7168 2577 PDF

Clarus 600/560 D MS
Hardware Guide
Release History
Part Number Release Publication Date

09936768 C March 2008
Any comments about the documentation for this product should be addressed to:
User Assistance
PerkinElmer, Inc.
710 Bridgeport Avenue
Shelton, Connecticut 06484-4794
U.S.A.
Or emailed to: [email protected]
Notices
The information contained in this document is subject to change without notice.
Except as specifically set forth in its terms and conditions of sale, PerkinElmer makes no
warranty of any kind with regard to this document, including, but not limited to, the
implied warranties of merchantability and fitness for a particular purpose.
PerkinElmer shall not be liable for errors contained herein for incidental consequential
damages in connection with furnishing, performance or use of this material.
Copyright Information
This document contains proprietary information that is protected by copyright.
All rights are reserved. No part of this publication may be reproduced in any form
whatsoever or translated into any language without the prior, written permission of
PerkinElmer, Inc.
Copyright © 2008 PerkinElmer, Inc.

Produced in the US.
Trademarks
Registered names, trademarks, etc. used in this document, even when not specifically marked
as such, are protected by law.
PerkinElmer is a registered trademark of PerkinElmer, Inc.

Clarus 600 is a trademark of PerkinElmer, Inc.
Swagelok is a registered trademark of the Crawford Fitting Company.
Teflon and Vespel are registered trademarks of E.I. duPont de Nemours and Company, Inc.
Microsoft is a registered trademark of the Microsoft Corporation.
Windows XP SP2 is a trademark of the Microsoft Corporation
Contents
Contents
Warnings and Safety Information .................................................... 7

Conventions Used in this Manual................................................................... 9
Customer Service................................................................................... 12
Electromagnetic Compatibility (EMC)......................................................... 13
Regulatory Information ......................................................................... 13
Electrical Symbols Used on ClarusMS ................................................. 14
Label Location and Content .................................................................. 15
Clarus MS Safety Practices .......................................................................... 18
Generic Warnings.................................................................................. 18
Moving the Clarus MS .......................................................................... 19
Decontamination and Cleaning..................................................................... 21
Decontamination.................................................................................... 21
Cleaning the Instrument ........................................................................ 21
Compressed Gases................................................................................. 22
Ventilation ............................................................................................. 22
Heated Zones ......................................................................................... 23
Using Hydrogen, Methane or Isobutane................................................ 24
Using Ammonia Gas ............................................................................. 24
Hazardous Chemicals ............................................................................ 24
Definitions in Warnings for Hazardous Chemicals ............................... 26
Temperature, Humidity and Environment .................................................... 27
Operating Conditions............................................................................. 27
Storage Conditions ................................................................................ 28
General Laboratory Safety............................................................................ 29
WEEE Instructions for PerkinElmer Products.............................................. 30
Pre-Installation Requirements ...................................................................... 31
Laboratory Space Requirements............................................................ 31
Environmental Requirements ................................................................ 32
Power Requirements.............................................................................. 33
Safety Requirements.............................................................................. 35
Computer and System Software Requirements ..................................... 37
PC Requirements ................................................................................... 37
Operating System .................................................................................. 37
Software................................................................................................. 38
Instrument Firmware Versions .............................................................. 38
3
Clarus 600/560 D MS Hardware Guide
Printers................................................................................................... 38
Pre-Installation Checklist.............................................................................. 39
Introduction ...................................................................................... 41
Preface .......................................................................................................... 43
System Overview................................................................................... 43
Summary of this Guide.......................................................................... 44
Related Documentation ......................................................................... 44
About Part Numbers Listed in this Manual ........................................... 45
About the Clarus 600/560 D System ............................................... 47

About the Clarus 600/560 D System ............................................................ 49
Clarus 600/560 D GC ................................................................................... 51
GC Interface (Transfer Line) ........................................................................ 53
Reference Gas Inlet....................................................................................... 54
Ion Optics Path ............................................................................................. 57
Vacuum System............................................................................................ 59
Rotary Pump.......................................................................................... 59
Vacuum Pump Options.......................................................................... 61
Diffusion Pump Operating States .......................................................... 62
Diffusion Pump Operating States Continued ........................................ 63
Turbomolecular Pump ........................................................................... 64
Diffusion Pump ..................................................................................... 64
Vacuum Gauge ...................................................................................... 67
TurboMass Software..................................................................................... 68
Top Level Screen................................................................................... 68
Tune Page .............................................................................................. 69
Analytical Column........................................................................................ 70
Pre-Operational Checklist............................................................................. 71
Maintenance ...................................................................................... 73
Overview ...................................................................................................... 75
Typical Overall Maintenance Schedule........................................................ 77
Daily ...................................................................................................... 77
Weekly................................................................................................... 77
Monthly ................................................................................................. 78
Every Six Months .................................................................................. 78
Yearly .................................................................................................... 78
4
Contents
Leak Checking .............................................................................................. 79

Tuning Clarus 600/560 D MS....................................................................... 82
Preparing Clarus 600/560 D MS for Hardware Maintenance...................... 85
Changing a Column ...................................................................................... 88
Tools and Items Required...................................................................... 88
Removing a Column.............................................................................. 88
Connecting the New Column to the Split/Splitless Injector.................. 91
Connecting a New Column to Clarus 600 MS ...................................... 94
Refilling the Reference Gas Vial ................................................................ 100
Items Required .................................................................................... 100
Inner Source Maintenance .......................................................................... 104
Removing the Inner Source ................................................................. 105
EI Inner Source Maintenance .............................................................. 106
CI Inner Source Maintenance .............................................................. 113
Reinstalling the Source........................................................................ 119
Replacing a Filament .................................................................................. 121
Items and Tools Required.................................................................... 121
Replacing the Head Amplifier .................................................................... 126
Mass Analyzer Maintenance....................................................................... 128
Items and Tools Required.................................................................... 128
Cleaning Materials............................................................................... 129
Removing the Ion Optics Assembly.................................................... 129
Replacing an Outer Source Thermocouple.......................................... 139
Removing the Outer Source from the Ion Optics ................................ 141
Replacing Outer Source Heaters ......................................................... 142
Replacing the Quadrupole Heater........................................................ 144
Cleaning the Outer Source Lens.......................................................... 146
Reassembling the Ion Optics Assembly .............................................. 149
Reassembling the Clarus 600/560 D MS............................................. 152
Vacuum System Maintenance .................................................................... 154
Maintanenace of the Turbomolecular and Diffusion Pump ................ 154
Checking the Forepump Oil Level ...................................................... 154
Adding Oil to the Forepump Reservoir ............................................... 156
Decontaminating the Oil...................................................................... 156
Replacing the Oil................................................................................. 156
Inline Gas Purifiers ..................................................................................... 159
Changing from EI to CI Mode.................................................................... 160
Connecting the CI Gas......................................................................... 160
5
Changing to CI .................................................................................... 162

Leak Checking..................................................................................... 163
Setting-Up CI ...................................................................................... 165
Troubleshooting .............................................................................. 175

Overview .................................................................................................... 177
Spare Components............................................................................... 178
Logical Troubleshooting Steps............................................................ 178
Troubleshooting Chart ................................................................................ 180
Chromatography Related..................................................................... 191
Spectral Related................................................................................... 195
Communications Related..................................................................... 197
Forepump Related ............................................................................... 198
Message Dialogs......................................................................................... 201
Replacement Parts ...................................................................................... 207
Index ................................................................................................ 209
6
Warnings and
Safety Information 1
Warnings and Safety Information
Conventions Used in this Manual
Normal text is used to provide information and instructions.
Bold text refers to text that is displayed on the touch screen.
All eight digit numbers are PerkinElmer part numbers unless stated otherwise.
Notes, warnings and cautions
Three terms, in the following standard formats, are also used to highlight special
circumstances and warnings.
NOTE: A note indicates additional, significant information that is provided with some
procedures.
Terminology
Throughout the manual, the term ‘mass spectrometer’ or MS specifically refers to

