw and washer, install the vacuum hose support. Do not
tighten the screw.
6. Using 20 screws, secure the terminal and the seven cable tie clamps.
Loosely fasten the motherboard assembly to the card cage bars.
Observe the orientation of the motherboard.
7. Place the card cage on a flat surface and fully tighten the motherboard
screws.
8. While the card cage assembly is still on the flat surface, fully tighten
the 10 screws holding the end plates to the bars.

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 Power and Electronics

9. Using the screws, lock washers and flat washers, install the front cover
mount bracket to the Vacuum Chamber support.
10. Using the four cap screws and lock washers, fasten the completed
Vacuum Chamber bracket to the top of the card cage. Fully tighten the
screws.
11. Install the quarter-turn screw clips to the support bracket.
12. Using the clamp and screw, mount the temperature sensor to the
vacuum hose support bracket.
13. Install the 14 card guides.
Assembling the Fan Assembly
1. Prepare the electrical cable on the fan by trimming the jacket and con-
ductors to the appropriate length. Strip the insulation from the conduc-
tors to the appropriate strip length.
2. Solder the fan power connector to the connectors.
3. Using the four flat-head screws, attach the fan to the fan plate. The
electrical conductors should exit the fan toward the connector hole in
the fan housing plate.
4. Using the washer and nut provided, install the fan power connector in
the insulating bracket.
5. Dress the fan conductors so that they are held against the fan plate by
using the insulating bracket. Using the two screws, fasten the
insulating bracket to the fan plate.
6. Using the four screws, fasten the fan plate to the fan housing. Ensure
that the fan spins freely without interference with the fan housing or
connection wires.

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Power and Electronics

6.8 Power Distribution Module Service

The Power Distribution module consists of the AC Distribution Board and
the DC Power Supply. The AC Distribution Board can not be removed with
the DC Power Supply mounted. To remove the DC Power Supply, the AC
bracket must be disconnected to expose four screws that attach the DC
Power Supply to the back of the AC bracket.

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

Procedures to remove the Power Distribution Module components must be

performed in the following order:
• Remove the Power Distribution Module cover.
• Disconnect the AC bracket.
• Remove the DC Power Supply.
• Remove the AC Distribution Board.
Removing the DC Power Supply
1. Shut down the instrument.
2. Remove the Back Cover.
3. Open the Front Cover.

WARNING Do not touch the DC power supply until five minutes after
switching off the main switch. The delay allows the
capacitors in the DC power source to safely discharge.

4. Disconnect all electrical connections to the AC Power Supply and all

other cable connections.
5. Disconnect the AC Power Supply at the other end of the AC
Distribution Box.
6. Remove the two bolts that secure the AC Distribution Box to the back
panel.
7. If the handles are attached to the chassis, remove the handle from the
detector end of the chassis.

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 Power and Electronics

Note To open the power module cover, you must remove the handle.

8. Slide the bottom of the Power Distribution Module Cover off the edge
of the chassis and lay the cover down close to the instrument.
9. With a 3 mm Allen key, remove the two hex-head screws that connect
the two bottom front corners of the AC bracket to the Chassis.
10. Carefully cut the cable tie that secures the following cables to the
Chassis between the line filter and the AC bracket:
• AC Main Input cable
• AC Power Input for DC Power Supply
• 230 VAC input to the AC Distribution Board cable ACJ2
11. Unscrew and remove the two hex-head screws that secure the top of
the AC bracket to the Q3 Vacuum Feedthrough Housing. See the
figure below.
12. Disconnect the ion optics cable.

Figure 6-13. Power Connectors Layout

13. Turn the Power Distribution Module counter-clockwise so the rear of

the AC bracket is accessible from the front of the instrument.

Note The Power Distribution Module remains connected to the main

console by cabling, but it is maneuverable enough to expose the
DC Power Supply mounting screws at the back of the AC bracket.

14. Disconnect the 12 DC Power Input Cable leads from the top of the DC
Power Supply.

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Power and Electronics

15. Remove the eight Philips head screws that fasten the DC Power
Supply to the AC bracket.
16. Remove the DC Power Supply from the AC bracket. Guide the AC
Power Input Cable connected to the bottom of the Power Supply
through the opening in the AC bracket below the AC Distribution
Board.
Removing and Replacing the AC Distribution Board

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

1. Shut down the instrument.

Caution Remove power cord from the instrument for safety

2. Remove the DC Power Supply.

3. Disconnect all the connections to the AC Distribution Board.
4. Using a 2.5 mm Allen key, remove the screws securing the AC
Distribution Board to the AC bracket standoffs and remove the AC
Distribution Board.
5. Turn each of the four Fuse Caps on the replacement AC Distribution
Board counter-clockwise 1/4 turn to release the caps. Verify that the
proper fuses are inserted in the fuse caps as listed below.

