Thermo Scientific DSQ II User manual

DSQ II
Hardware Manual
120299-0002 Revision C December 1, 2009

© December 2009 Thermo Fisher Scientific Inc. Xcalibur™, DSQ, DSQ II, TRACE DSQ, TRACE GC,
TRACE GC Ultra, FOCUS GC, PolarisQ, and ITQ are trademarks and/or product names of Thermo Fisher
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Ion Trap series refers to ITQ and PolarisQinstruments. DSQ series refers to all DSQ and DSQ II instruments.
Information about the TRACE GC and FOCUS GC instruments is included in this document.
INSTRUMENT USAGE: Thermo Scientific systems operate safely and reliably under carefully controlled
environmental conditions. If the equipment is used in a manner not specified by the manufacturer, the
protections provided by the equipment may be impaired. If you maintain a system outside the specifications
listed in this guide, failures of many types may occur. The repair of such failures is specifically excluded from
the standard Warranty and service contract coverage.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
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document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
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Release history: Rev A, August 2006. Rev B, December 2008, Rev C, December 2009.
For Research Use Only. Not regulated for medical or veterinary diagnostic use by U.S. Federal Drug
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Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described below.
EMC Directive 89/336/EEC
EMC compliance has been evaluated by Professional Testing.
•PolarisQ, ITQ, and Ion Trap Series standards: EMC EN 55011:1998 + EN 50082-1:1998,
Safety EN 61010-1:1990 + A1:1992 + A2:1995
• DSQ standards: EMC EN 61326-1:1998 + A1:1998. Safety EN 61010-1:1990 + A1:1992 + A2:1995
• DSQ II standards: EMC EN 61326-1:1997 + A1:1998 + A2:2001. Safety EN 61010-1:2001
• Direct Probe Controller (DPC) standards: EMC EN 55011:1991 + EN 50082-1:1992. Safety EN 61010-1:1994
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001. Changes
that you make to your system may void compliance with one or more of these EMC and safety standards. Changes to
your system include replacing a part or adding components, options, or peripherals not specifically authorized and
qualified by Thermo Fisher Scientific. To ensure continued compliance with EMC and safety standards, replacement
parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific or one of its
authorized representatives.
FCC Compliance Statement
Certifications, FCC part 15, Class A
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. If it is not installed and used in accordance with the instruction
manual, it may cause harmful interference to radio communication. Operation of this equipment in a
residential area is likely to cause harmful interference. In this case, users will be required to correct the
interference at their own expense. Detailed installation requirements are in the respective instrument’s
preinstallation guide.

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Notice on the Proper Use of Thermo Scientific Instruments
In compliance with international regulations: Use of this instrument in a manner not specified by Thermo Fisher
Scientific could impair any protection provided by the instrument.
Notice on the Susceptibility to Electromagnetic Transmissions
Your instrument is designed to work in a controlled electromagnetic environment. Do not use radio frequency
transmitters, such as mobile phones, in close proximity to the instrument.
For manufacturing location, see the label on the instrument.
WEEE Compliance
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Directive 2002/96/EC. It is marked with the following symbol:
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WARNING Read and understand the various precautionary notes, signs, and symbols
contained inside this manual pertaining to the safe use and operation of this product
before using the device.

WEEERoHS for further information on Thermo Fisher Scientific’s compliance with these Directives and the recyclers
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Thermo Scientific DSQ II Hardware Manual ix
C
Contents
Chapter 1 Basic Operations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Getting the Right Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Installing a Column into the GC/MS System . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Removing a Column from the GC/MS System . . . . . . . . . . . . . . . . . . . . . . . . . 15
Starting Up the GC/MS System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Shutting Down the GC/MS System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Chapter 2 Maintaining the DSQ II. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Components That Require Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
List of Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Recommended Maintenance Schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Running Benchmark Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Preparing the DSQ II for Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Removing the Front and Top Covers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Removing the Right Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Removing the Left Cover. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Removing the Vacuum Manifold Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Cleaning Stainless Steel Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Cleaning Non-Stainless Steel or Hybrid Components . . . . . . . . . . . . . . . . . . 36
Cleaning the Ion Source Components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Cleaning the Ion Volume with an Inlet Valve . . . . . . . . . . . . . . . . . . . . . . . . 38
Cleaning the Ion Volume Without an Inlet Valve . . . . . . . . . . . . . . . . . . . . . 43
Cleaning the Ion Source, Lenses and Prefilter . . . . . . . . . . . . . . . . . . . . . . . . 45
Cleaning the Ion Source and Lenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Cleaning the Prefilter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Replacing the Ion Source Filament . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Replacing the Electron Multiplier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Maintaining the Turbomolecular Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Contents
xDSQ II Hardware Manual Thermo Scientific
Maintaining the Rotary-Vane Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Checking the Oil Level of a Rotary-Vane Pump . . . . . . . . . . . . . . . . . . . . . . 63
Adding Oil to a Rotary Vane Pump. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Purging Gas from the Oil in a Rotary-Vane Pump . . . . . . . . . . . . . . . . . . . . 65
Changing the Oil in a Rotary-Vane Pump. . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Maintaining Components Outside the Vacuum Manifold . . . . . . . . . . . . . . . . 70
Replacing the Analog Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Replacing the Analog Board Fuse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Replacing the Calibration Gas Flow Module . . . . . . . . . . . . . . . . . . . . . . . . . 75
Refilling the Calibration Gas Flow Module . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Replacing the CI Reagent Gas Flow Module . . . . . . . . . . . . . . . . . . . . . . . . . 79
Replacing the Conversion Dynode/Electron Multiplier Power Supply. . . . . . 81
Replacing the DC Driver. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Replacing the DC Driver Fuse. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Replacing the Digital Board. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Replacing the Electrometer Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Replacing the Foreline Pressure Gauge and Foreline Adapter. . . . . . . . . . . . . 91
Replacing the Inlet Valve Seal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Replacing the Ion Gauge (Optional Upgrade) . . . . . . . . . . . . . . . . . . . . . . . . 94
Replacing the Lens Interface Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Replacing the Low Pass Filter Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Replacing the Power Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Replacing the Power Module Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Replacing the Rear Cooling Fans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Replacing the RF Detector Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Replacing the RF Generator Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Replacing the RF Generator Board Fuses. . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Replacing the Transfer Line. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Replacing the Turbomolecular Pump Power Supply . . . . . . . . . . . . . . . . . . 114
Replacing the Vacuum Control Board. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Replacing the Vent Valve Solenoid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Chapter 3 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .121
Using Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Running Tune Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Communication Symptoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Contamination Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Filament and Lens Control Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Heated Zone Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
High Vacuum Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Linearity Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Power Supply Symptoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139