the Clarus MS; while for ‘GC’ Clarus GC is implied.
Caution
We use the term CAUTION to inform you about situations that could
CAUTION result in serious damage to the instrument or other equipment. Details
about these circumstances are in a box like this one.
9
D Caution (Achtung)
Bedeutet, daß die genannte Anleitung genau befolgt werden muß, um
einen Geräteschaden zu vermeiden.
DK Caution (Bemærk)
Dette betyder, at den nævnte vejledning skal overholdes nøje for at
undgå en beskadigelse af apparatet.
Caution (Advertencia)
E Utilizamos el término CAUTION (ADVERTENCIA) para advertir
sobre situaciones que pueden provocar averías graves en este equipo o
en otros. En recuadros éste se proporciona información sobre este tipo
de circunstancias.
F Caution (Attention)
Nous utilisons le terme CAUTION (ATTENTION) pour signaler les
situations susceptibles de provoquer de graves détériorations de
l'instrument ou d'autre matériel. Les détails sur ces circonstances
figurent dans un encadré semblable à celui-ci.
I Caution (Attenzione)
Con il termine CAUTION (ATTENZIONE) vengono segnalate
situazioni che potrebbero arrecare gravi danni allo strumento o ad
altra apparecchiatura. Troverete informazioni su tali circostanze in un
riquadro come questo.
NL Caution (Opgelet)
Betekent dat de genoemde handleiding nauwkeurig moet worden
opgevolgd, om beschadiging van het instrument te voorkomen.
P Caution (Atenção)
Significa que a instrução referida tem de ser respeitada para evitar a
danificação do aparelho.
Warning
We use the term WARNING to inform you about situations that could
result in personal injury to yourself or other persons. Details about
these circumstances are in a box like this one.
WARNING
10
D Warning (Warnung)
Bedeutet, daß es bei Nichtbeachten der genannten Anweisung zu einer
Verletzung des Benutzers kommen kann
DK Warning (Advarsel)
Betyder, at brugeren kan blive kvæstet, hvis anvisningen ikke
overholdes.
Warning (Peligro)
E Utilizamos el término WARNING (PELIGRO) para informarle sobre
situaciones que pueden provocar daños personales a usted o a otras
personas. En los recuadros como éste se proporciona información
sobre este tipo de circunstancias.
F Warning (Danger)
Nous utilisons la formule WARNING (DANGER) pour avertir des
situations pouvant occasionner des dommages corporels à l'utilisateur
ou à d'autres personnes. Les détails sur ces circonstances sont données
dans un encadré semblable à celui-ci.
I Warning (Pericolo)
Con il termine WARNING (PERICOLO) vengono segnalate situazioni
che potrebbero provocare incidenti alle persone. Troverete
informazioni su tali circostanze in un riquadro come questo.
NL Warning (Waarschuwing)
Betekent dat, wanneer de genoemde aanwijzing niet in acht wordt
genomen, dit kan leiden tot verwondingen van de gebruiker.
P Warning (Aviso)
Significa que a não observância da instrução referida poderá causar
um ferimento ao usuário.
11
Customer Service
This instrument is manufactured by:
PerkinElmer Inc.
710 Bridgeport Avenue
Shelton, Connecticut 06484-4794
U.S.A.
Tel: 1 (800) 762-4000

Internet: http://www.perkinelmer.com
12
Electromagnetic Compatibility (EMC)
Regulatory Information
United States (FCC)
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 user will be required to correct the interference at his own
expense.
NOTE: Changes or modifications not expressly approved by PerkinElmer could cause the
instrument to violate FCC (U.S. Federal Communications Commission) emission
regulations, and because of this violation could void the user’s authority to operate
this equipment.
Europe
All information concerning EMC standards is in the Declaration of Conformity, and

these standards may change as the European Union adds new requirements.
The Clarus MS contains protective circuitry. Contact PerkinElmer

Service before performing any AC line tests.
CAUTION
13
Clarus 600 GC-MS Hardware Guide
Electrical Symbols Used on ClarusMS
Alternating current.
Protective conductor terminal. Ground.
Off position of the main power switch.
On position of the main power switch.
Warning: Risk of electric shock.
Warning: Hot surface.
Caution, risk of danger

Documentation must be consulted to determine the nature of the
potential hazard and any actions which have to be taken.
14
Label Location and Content
Clarus 600
Clarus 600 Mass Spectrom eter
Mass Spectrometer
Figure 1 Front View of Clarus 600 MS Front View of Clarus 560 D
15
Mass Spectrometer
GC Air
Interface Vents PC
Ethernet
Connection
Mass Spectrometer
ETHERNET
Processor
FCC Compliance
Reset
This device complies with Part 15 of the FCC Rules.
Operation is subject to the following two conditions:
S1 Switch
1) this device may not cause harmful interference, and
2) this device must accept any interference received,
Warning including interference that may cause undesired

operation.
Warning
Disconnect AC power cord from oulet Disconnect AC power cord from oulet
before removing any cover or parts.
before removing any cover or parts. Do not operate the instrument with any
cover or parts removed.
Do not operate the instrument with any

!
Caution
cover or parts removed. Do not re strict air intake or exhaus t
Air
Caution Intakes
Do not restrict air intake or exhaust.
Air
Exhaust
ROTARY PUMP
Warning Warning POWER IN

!
NH 3 120 VAC ~ 50/60Hz
CH 4 230 VAC ~ 50/60Hz
C 4H 10 N2 WATER WATER MAX POWER 1000 VA
CI GAS VENT IN OUT EN 55011-Class A, Group 1
Caution
This unit contains protective circuitry.
15 psi
MAX
5 psi
(103 kPa) (35 kPa)
MAX
50 psi
(345 kPa)
MAX
! Contact PerkinElmer qualified service
personnel before performing any
AC line tests
120 VAC ~ 50/60Hz

230 VAC ~ 50/60Hz
MAX POWER 1000 VA
EN 55011-Class A, Group 1
Caution
Contact PerkinElmer qualified service
AC line tests.
Figure 2a Rear View of the Clarus 600 MS
16
PerkinElmer
precisely.
Shelton, CT 06484 USA
Clarus 560 D
Mass Spectrometer
Part No. Nx xx xxx x
GC Air
Interface Vents PC
Ethernet Serial No. Xxx xx xx
Connection
FCC Compliance
This devi ce compli es with Part 15 of the FCC Rules.
Operation is subject to the follow ing tw o conditions:
1) this device may not cause harmful interference, and
2) this device must accept any interference r eceived, Processor
including interference that may cause undesi red
operation. FCC Compliance
Reset
S1 Switch
Warning Warning
Disc onnect AC power cord from oulet
before removing any c over or parts .
Do not opera te the instrument with any
!
Caution
cover or parts removed.
Air
Caution Intakes
D o not r estrict air in take o r exhaust.
Air
Exhaust
120 VAC ~ 50/60Hz
ROTA RY PU MP
230 VAC ~ 50/60Hz
MAX POWER 1000 VA
Warning POWER IN EN 55011-Class A, Group 1
!
REMOVE VENT LINE BLANKING CAP
AT INSTALLATION. 2
On/Off Switch
!
Caution
Caution
Contact PerkinElmer qualified service
AC line tests.
Figure 2b Rear View of the Clarus 560 D MS
17
Clarus MS Safety Practices
NOTE: This equipment requires no specified inspection or preventive maintenance to ensure

the continuous functioning of its safety features.
The Mass Spectrometer should be used in accordance with the instructions provided
in the user’s manuals and tutorial supplied with the instrument. If used otherwise,
the protection provided by the instrument may be impaired.
Do not attempt to make adjustments, replacements or repairs to this

instrument except as described in the accompanying user documentation.
WARNING
Explosive Atmosphere. This instrument is not designed for operation in an

explosive atmosphere.
WARNING
Generic Warnings
Before installing or operating the MS, read the following topics concerning hazards
and potential hazards. Ensure that anyone involved with installation and/or operation
of the MS is knowledgeable in both general safety practices for the laboratory and
safety practices for this instrument. Get advice from your safety engineer, industrial
hygienist, environmental engineer, or safety manager before you install or use this
instrument.
This equipment requires no specified inspection or preventive maintenance to ensure

18
Moving the Clarus MS
Depending on the Clarus 600 MS GC pump option selected, the

instrument weight will range from 46.8 kg (102 lb) to 49.9 kg (110 lb).
The Clarus 560 D MS is 48 kg (105 lb) in weight.
The mass spectrometer requires two people to safely lift it and should
WARNING be lifted from the bottom. Use the following lifting posture to avoid
back injury: With knees bent, simultaneously lift the instrument out of
the carton as you end up in a standing position.
Connect the mass spectrometer to an AC line power outlet that has a

protective ground connection. To ensure satisfactory and safe
operation of the mass spectrometer, it is essential that the protective
ground conductor (the green/yellow lead) of the line power cord is
connected to a true electrical ground. Any interruption of the protective
WARNING ground conductor, inside or outside the mass spectrometer, or
disconnection of the protective ground terminal may impair the
protection provided by the mass spectrometer.
Never operate the mass spectrometer with any covers or parts removed.
WARNING
Do not make adjustments, replacements or repairs to the mass

spectrometer except as described in this manual. Only a PerkinElmer
Service Representative or similarly trained and authorized person
WARNING should be permitted to service the mass spectrometer.
Ensure that the power cord is correctly wired and that the ground leads of all
electrical units (for example, recorders, integrators) are connected together via the
19
circuit ground to earth. Use only three-prong outlets with common earth ground
connections.
• Servicing of electrical components within the mass spectrometer should be
performed only by a PerkinElmer Service Representative or similarly trained
and authorized person.
• Servicing of the incoming AC power line components in your laboratory
should be performed only by a licensed electrician.
Electrical shock hazard. To prevent electrical shock, disconnect the

power cord from the AC outlet before servicing.
WARNING
Disconnect AC power cord from outlet before removing any cover or

parts. Do not operate the instrument with any covers or parts removed.
WARNING
Under no circumstances should circuit boards be removed or inserted unless the

instrument is disconnected from line power.
20
Decontamination and Cleaning
Before using any cleaning or decontamination methods except those specified by

PerkinElmer, users should check with PerkinElmer that the proposed method will
not damage the equipment.
Decontamination
Customers wishing to return instrumentation and/or associated materials to
PerkinElmer for repair, maintenance, warranty or trade-in purposes are
advised that all returned goods must be certified as clean and free from
contamination.
The customer’s responsible body is required to follow the "Equipment