Table 6-6. Power Distribution Board - Fuse Distribution

Fuse 1 Turbo Cooling 2.5A -250V Time-lag

Fuse 2 Divertor Valve 4.0A - 250V Time-lag

Caution When replacing fuses, always use the correct replacement

type and amperage

6. Position the AC Distribution Board so that the connectors line up with

the slots in the AC bracket and tighten the four screws that attach the
AC Distribution Board to the AC bracket standoffs.
7. Replace the DC Power Supply. See the next procedure.5
Replacing DC Power Supply

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 Power and Electronics

1. Attach the AC Input Cable to the replacement DC Power Supply as

shown in the DC Power Supply Connections figure.
2. Feed the AC Input Cable through the cable opening in the AC bracket
below the AC Distribution Board while maneuvering the replacement
DC Power Supply into position inside the AC bracket.
3. Remove and discard the six straps across the replacement DC Power
Supply output terminals.

Note Removing these straps enables the sensing circuit. If the straps
are not removed, the sensing circuit will monitor the voltage drop
across the DC Power Supply output terminals not across the load
on the motherboard.

Figure 6-14. DC Power Supply AC Input Connection

4. Align the threaded mounting holes on the back and left sides of the
Power Supply with the corresponding holes in the Bracket and screw
the four Philips screws through the AC bracket into the Power Supply.
See the figure above.
5. Attach the DC Input Cable to the 12 DC output connectors as shown
in the Main Switch Connections figure.

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Power and Electronics

Figure 6-15. DC Power Supply Connections

6. Slide the module into position and thread the two screws with lock
washers and flat washers through the bottom front corners of the AC
bracket assembly to the chassis. See the DC Power Supply AC Input
figure.
7. Replace and tighten the two screws that secure the top of the
assembly to the Q3 RF Feedthrough Housing. See the DC Power
Supply AC Input Connection figure.
8. Fit a cable tie through the clamp on the chassis between the line filter
and the AC bracket and tighten it around the following cables:
• the AC Main Input cable from the AC line filter
• the 230 VAC input cable to the AC Distribution Board
• the AC Input cable to the DC Power Supply
9. Re-connect the AC output cables to the appropriate connector on the
AC Distribution board.
10. Replace the Power Distribution Module Cover and tighten the four
hex-head screws that secure it in position. Ensure that the flat washer
and the lock washer are in place. See the Power Distribution Module
Assembly figure.
11. Connect the ETP Cable to the Signal Handling Board.
12. Connect the Ion Optics Power Cable to the Vacuum Chamber rear
flange.

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 Power and Electronics

6.9 Main Circuit Breaker Switch

The Main Circuit Breaker Switch on the Power Distribution Module Cover
controls the flow of power from the 230 VAC supply to the Power
Distribution Module. When the Switch is “ON”, the power is directed via the
AC Distribution input cable to the AC Distribution Board.
The Switch also acts as a circuit breaker to protect the instrument from
power surges. If the voltage (current) in the input line exceeds 12 A, the
circuit breaker trips disabling power to the AC Distribution Board.

WARNING BIOHAZARDOUS MATERIAL Do not dispose of system

components or subassemblies, including computer parts, in
municipal waste. Dispose of replaced components and
instruments according to established waste electrical
equipment procedures.

Removing the Switch

1. Shut down the instrument.

Caution Remove power cord from the instrument for safety

2. Open the Source Cover.

3. Remove the Back Cover.
4. Open the Front Cover.
5. Remove the four hex-head screws that connect through the AC
bracket to the side corners of the Power Distribution Module Cover.
See the Power Distribution Module Assembly figure.
6. Carefully slide the bottom of the Power Distribution Module Cover off
the chassis and lay it down in front of the assembly.

Caution The Power Distribution Module Cover cannot be moved from

the instrument because the Switch and the Reset buttons on
the Cover are wired to the main console.

7. Disconnect the four leads from the switch.

8. To remove the switch, squeeze the spring catches and push the switch
through the front of the Power Distribution Module Cover. See the Coil

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Power and Electronics

Box Connections - Rear and Side View figure.

Replacing the Switch
1. Push the replacement switch through the front of the Power Distribu-
tion Module Cover until it snaps into position.
2. Connect the leads from AC Distribution Input Cable and the AC Main
Circuit Breaker Cable to the connectors on the switch as shown in the
next figure.
3. Replace the Power Distribution Module Cover.

Figure 6-16. Main Switch Connections

192