Decontamination Procedure" and complete the “Certificate of Decontamination”.
These documents are available on the PerkinElmer public website:
http://las.perkinelmer.com/OneSource/decontamination.htm
If you do not have access to the internet and are located in the U.S., call toll free at
1-800-762-4000 or (+1) 203-925-4602, 8:30 a.m. – 7 p.m. EST and speak to
Customer Support.
In Canada, call toll free 800-561-4646 and speak to Customer Support.
If you are located outside of the United States or Canada, please call your local
PerkinElmer sales office for more information.
Cleaning the Instrument

Exterior surfaces may be cleaned with a soft cloth, dampened with a mild detergent
and water solution. Do not use abrasive cleaners or solvents.
21
Compressed Gases
Compressed Gases. High pressure gas cylinders can be dangerous if

mishandled or misused. Always handle gas cylinders with caution and
observe your local regulations for the safe handling of gas cylinders.
WARNING
Avoid banging the valves, and ensure that the correct valves and gauges are
installed. It is recommended that gas cylinders be stored and placed outside the
laboratory and connected to the instrument through specially cleaned copper tubing.
Take care not to kink or stress the gas tubing. For safety, cylinders must be firmly
clamped in an upright position.
Explosive hazard. When using hydrogen, methane or isobutane, special

care must be taken to avoid buildup of explosive gas mixtures either in the
GC oven or the mass spectrometer vacuum manifold.
WARNING
Ensure that all hydrogen line couplings are leak-free and do not allow hydrogen to
vent within the oven.
Ventilation
Hazardous vapors. When analyzing hazardous compounds, such as

pesticides, or running in the chemical ionization (CI) mode, it is
necessary to vent the mass spectrometer effluent from the forepump
exhaust into a fume hood or charcoal trap.
WARNING
22
Toxic Gases-Fume Ventilation System. Without adequate ventilation

potentially toxic vapors can build up in the laboratory. Your laboratory
must have reliable fume ventilation system before you use this
instrument.
WARNING
Adequate ventilation must be provided, particularly if a liquid nitrogen or carbon

dioxide subambient accessory is in constant use. The area underneath the bench
(around the forepump) should be well ventilated. An oil separation filter and
charcoal trap should be installed at the outlet of the forepump exhaust to prevent
contamination if fume hood venting is unavailable.
To ensure adequate cooling of the instrument electronics, do not obstruct the gap at
the base of the Clarus MS/Clarus GC, and if practical, leave a minimum 6 inch
clearance between each instrument in the system (for example, the ATD or HS
40XL). This does not include the Clarus MS/Clarus 600 GC as they are connected
together.
Heated Zones
Risk of burns. Never touch a heated mass spectrometer transfer line or

a GC injector cap with unprotected (bare) fingers.
WARNING
Heated zones should be treated with caution, for example, the transfer line, injector
caps, and detectors. In addition, the detector cover may get hot, especially if flame
ionization detectors are operated at high temperatures. As a general rule, allow
heated zones to cool before attempting to work in the GC oven, on the transfer line,
on an injector, around the detector areas or inside the mass spectrometer manifold.
Cooling of the transfer line may require a wait of ½ to 1 hour.
23
Using Hydrogen, Methane or Isobutane
Explosive Hazard. If the hydrogen is turned on without a column

attached to the injector and/or detector fittings inside the oven, the gas
could diffuse into the oven creating the possibility of an explosion.
If the mass spectrometer is not under vacuum, hydrogen, methane, or

isobutane can fill the vacuum chamber thereby creating an explosive
hazard.
WARNING
To avoid possible injury, do not turn on the hydrogen unless a column
is attached, all joints have been leak-tested, and the mass spectrometer
is under vacuum with the forepump exhaust properly vented to a fume
hood.
Using Ammonia Gas
Hazardous gas vapors. When using ammonia gas while running in the
chemical ionization (CI) mode, it is necessary to vent the mass
spectrometer effluent from the forepump exhaust into a fume hood or
outside the building.
WARNING
Hazardous Chemicals
Hazardous chemicals. Before using samples, thoroughly familiarize

yourself with all hazards and safe handling practices. Observe the
manufacturer’s recommendations for use, storage and disposal. These
recommendations are normally provided in the Material Safety Data
WARNING Sheets (MSDS) supplied with the solvents, chemicals, and pump oils.
Be aware that the chemicals that you use in conjunction with the mass spectrometer
may be hazardous. Do not store, handle, or work with any chemicals or hazardous
24
materials unless you have received appropriate safety training and have read and
understood all related Material Safety Data Sheets (MSDS). MSDSs give
information on physical characteristics, precautions, first aid, spill clean up and
disposal procedures. Familiarize yourself with the information and precautions
contained in these documents before attempting to store, use or dispose of the
reagents. Comply with all federal, state, and local laws related to chemical storage,
handling and disposal.
You must work under a suitable hood when handling and mixing certain chemicals.
The room in which you work must have proper ventilation and a waste collection
system. Always wear appropriate safety attire (full-length laboratory coat, protective
glasses, gloves etc.) as indicated on Material Safety Data Sheets.
When using toxic samples, the mechanical pump oil is toxic waste.
WARNING
Some chemicals used with the mass spectrometer may be hazardous or

may become hazardous after completion of an analysis. The
responsible person (for example, the Lab Manager) must take the
necessary precautions to ensure that operators and people in the
surrounding workplace are not exposed to hazardous levels of toxic
substances (chemical or biological) as defined in the applicable
WARNING Material Safety Data Sheets (MSDS) or OSHA, ACGIH, or COSHH
documents. Venting for fumes and disposal of waste must be in
accordance with all national, state and local health and safety
regulations and laws.
25
Definitions in Warnings for Hazardous Chemicals

Responsible body: Individual or group responsible for the use and maintenance of
equipment, and for ensuring that operators are adequately
trained. [per EN/IEC 61010-1].
Operator: Person operating equipment for its intended purpose. [per

EN/IEC 61010-1].
OSHA: Occupational Safety and Health Administration (United States).
ACGIH: American Conference of Governmental Industrial Hygienists.
COSHH: Control of Substances Hazardous to Health (United Kingdom).
26
Temperature, Humidity and Environment

Operating Conditions
The Clarus MS is designed for indoor use only in a laboratory

CAUTION environment that is clean and is free of drafts, direct sunlight and
vibration.
Do not operate the mass spectrometer in a Cold Room or a refrigerated

area. Clarus MS operates under the following conditions:
Ambient temperature is 10 °C to 35 °C (50 °F and 95 °F) with a
variability of less than ± 4 °C (± 7 °F).
CAUTION
The Clarus MS will operate safely between 5°C and 40 °C
(41 °F and 104 °F).
If operating at ambient temperatures between 30°C and 35 °C, you will
need the water-cooling option for the turbopump.
Ambient relative humidity is 20 % to 80 % non-condensing.
Operating altitude is in the range of 0 to 2000 m.
The mass spectrometer is not designed for operation in an explosive

environment. The laboratory should be free of flammable, explosive,
toxic, caustic, or corrosive vapors or gases and should be relatively
free of dust.
WARNING
Pollution Degree: Clarus MS will operate safely in environments that contain

non-conductive foreign matter up to Pollution Degree 2 in
EN/IEC 61010-1.
27
Storage Conditions
The mass spectrometer may be stored under the following conditions:
• Ambient temperature is -20 °C to +60 °C (-4 to 140 °F).
• Ambient relative humidity is 20 to 80 %, non-condensing.
• Altitude is in the range 0 to 12000 m.
• The instrument is stored in an upright position.
28
General Laboratory Safety
Your laboratory should have all equipment ordinarily required for the safety of
individuals working with chemicals (fire extinguishers, first-aid equipment, safety
shower and eye-wash fountain, spill cleanup equipment, etc.).
29
WEEE Instructions for PerkinElmer Products
or
A label with a crossed-out wheeled bin symbol and a rectangular bar indicates that
the product is covered by the Waste Electrical and Electronic Equipment (WEEE)
Directive and is not to be disposed of as unsorted municipal waste. Any products
marked with this symbol must be collected separately, according to the regulatory
guidelines in your area.
The objectives of this program are to preserve, protect and improve the quality of
the environment, protect human health, and utilize natural resources prudently and
rationally. Specific treatment of WEEE is indispensable in order to avoid the
dispersion of pollutants into the recycled material or waste stream. Such treatment is
the most effective means of protecting the customer’s environment.
Requirements for waste collection, reuse, recycling, and recovery programs vary by
regulatory authority at your location. Contact your local responsible body (e.g., your
laboratory manager) or authorized representative for information regarding
applicable disposal regulations. Contact PerkinElmer at the web site listed below for
information specific to PerkinElmer products.
Web address:
http://las.perkinelmer.com/OneSource/Environmental-directives.htm
For Customer Care telephone numbers select “Contact us” on the web page.
Products from other manufacturers may also form a part of your PerkinElmer
system. These other producers are directly responsible for the collection and
processing of their own waste products under the terms of the WEEE Directive.
Please contact these producers directly before discarding any of their products.
Consult the PerkinElmer web site (above) for producer names and web
addresses.
30
Pre-Installation Requirements
Laboratory Space Requirements
Size Weight
Clarus 600 MS 32 cm (13 in.) wide x 50 cm Depending on the pump option

(20 in.) high x 77 cm (30 in.) deep selected, the weight will range from
46.8 kg (102 lb) to 49.9 kg (110 lb).
Clarus 560 D MS 32 cm (13 in.) wide x 46 cm 48 kg (105 lb)

(18 in.) high x 77 cm (30 in.) deep
Forepump 30.5 cm (12 in.) wide x 44 cm (17.3 in.) high 25.9 kg (57 lb)
x 72 cm (28.4 in.) deep.
Clarus 600 GC 99 cm (39 in.) wide x 53 cm 49 kg (108 lb)

(21 in.) high x 82 cm (32 in.) deep
Autosampler Tower 13 cm (5 in.) wide x 36 cm (14 in.) high x 24 4.5 kg (10 lb)
cm (9.5 in.) deep
Physical Single unit for use on standard laboratory bench that can be interfaced to a computer
Configuration and printer.
Bench Space The laboratory bench should be sturdy enough to support the full weight of the GC/MS
as well as additional equipment (for example, computer and/or printer). Expect the
total weight of the GC/MS and accessory equipment to weigh at least 159 kg (350 lb).
Allow a minimum clearance of 15 cm (6 in.) on each side, 22.9 cm (9 in.) at the rear,
and 137.2 cm (54 in.) at the top of the GC/MS. If this is not possible, install the
GC/MS on a bench that has wheels. The bench requires an area underneath for the
forepump.
Do not position the Clarus 600 MS so that it is difficult to operate the
AC power on/off switch on the lower left side of the instrument in case of a
malfunction of the instrument. For the Clarus 650 D the AC power on/off switch on
the back of the instrument.
Peripherals, Printers Allow at least 94 cm (36 in.) on either side of the instrument to accommodate
etc. additional equipment (for example, the computer).
31
Environmental Requirements
Pollution Degree This instrument will operate safely in environments that contain
non-conductive foreign matter up to Pollution Degree 2 as
defined in EN/IEC 61010-1.
Laboratory Install the GC/MS in an indoor laboratory environment that is

Environment clean and free of drafts and direct sunlight.
The laboratory should be free of flammable, explosive, toxic,
caustic or corrosive vapors or gases, and should be relatively
free of dust.
The ambient laboratory temperature should be between 10 °C
and 30 °C (50 °F and 86 °F) for Clarus 600 C, 600 T, and 600 S
systems unless the turbomolecular pump is water cooled, and
between 10 °C and 35 °C (50 °F and 95 °F) for Clarus 600 D, or
for Clarus 600 C, 600 T, and 600 S systems with water cooling.
32
Clarus 600 GC-MS User’s Guide
Power Requirements
Clarus MS All electrical supplies must be smooth, clean, and free of line transients
greater than 40 V peak to peak, and must meet and remain within the
following tolerances:
120 VAC ±10 % @ 50/60 Hz ±1 % 1000 VA maximum
230 VAC ±10 % @ 50/60 Hz ±1 % 1000 VA maximum
Add 100 VA for the computer and 108 VA for a printer.
Clarus GC All electrical supplies must be smooth, clean, and free of line transients
greater than 40 V peak to peak, and must meet and remain within the
following tolerances:
For GC with slow heating rate as standard;
120 VAC ± 10% @ 50/60 Hz ± 1% @ 20 Amps, 2400 VA maximum
For GC with optional oven heater for fast heating rate;

240 VAC ± 5% @ 50/60 Hz ± 1% @ 13 or 16 Amps, 3120 VA max
Instruments and peripherals must not be connected to circuits with large
inductive or large and frequent loads (for example, large motors,
discharge lamps, photocopy systems, radio transmitters, etc.).
33
Power Outlets Clarus MS: A minimum requirement of a power line separate from the
GC at 15 amps or greater.
Clarus GC: A minimum of one dedicated 120 VAC outlet at 20 A or
one 230 VAC outlet at 10 A (minimum) is required for the Standard
GC. When the optional oven heater is ordered, the outlets will be as
indicated above.
Additional equipment, such as computers and printers, should be

connected per their specifications.
34
Safety Requirements
Gas Delivery Copper tubing that is free of grease, oil and organic material must
Lines always be used with the Clarus 600 MS on all gas lines, except
ammonia reagent gas. Ammonia reagent gas requires stainless steel.
Solvent-washed copper tubing must be used to avoid contamination
of the Gas Chromatograph. Suitable solvents are acetone or
dichloromethane (do not use if negative chemical ionization is
planned) followed by methanol. Clean helium or nitrogen should be
used to blow any residual solvent from the tubing. Cap all unused
tubing.
Care must be taken not to kink or overstress the gas delivery lines.
Strain relief consisting of two one inch coils of tubing should be
installed at every gas line connection.
Gas Cylinders All gas cylinders should be firmly clamped to a suitable surface.
Gas cylinders should be located outside of the laboratory whenever

possible, and should always be stored and operated in a vertical
position.
Hydrogen Ensure that all hydrogen lines and connections are leak-free. When
using a hydrogen tank, install an in-line hydrogen snubber (part
number 00090038) between the tank regulator and the delivery
tubing.
Ventilation Always provide adequate ventilation. When analyzing hazardous

compounds such as pesticides, it may be necessary to arrange to
vent the mass spectrometer effluent from the forepump into a fume
hood. To prevent contamination if a fume hood is unavailable, an
oil separation filter should be installed at the outlet of the forepump
vented to a fume hood or an oil mist separator (Alcatel 68316) with
a charcoal trap (Koby KA1). An acceptable alternative is to attach a
½ inch Tygon tube and vent to a hood. Pump oil vapor is considered
toxic and must be vented properly.
35
Gas Requirements
Carrier gases used with the mass spectrometer require a minimum purity of
99.999%. Gas cylinders should be located outside of the laboratory whenever
possible, and should always be stored and operated in the vertical position.
For all gases delivered to the mass spectrometer, always use copper tubing
CAUTION that is free of grease, oil, and organic material. If in doubt about the
condition of your tubing, clean it before use.
Gases
GC/MS Carrier Minimum purity of 99.999% for helium or hydrogen. Carrier gas tubing
Gases: should be ultra-clean.
A number 1A (200 ft3) gas cylinder should be used for all carrier gases with a
Helium high-purity, stainless-steel diaphragm, two-stage regulator. Filter through a
moisture filter and/or hydrocarbon trap and de-oxo filter designed for MS.
Gas delivery pressure to the GC should be 70 – 100 psi (483 – 689 kPa). Do
not exceed 100 psi (689 kPa) on the carrier gas inlet.
Reagent Gases: Minimum purity of 99.999% for methane, minimum purity of 99.98% for
isobutane, minimum purity of 99.998% for ammonia. Carrier gas tubing
should be ultra-clean.
The gas delivery pressure required is 15 psi (103 kPa) to the bulkhead fitting
(1/8 in. Swagelok) on the mass spectrometer.
Ammonia If ammonia is used for chemical ionization, all fittings and tubing must be
stainless steel to avoid corrosion. A single-stage regulator is required for
ammonia, rated for corrosive service. Also, the forepump must be vented to a
fume hood or outside the building.
Methane and A high-purity, stainless-steel diaphragm, two-stage regulator is required for
Isobutane methane and isobutane with a final delivery pressure of 15 psi (103 kPa).
Clean tubing must be used. It must be solvent-washed and nitrogen-dried. The
bulkhead connector at the rear of the instrument is a 1/8 in. Swagelok fitting.
The use of commercial gas purifiers for reagent gas is recommended.
36
Computer and System Software Requirements

To ensure that your system performs at the expected high level, your computer must
be configured to the minimum capabilities indicated below.
These requirements may be updated as the requirements for TurboMass software

and/or Microsoft Windows XP SP2 are changed. Consult the latest Product
Description List for current requirements.
NOTE: This guide does not cover the installation and configuration of your computer. If
you have purchased a complete system from PerkinElmer, the computer will be
configured by your Service Engineer during product installation.
PC Requirements
The TurboMass software is installed at PerkinElmer prior to shipment and tested
using the following minimum PC system specifications. If you need to reinstall the
software, verify that the PC meets the following minimum requirements:
• Dell OptiPlex 745, GX620, GC270, or GX 280
• Intel® Pentium processor
• 512 MB of Random Access Memory (RAM)
• High Color (16 bit) at 1024 x 768 SVGA
• Hard disk with 2.0 GB free space
• 8x speed CD-ROM drive
• 1 RS-232 port
• 2 RJ-45 10/100Base-T ports
• A keyboard and PS/2®-style mouse
Operating System
Windows XP SP2
37
Software
TurboMass Software.
Instrument Firmware Versions

Internal dotLINK
Printers
• HP LaserJet 4200 Printer Series (HP 4200, 4210, and 4250)
• HP DeskJet 5650 Color InkJet Printer
NOTE: Using any printers other than the ones recommended above may not correctly
display the Communiqué reports.
38
Pre-Installation Checklist
MODEL: __________________________ DATE: _____________________
CUSTOMER: __________________________________
SPO#: __________________________________
Requirements OK Needs Prior To Installation
Customer Responsibility
Lab Space Requirements
Power Requirements
Gas Requirements
Environmental Requirements
Safety Requirements
Preparation of Samples
(Customer Responsibility)
Computer Configuration
Customer Experience
39
40
Introduction 2
Introduction
Preface
The Clarus MS is a benchtop mass spectrometer designed with the user in mind. The
small profile of combination Gas Chromatograph and Mass Spectrometer (GC/MS)
allows it to fit on a standard six foot long laboratory bench. Sophisticated software
controls the GC/MS from a Windows XP SP2 computer.
System Overview
The system consists of:
• Clarus GC.
• Clarus MS.
• Computer.
• TurboMass Software.
• Foreline Pump.
43
Introduction
Summary of this Guide

Thoroughly read and understand the Safety and Regulatory Information chapter
before using the mass spectrometer.
Chapter 1: Warnings and Safety Information

Contains all of the safety information and topics to comply
with EN/IEC 61010.
Chapter 2: Introduction
Provides an instrument overview and the references to related
documentation.
Chapter 3: About the Clarus 600/560 D System

Describes each of the components in the system and includes a
list of items to check before using the instrument.
Chapter 4: Maintenance
Contains preventive and routine maintenance procedures that
typical users can perform.
Chapter 5: Troubleshooting
Provides helpful troubleshooting tips and a table to help you
identify and solve typical problems.
Related Documentation
The Clarus 600/560 D family of manuals includes the following:
• Clarus 600/560 D MS Tutorial (part number 09936769): The tutorial provides
a step-by-step guide to performing a number of tasks using the instruments and
software.
44
• Software User’s Guide (part number 09936767): A comprehensive manual

describing the functionality of each part of the TurboMass software. It
describes the keys and fields on each screen.
• Clarus 600/560 D MS Hardware Manual (part number 09936768): Contains

the required safety and regulatory information required for EN/IEC 61010. It
contains an overview of mass spectrometry and of each component in this
system; a pre-operational checklist, typical user maintenance and a
troubleshooting guide.
• Service Manual (not included): Contains information for trained service

engineers to completely service the Clarus.
About Part Numbers Listed in this Manual

The part numbers listed in this manual are available from PerkinElmer’s catalog
service.
Supplies, Accessories and Replacement Parts
Supplies, accessories, and replacement parts can be ordered directly from

PerkinElmer's catalog service. PerkinElmer offers a full selection of high-quality
chromatography data handling products and gas chromatography supplies and
columns through e-essentials.
To place an order for supplies and many replacement parts, request a free
e-essentials catalog, or ask for information:
Telephone:
• U.S. only: Call toll free 1-800-762-4000, 8:30 a.m. to 7 p.m. EST. Your order
will be shipped promptly, usually within 24 hours.
• Worldwide: Call your local PerkinElmer sales or service office or call

PerkinElmer, Shelton, CT USA
45
Clarus 600 MS User’s Guide
46
About the
Clarus 600/560 D System 3
About the Clarus 500 System
About the Clarus 600/560 D System
The Clarus 600/560 D mass spectrometer is a compact benchtop instrument that

produces positive identification and quantitation of compounds separated by the
Clarus 600/560 D GC. Even if the compounds coelute, the mass spectrometer can
still positively identify and quantitate each compound. Clarus 600 MS is designed to
run analyses that best identify your sample by using the electron impact (EI) or
chemical ionization (CI) mode. The Clarus 560 D MS runs analyses that identify
your sample by using the electron impact (EI) mode.
The Clarus 600/560 D system is controlled by a PC using TurboMass Software. The

application runs in a Microsoft Windows XP SP2 operating environment. The
software user interface contains color graphics and provides full user interaction
with either the keyboard or the mouse. TurboMass completely controls the GC/MS
system from tuning and data acquisition (scanning or selected ion recording mode),
through quantifying your results. Complete operating instructions of all TurboMass
controls are in the TurboMass Software Guide (part number 0993-6767), supplied
with the system.
A high-performance, research-grade analytical quadrupole mass analyzer with a

quadrupole prefilter assembly transmits only those ions having your selected mass-
to-charge ratio. The prefilter rod set improves sensitivity and protects the analytical
quadrupole rods from contaminating ion deposits. Ions emerging from the
quadrupole mass analyzer are converted to photons and detected by the
photomultiplier detector system. The low noise photomultiplier typically operates
with a gain of 105.
49
Clarus 600 MS Hardware Guide
Figure 3 Clarus MS with Clarus GC
The system consists of two major components: Clarus MS and the Clarus GC. Brief
descriptions of each major component follow.
50
Clarus 600/560 D GC
The Clarus 600/560 D Gas Chromatograph is a dual-channel, temperature-

programmable gas chromatograph (GC). It is available in many configurations, such
as with or without, an autosampler, programmable pneumatic control (PPC), and a
variety of injector/detector combinations to provide you with total GC flexibility.
The Clarus 600/560 D GC is microprocessor controlled, where you enter the
operating parameters and view the prompting text and monitor instrument functions
on a large full-color touch screen display.
Figure 4 Clarus 600/560 D GC
The Programmed Pneumatic Control (PPC) Version of the Clarus 600/560 D GC

is used where the carrier gas and detector gases are monitored and controlled by the
microprocessor, thereby producing a fully automated system that is capable of
managing all pneumatic functions within the gas chromatograph.
51
The Clarus 600/560 D GC can store up to five GC methods. Methods can be

generated, copied, deleted, edited, set up, and printed. These methods are normally
developed and stored on the TurboMass data system. The automatic liquid
autosampler can run up to 15 injections per vial from as many as 82 vials and one
priority vial using one or two autosampler programs (if not under TurboMass
control). In the latter case, a different GC method can be used by each program if
desired.
PPC provides real-time digital readouts to simplify setting carrier gas pressures and
flows.
Figure 5 Clarus 600 Mass Spectrometer
52
GC Interface (Transfer Line)
The detector end of a capillary GC column in the Clarus 600/560 D GC oven is

inserted through a temperature-controlled transfer line and optimally positioned so
that the column end is flush with the inner wall of the EI or CI ion source. The
transfer line is temperature controlled by Clarus MS and has a 350 °C upper limit. If
the Clarus 600 GC detects improper operation (for example, no carrier gas) and goes
into an alarm condition, it will turn off the temperature to the transfer line.
Do not use metal capillary columns in the transfer line. They may
CAUTION
electrically short-out the source.
Figure 6 The transfer line
53
Reference Gas Inlet
The reference gas inlet system consists of a glass bulb filled with heptacosa (FC43)
connected to tubing which directs it to the ion source. You can switch the reference
gas solenoid valve on and off and also purge the reference gas lines from the Tune
screen.
Figure 7 and 8 shows the components or assemblies that comprise the Clarus
600/560 D MS with the manual vent switch (Clarus 600 D and Clarus 560 D) or the
CI adjustment valve (Clarus 600 C) configuration (see the following two pages).
54
RF Generator
Reference Gas Vial
Head Amplifier
Wide
Access Door Range
Gauge
Inner Source Forepump Line
Transfer Line
On/Off Switch
Diffusion Pump
Manual Vent Valve
For Diffusion Pump
Phosphor Plate
Conversion
Dynode
Photomultiplier
Tube
Grounding Plate
Lens 2
Exit Aperture
Lens 1
Analytical Quads
Pre-Quads
Outer
Source
Inner
Source
Figure 7 Components of the Clarus 600/560 D MS and a detail of the ion optics
path (manual vent valve for diffusion pump configuration)
55
RF Generator
Reference Gas Vial
Head Amplifier
Wide
Access Door Range
Gauge
Forepump Line
Inner Source
Transfer Line
On/Off Switch
CI Needle Valve Turbo Pump

For Large Turbo Pump
Phosphor Plate
Conversion
Dynode
Photomultiplier
Tube
Grounding Plate
Lens 2
Exit Aperture
Lens 1
Analytical Quads
Pre-Quads
Outer
Source
Inner
Source
Figure 8 Components of the Clarus 600 MS and a detail of the ion optics path
(CI needle valve for large turbo pump configuration)
56
Ion Optics Path

Ion Source The ion source consists of a removable EI or CI inner source and
a fixed outer source for the Clarus 600. The Clarus 560 D uses an
EI source only. In the EI source, molecules exit the column where
they are bombarded by electrons from the filament and ionized
into positive and negative ions as well as neutral species. The
positive electron trap attracts the negative ions and electrons to
the repeller that directs the positive ions out of the inner source
through focusing lens to the mass analyzer. Those remaining
molecules and neutral fragments are pumped away by the
vacuum. Heaters in the outer source raise the source temperature
high enough to prevent sample molecules from condensing in the
source and minimize any contamination.
Mass Analyzer The mass analyzer element of this high performance quadrupole
mass spectrometer is a finely machined assembly that has been
precisely aligned using specialized equipment. Under no
circumstances should the main analyzer rod set assembly ever be
dismantled.
The mass spectrometer is fitted with a quadrupole prefilter
assembly that is designed to protect the main analyzer by
intercepting the majority of any contamination. As a
consequence, the main analyzer should never require cleaning.
On occasion, it may be necessary to remove the prefilter rods for
cleaning. The need to clean these rods is usually indicated by
poor peak shape or loss of resolution, although other more likely
causes, such as source contamination, should be eliminated first.
It is necessary to remove the inner and outer ion source assembly
before the prefilter assembly can be removed.
Detector The detector consists of a conversion dynode, phosphor plate, and

photo-multiplier tube. The detector works by accelerating
positive or negative sample ions onto a dynode surface that emits
electrons. The electrons are then accelerated to strike a phosphor,
which produces photons of light that are amplified by the
photomultiplier and collected as the signal.
57
Photomultiplier The photomultiplier consists of a photosensitive surface and

electron multiplier sealed in a glass tube. The light strikes the
front window, electrons are emitted and accelerated onto the first
dynode of the electron multiplier and avalanche down the chain
of dynodes. The multiplier is sealed in its own permanent vacuum
chamber (glass tube) and cannot be contaminated. However,
contamination on the front window will raise the noise level and
lower the sensitivity.
Electronics The Clarus 600/560 D MS electronics consist of a port in the PC,

an embedded processor & digital I/O board, analog board
(GC/MS), backplane board, PMT electrometer board, and high
voltage and low voltage power supply boards. The embedded
processor controls all aspects of instrument and data acquisition.
Ions exiting from the quadrupole are accelerated into a cup-
shaped dynode where they strike the inner surface. Electrons are
emitted into an electric field, which extracts them from the
conversion dynode and passes them onto the phosphor. The
phosphor is held at a higher positive potential than the dynode.
Light is emitted when the electrons strike the phosphor. The
resulting optical signal is detected by the photomultiplier (PMT).
58
Vacuum System
The source, ion optics, analyzer, and detector are fitted inside a cast aluminum
chamber. Vacuum is applied to the chamber using a rotary pump and a
turbomolecular pump. The vacuum is monitored through a wide range gauge. The
rotary pump sits on the floor and a turbomolecular high vacuum pump or an air-
cooled oil diffusion pump (Clarus 600 D) is mounted under the ion optics chamber:
Rotary Pump
The Clarus 600 MS has a 3 m3/hr computer controlled mechanical pump. The
turbomolecular or diffusion pump is backed by this direct drive rotary pump. The
rotary vane pump rests on the lab floor and may be positioned beneath the
instrument. Care should be taken to avoid mechanically coupling vibrations from
this pump to the mass spectrometer. Operation and maintenance details about these
pumps can be found in the manuals provided with the pump.
The rotary vane pump (also called the forepump) provides the first level of vacuum
to approximately 2 x 10-3 Torr. The pump has a switchable dual voltage.
59
Voltage Selection
Switch Under Cover
Handle
TurboMass
Connection Port
Oil Filler Plug
Exhaust Port
Max
On/Off Min
Switch
Gas Ballast
Switch
Mode Selection
Switch Drain Plug
Oil Level
Indicator
Figure 9 The rotary (fore) pump
Connect the rotary pump exhaust to a line vented to the atmosphere outside the
laboratory or use an appropriate exhaust line filter.
The AC line cord for the rotary vane pump must be plugged into the
designated receptacle on the back of the Clarus 600 MS. The pump is
CAUTION controlled by the TurboMass software.
Connecting the vacuum hose to the exhaust connection of the rotary

pump will severely contaminate the Clarus 600 MS.
60
Vacuum Pump Options

The Clarus 600 MS offers three different vacuum pump capacities. The
tubomolecular and diffusion pump options are designed to fit your applications,
performance and budgetary needs. The Clarus 560 D only utilizes a diffusion pump.
Turbomolecular Pump
Clarus 600 MS has two turbomolecular pump options in three configurations.
Turbomolecular pumps are high-speed turbines which transport the sample and
carrier gas molecules away from the mass spectrometer.
Clarus 600S - The 75 L/sec turbomolecular pump supports Electron Ionization
operation (EI) and has optional water cooling.
Clarus 600 T – All of the functions and options of the 600 S with a 255 L/sec
turbomolecular pump for higher column flow rates, pump-down time under three
minutes, and lower detection limits
Clarus 600 C - All of the functions and options of the 600 T with positive and
negative Chemical Ionization (CI) operation.
Diffusion Pump
Clarus 600 D and the 560 D MS has an air-cooled oil diffusion pump. This pump is
only available for Electrical Ionization (EI) operation.
Pump fluid is heated in the base of the pump to produce a vapor which passes
through the interior of the jet assembly and emerges from the jets as high-velocity
vapor streams. These streams entrain eluting compounds and carrier gas, condense
on the cooled pump body wall, and drain into the base of the pump for recirculation.
The entrained compounds are transferred to the forepump.
The diffusion pump system has a manual vent switch. This manual vacuum venting
is controlled by a push button toggle switch and a pump temperature sensing
switch. When you push the button in, the vent is opened. When the button is up
(not pushed in), the vent is closed. See the following illustration.
The mass spectrometer's vacuum system is controlled from the Tune page. Be sure that
this is done in accordance with the information provided in your Mass Spectrometry
Hardware Guide. The following procedures describe a Turbomolecular Pump system
and a Diffusion Pump system.
61
Diffusion Pump Operating States

System Description System Diagram
Vacuum System Off.
Backing pump turned on.
High vacuum pump is on.
Proper operating conditions reached.
Fault with high vacuum pump.
When vacuum system off has been initiated
62
Diffusion Pump Operating States Continued

System Description System Diagram
When system has cooled and diffusion pump is
turned off.
When backing pump is turned off.
When vacuum leak is detected.
When vacuum gauge failure is detected.
When vacuum gauge failure is detected on start

up.
High vacuum pump is on. Display count down

timer.
When system has cooled and diffusion pump is Display count down
turned off. timer.
63
Turbomolecular Pump
Pumping Down a Turbomolecular Pump Vacuum System
¾ Select Pump/Vacuum System On from the Options menu on the Tune

page.
The menu name will change from Pump/Vacuum System On to
Vent/Vacuum System Off, and the system will begin its pump-down
sequence. Once OPERATE is enabled, it remains enabled unless the
Vent/Vacuum System Off command is given.
Venting the Vacuum System (Turbomolecular Pump)
1. Cool the source and inlet to below 100 °C.
2. Select Vent/Vacuum System Off from the Options menu on the Tune
page, and confirm that you want to vent the system.
Diffusion Pump
Pumping Down a Diffusion Pump Vacuum System
¾ Select Pump/Vacuum System On from the Options menu on the Tune

page.
The menu name will change from Pump/Vacuum System On to Vent/Vacuum

System Off, the roughing pump turns on and waits for the system to achieve a
minimum vacuum level of 3.7 x 10-1 Torr. Once that vacuum level has been
achieved, a relay turns on the diffusion pump heater and a countdown timer
starts. A typical vacuum level will stay constant until the count down timer
reaches 10 minutes, the vacuum drops quickly to 1 x 10-4 Torr, and continue to
4 x 10-5 Torr before the countdown timer ends.
When the timer reaches 5 minutes, the software will enable OPERATE. If you
attempt to use the system prior to achieving a safe operating vacuum
(5 x 10-5 Torr), a warning message will appear.
64
CAUTION The software will not prohibit the use of the system prior to reaching
the desired vacuum. The software will monitor the vacuum gauge
pressure to determine when the system has reached the proper
operating vacuum (5 x 10-5 Torr).
Once OPERATE is enabled, it remains enabled unless the Vent/Vacuum

System Off command is given.
Venting the Diffusion Pump Vacuum System
1. Cool the transfer line and source to under 100 °C.
2. Select Vent/Vacuum System Off from the Options menu on the Tune
page, and confirm that you want to vent the system.
The system will start its automatic venting sequence. The software monitors
the temperature of the source and the inlet. When the temperatures of both
of the source and the inlet are less than 100 °C, the software turns off the
diffusion pump heater and starts a 20 minute countdown timer.
During the cooling down period, the countdown timer will display the time
remaining in minutes and seconds. When the count down timer reaches 0,
the backing pump turns off.
Once the backing pump has been turned off, the software will display a
message indicating that the system is now cool enough to vent. The message
also reminds you to turn off the carrier gas.
3. Vent the mass spectrometer by pressing the push-button behind the front
door of the mass spectrometer. It will lock in the pressed-in position and
turn red indicating the vent valve is open.
CAUTION If you try to vent a hot diffusion system, oxidation of the pump oil may
occur and cause oil to enter the analyzer tub which will damage the
mass spectrometer.
65
Access Door
Source
Manual Vent Valve

for the Diffusion Pump
The depressed push button vent switch lights when venting is allowed. Before
pressing Pump/Vacuum System On, make sure the vent switch is closed (the
button is out and the light is off)
Never vent when:
• The diffusion pump is hot
• During the 20 minute cool-down period
Always check that the front panel vent button is out and the lamp is off when
starting to pump the system down.
66
NOTE: The vent valve will operate if the vent switch is pushed in (on) before the diffusion
pump becomes hot. This includes the first few minutes of Pump/Vacuum System
On. Venting during this period may cause a vacuum fault to occur and risk back
streaming the diffusion oil into the analyzer. It is a good reminder to leave the
instrument front door open whenever the push button switch is pushed in (on).
NOTE: When the diffusion pump is hot, the vent switch is deactivated and will not light
when pushed in (on). Since the vent switch may be left in the depressed position at
any time, you should be careful to avoid closing the instrument door and forgetting
that the push button switch is pushed in. (When the diffusion pump cools, the
pushed in push button switch will light and automatically vent the system).
Vacuum Gauge
The single wide range vacuum gauge monitors the system pressure from atmosphere
down to 10-9 Torr using a combined Pirani/Inverted Magnetron ionization sensor.
Normal operating pressure with 1 mL/min helium for the 255 L/sec turbomolecular
pump is between 9x10-6 Torr and 2x10-5 Torr after pump-down and ion source bake-
out. The 75 L/sec turbomolecular and the diffusion pumps will operate at somewhat
higher pressures, typically below 4x10-5 Torr.
67
TurboMass Software
TurboMass software is the user interface of the Clarus system. The following
screens show some examples of how you can control Clarus. Interaction is via the
mouse and keyboard using menu-driven commands. Printing, file management and
other routine procedures are performed using the appropriate Microsoft Windows
modules.
Top Level Screen

This screen contains the GC/MS status, sample list, sequence queue, and provides
you with access to all other functions.
68
Clarus 600 GC-MS User’s Guide
Tune Page
The Tune Page allows you to tune the mass spectrometer, control the gases, set the
GC interface temperature, and monitor the instrument vacuum pressure.
69
Analytical Column
The analytical column inside the Clarus GC oven provides the sample separation.
Make sure you select the proper column for your analysis. PerkinElmer offers a
wide range of columns in the Gas Chromatography Column Catalog. The
TurboMass Tutorial provides additional column selection tips.
There are several things to consider when choosing an analytical capillary column:
1. Know the types of samples you will be analyzing. Are they volatile, semi-volatile,
pesticides, solvents, etc?
2. Select a stationary phase based on polarity of the sample. A very general rule in
column selection is that like dissolves like. Column polarity has the greatest effect
on how the column separates the compounds of interest as the sample interacts with
the stationary phase. There are different degrees of polarity from non-polar to very
polar. When compounds are separated primarily on their boiling points the phase is
considered to be non-polar. Polar phases typically separate compounds based on the
chemical interactions between the sample components and the stationary phase.
3. The inside diameter of the capillary column has an effect on the column’s resolving
power and its capacity or concentration range. In general, the larger the inside
diameter of the column, the larger the sample capacity. However, the larger the
inside diameter, the higher the flow necessary to achieve good performance.
4. The next parameter is the phase or film thickness. Film thickness will primarily
affect the retentive character and the capacity of the column. Increasing the film
thickness will cause an increase in the retention of the compounds being analyzed.
Thick film columns are primarily used for extremely volatile compounds. The
thicker phases will retain components longer, allowing them to interact longer with
the stationary phase, thereby increasing the separation of closely eluting compounds.
5. The last variable to consider is column length. The effect of column length on a
separation becomes less important as column length increases. Resolution is a
function of the square root of the column length. An example of this relationship is
that, if you want to double the separation between two peaks without changing the
stationary phase, inside diameter, film thickness, or GC conditions, it would take a
four-fold increase in the column length. A 30 meter column is the most common
length and is usually sufficient for analyzing most samples. Typically, users doing
environmental EPA type analysis will use a 30 meter column for semi-volatile
compounds and 60 to 105 meter columns for volatile compounds.
70
Pre-Operational Checklist
This checklist provides you with a list of items to check to make sure everything are
in working order before you begin to use Clarus.
Item OK
Are the gases connected to the GC?
Is the proper column connected?
Is the proper liner installed in the injector?
Are your samples prepared?
Is there a GC method?
Is the GC split vent open?
Is the proper mass spectrometer vacuum achieved?
Is the system leak-free?
Is there a mass spectrometer method?
Are the autosampler wash vials filled with solvent?
Are you using the proper column flow or pressure?
Did you check the air/water spectrum on the TurboMass Tune screen?
Is the injector hot and set to the proper temperature?
Is the transfer line hot and set to the proper temperature?
Is the source hot and set to the proper temperature?
71
72
Maintenance 4
Overview
High electrical voltage is present inside the mass spectrometer. To

prevent the risk of electrical shock or injury from high voltage, unplug
the AC line cord from the AC outlet and wait at least one minute before
opening or removing an instrument panel.
WARNING
Disconnect AC power cord from outlet before removing any cover or

parts. Do not operate the instrument with any covers or parts removed.
WARNING
Do not attempt to make adjustments, replacements or repairs to this

instrument except as described in the accompanying user
documentation.
WARNING
NOTE: This equipment requires no specified inspection or preventive maintenance to ensure

Cleanliness and care are of critical importance whenever internal assemblies are
removed from the instrument.
• Always prepare a clear, clean work area.
• Make sure that any required tools or spare parts are close at hand.
• Obtain small containers to store screws, washers, spacers etc.
• Never touch any internal source parts with your bare fingers.
• Use tweezers and pliers whenever possible.
• If nylon or cotton gloves are used, prevent leaving fibers in sensitive areas.
NEVER use rubber gloves.
• Before reassembling and replacing dismantled components, inspect O-rings

and other vacuum seals for damage. If you in doubt, replace the O-rings and
vacuum seals with new ones.
If a fault occurs soon after repairing or disturbing a particular part of the system,
ensure that this part has been correctly refitted and/or adjusted and that any adjacent
components have not been inadvertently disturbed.
Many of the procedures described in this chapter involve removing

potentially toxic contamination deposits using flammable or caustic
agents. Anyone performing these operations should be aware of the
inherent risks and should take the necessary precautions.
WARNING
76
Maintenance
Typical Overall Maintenance Schedule
Performing maintenance tasks on a routine basis can reduce the overall costs of
operation. If a fault occurs, you can correct it with minimum difficulty.
Advanced maintenance should be performed by a skilled person capable of

removing complicated mechanical assemblies. For example, an untrained individual
should not attempt to remove the manifold but may be able to perform basic
maintenance such as draining and filling the forepump.
Exterior surfaces may be cleaned with a soft cloth dampened with a mild detergent
and water solution. Do not use abrasive cleaners or solvents.
Factory trained service personnel can assist in any advanced training needs. All
tasks should be logged into a logbook to keep a record of any problems or trends.
Daily
• Make sure all system components are in working order.
• Check and ensure that there are gas supplies to the GC and to the mass
spectrometer.
• Check the air/water spectrum. Perform leak checking if necessary.
• Enter information into a logbook.
Weekly
• Check the tune and mass calibration. Tune if necessary.
• Check the forepump oil level and color. Replace if necessary.
• If equipped with a water chiller, check the water level and temperature.
• If using CI, at the end of the day gas ballast the forepump lightly for 20
minutes.
77
Monthly
• Clean the fan filters on the rear of Clarus MS.
• Check the reference gas vial. Refill if necessary.
Every Six Months

• Replace the forepump oil.
• Check the inner source. Clean if necessary.
• Check the analyzer prequadrupole. Clean if necessary.
Yearly
• Check lens 1, lens 2, and analyzer prequadrupole. Clean if dirty.
• Check and clean the forepump inlet filter, gas ballast control, and the motor fan
cover and enclosure.
78
Maintenance
Leak Checking
Checking for leaks is actually checking the integrity of the vacuum system. You
observe masses 4 (helium), 18 (water), 28 (nitrogen), and 32 (oxygen).
To leak-check the system, follow this procedure:
1. Ensure that all connections are made to the mass spectrometer.
2. Set the GC split flow to 50 mL/min by pressing the PSSI injector icon on the
Clarus GC touch screen. On the next screen, press the split flow setpoint and use
the up and down arrow or keypad buttons to set the split flow to
50mL. For example, if the capillary injector is in position 1 and you selected split
flow in the PPC configuration software, the following screen is displayed.
The total flow (split vent + septum purge + column) is displayed in the lower left
of the screen. The split vent flow setpoint is displayed in the setpoint box in the
lower right.
3. Start the TurboMass software by clicking on the Windows Start button at the bottom
left of the screen and selects TurboMass under the
Programs/TurboMass/TurboMass path, or double-click on the TurboMass icon if it
is on your Windows desktop.
79
The initial TurboMass window is displayed.
4. Display the Tune dialog by clicking .

The Tune dialog is displayed.
5. Make sure the Tune parameters are similar to the values displayed.
NOTE: The inlet and source temperatures should be less than 100°C only when venting the
system.
80
Maintenance
6. Click Press for Operate next to the red indicator box.

The indicator box color changes to green and the name of the button changes to
Press for Standby.
7. Select Pump from the Options menu.

This starts the forepump and the turbomolecular pump or diffusion pump
depending on which pump you have installed. Watch the vacuum gauge readout
and allow time for the gauge to achieve 4 x 10-5 Torr.
8. Observe the displayed masses.

Mass 4 (helium) should be much larger than mass 18 (water), which should be
larger than mass 28 (nitrogen), which should be about 4 times larger than mass 32
(oxygen).
9. If the nitrogen and oxygen are larger it indicates an air leak, which could damage
the filament. Immediately click Press for Standby to turn off the filament.
10. If a leak exists, locate and fix it.

Typical areas to check for leaks are around fittings and areas under vacuum.
81
Tuning Clarus 600/560 D MS
After determining that no leaks exist and before acquiring data, you may need to
check the mass spectrometer tuning conditions and, if necessary, modify one or
more of the tuning parameters. Clarus MS can be tuned either manually or
automatically from the Tune window.
The left side of the page holds the tuning parameters for a selected region of the
mass spectrometer. You can change the region by selecting an item from the
Window menu, or by pressing one of the buttons on the bottom-left of the Tune
page.
The panel in the top right of the Tune page displays the tune peak information and
instrument pressure information.
The tune peak display is located on the right side of the screen and allows you to
view up to four masses. The corresponding check boxes located above the peaks
allow you to control each peak display. Any one of the tune peaks can be zoomed so
that it occupies the entire tune peak area. When a tune peak has been zoomed, the
82
Maintenance
controls for the mass and span for that peak are displayed at the top of the display
window. This enables you to display the pressure information while having control
over the peak display.
To display the Tune page:
1. While displaying TurboMass sample list screen click .

The Tune page is displayed.
2. Turn on the filament and high voltages by clicking Press for Operate at the
bottom right of the window.
The indicator box turns green to indicate that it is on.
3. Select UltraTune/Custom (AutoTune) from the Options menu, then click

Start.
You will hear a click when the reference gas solenoid valve opens and
AutoTune begins. Upon completion, the message AutoTune completed
successfully is displayed.
4. Click OK.
83
5. Select Reference Gas On from the Gas menu to remove the check mark (9),
or click to set it in the up position.
6. Save this new Tune of the instrument by selecting Save As from the File menu
and entering a name for this tune in the File name field.
A way to keep track of the tunes is to use dates for the file names.
7. Click Save.
Your mass spectrometer is now Tuned.
To ensure proper operation, check the mass calibration.
84
Maintenance
Preparing Clarus 600/560 D MS for

Hardware Maintenance
To prepare Clarus MS for hardware maintenance, there are several steps that are
common and precursory to all maintenance procedures. They are as follows:
Turn off the Operate Mode
1. Display the Tune window.
2. If the Press for Standby button is green (indicating an operating instrument),

switch it off by clicking on it.
85
Cool the Transfer Line, GC Column Oven, and the Source
The transfer line, GC oven, and source are HOT. Touching them can
cause serious burns. To prevent personal injury, wait until the oven and
transfer line reach the lower setpoint temperature before touching
them. Only grab and hold the source by its handle.
WARNING
1. On the left side of the Tune page enter 20 in the Inlet Line Temperature to
cool the GC Interface (transfer line).
If the Clarus GC is off, then the PPC control is off and no gas is
CAUTION flowing through the system.
2. Open the GC oven door to cool the column oven.
3. On the Tune page, set the source temperature by entering 20 in the Source
Temp field.
4. Allow the transfer line, column oven, and source to cool before touching them.
Remember, the transfer line was heated and it may take at least
10 to 20 minutes to cool.
WARNING
Avoid venting to air whenever possible. This eliminates the

introduction of oxygen and water vapor into the mass
CAUTION spectrometer. The Clarus MS should be vented with UHP
nitrogen (99.9995%). Helium should not be used. To properly
connect a source of dry nitrogen to the instrument order the
manifold venting kit (Part No. N647-0045).
86
Maintenance
Vent the System
1. Once both the Inlet Line and Source temperatures have dropped below 100 °C,
select Vent/Vacuum System Off from the Options menu.
The Vent Pump dialog appears. All pumps are turned off.
2. Click OK.
3. Observe the Vacuum Pressure Gauges status on the Tune window.
The gauge goes to ZERO after the turbopump reaches 50 % speed and the vent
valve is opened.
NOTE: Mass Spectrometer venting may take several minutes depending on the helium flow
and/or vent gas flow into the manifold.
4. The system is now vented to atmosphere (or optional dry gas).
Turn off the GC Carrier Gas
Turn off helium carrier gas flow to the MS if you do not have a purge
flow of high purity nitrogen.
CAUTION
Do not allow the vented mass spectrometer to fill with helium for more
than 5 hours.
Failure to do so can damage the photomultiplier detector and require
a service call not covered by warrantee or contract.
Set all temperatures to ambient. Once the GC column oven, source, and transfer line
are cool you may then turn off the GC carrier gas.
87
Changing a Column
To ensure that the mass spectrometer remains contamination free, wear

CAUTION powder-free, lint-free gloves while performing this procedure.
Tools and Items Required

• New column.
• Column wafer scribe (Part No. N930-1376).
• Two high-temperature septa.
• Two ¼-inch open-end wrenches

• Lint-free, powder-free PVC gloves (Part No. N621-2495).
• 1/16-inch graphite/Vespel ferrules (0.8 mm i.d., Part No. 0992-0107, 0.25 mm

i.d., Part No. 0992-0104 or 0.325 mm i.d., Part No. 0992-0105).
Removing a Column
1. Prepare the mass spectrometer for hardware maintenance (see Preparing
Clarus 600/560 D MS for
Hardware Maintenance on page 85).
2. Using a ¼-inch open-end wrench, loosen the 1/16-inch column nut attached to
the injector fitting and slide the column tubing completely from the injector
and column nut.
88
Maintenance
3. Using a ¼-inch open-end wrench, loosen the 1/16-inch column nut on the
transfer line. Slide the column tubing completely from the transfer line and
column nut. Remove the column from the GC oven.
Remove Column
Injector
1/16-inch Column Nut
Remove Column
Transfer Line Septum

Figure 10 Removing a column
4. Open the Clarus 600 MS access door, loosen and remove the two black
thumbscrews, hold the source by the handle, and pull it out.
To prevent contamination, only hold the source by its handle. Never

CAUTION touch the part of the source that comes in contact with ions with your
bare fingers.
89
5. Place the source on a clean surface. Preferably place the handle end on a flat
surface so that the source stands in an upright position.
Access
Door
Inner Source
Black
Thumbscrews Handle
Figure 11 Removing the source
90
Maintenance
Connecting the New Column to the Split/Splitless

Injector
This procedure describes how to connect a column to a capillary injector. For
procedures to connect a column to a PSS or POC injector refer to “Installing a
Capillary Column” in Chapter 6 of the Clarus GC User’s Manual (Part Number
0993-6780).
This injector has a fragile 1/16-inch fitting. To preserve the integrity of

the fitting:
CAUTION • Carefully tighten the nut on the fitting.
• Do not cross-thread or overtighten the nut on the fitting.
• Allow the injector to cool before connecting a nut.
1. Unwind 20 cm (8 inches) from one end of the column.
20 cm
Column
Figure 12 Unwinding 20 cm from the injector end
91
2. Insert a septum, 1/16-inch column nut (part number 09903392), and 1/16-inch
graphite ferrule (0.8-mm i.d. Part Number 0992-0141, or 0.5-mm i.d. Part
Number 0990-3700) over one end of the column as shown in Figure 13 .
1/16-inch
Graphite/Vespel
Ferrule
Column
Septum
Column
Figure 13 Inserting the nut and ferrule on the column
NOTE: Verify that the tapered end of the ferrule is facing towards the nut as shown above.
3. Cut about 1 cm (3/8 inch) from the column end using a wafer scribe
(part number N930-1376, pkg. of 10 scribes). Break off the tubing at the score
mark so that the break is clean and square. Examine the cut with a magnifying
glass and compare it to the examples shown in Figure 14.
Good Cut
Bad Cuts
Figure 14 Good cut and bad cuts
92
Maintenance
4. Locate the capillary injector fitting inside the oven.
1/8-inch Capillary
Injector Fitting
Figure 15 Location of the capillary injector in the oven

5. Position the septum on the column as shown in the following table:
Injector Type Column Insertion Dept

(measured from the back of the nut to the end of the column)
CAP 4.44 to 5.1 cm (1¾ to 2 inches)
PSS 3.8 to 4.44 cm (1½ to 1¾ inches)
POC Flush with the septum end of the injector
6. Insert the column into the capillary injector fitting.

7. Hand-tighten the column nut ¼ turn past fingertight.
8. Using two ¼-inch wrenches tighten the column nut only until the column
cannot be pulled out of the fitting.
Do not overtighten column nuts. Overtightening can cause damage to

CAUTION the ferrule and/or column.
93
Connecting a New Column to Clarus 600 MS

1. Uncoil 50 cm (20 inches) from the new column. Place the column on the
column hanger in the oven.
50 cm
Column
Figure 16 Uncoiling 50 cm from the transfer line end
2. Slide the septum, 1/16-inch column nut and 1/16-inch graphite/Vespel ferrule
over the end of the column.
Column
1/16-inch Column
Graphite/Vespel
Ferrule Septum
Figure 17 Inserting a septum, column nut and ferrule on a column
3. Slide the septum, column nut, and ferrule along the column to the position
shown below. Score and break 1.0 cm off the end of the column. Wipe the
column with a methanol dampened lab tissue (for example, a Kimwipe).
94
Maintenance
Use glove.
1. Slide the septum, column nut,
and ferrule to this position.
1 cm
Column
2. Cut end of column

off here
3. Wipe the column

with a Kimwipe
dampened with MeOH.
Figure 18 Preparing to install the column in the transfer line
4. Carefully insert the end of the column through the transfer line and into the
mass spectrometer source until it is positioned midway between the hole and
the wall on the right side of the source. See Figure 19.
5. Hold the column in this position as you slide the column nut and ferrule to the
transfer line and tighten the nut fingertight. Slide the septum until it is flush
against the rear of the column nut. See Figure 20.
This marks the position of the column end in the source.
NOTE: Finger tight means just tight enough to hold the column in place so that you are still
able to move the column slightly if necessary to reposition it.
95
Clarus 600
Mass Spectrometer
Clarus 600
Gas Chromatograph
Insert Column into Transfer Line
Transfer Line
2 mm or midway
between the hole
and the wall
Hole
Column End
Wall
Figure 19 Positioning the column end in the source assembly
96
Maintenance
Septum
1/4-inch Column Nut 1/16-inch Column Nut
Figure 20 Marking the column position in the source
6. Pull the column back until the distance between the back of the nut and septum
is about 10 cm.
To prevent breaking the end off the column, you need to pull the column
CAUTION back to reinstall the source in the mass spectrometer.
97
1/16-inch Column Nut Septum Column
10 20 30 40 50 60 70 8
metric
Slide the column back until the

septum is 10 mm from nut.
Figure 21 Pulling the column back to reinstall the source
7. Position the inner source so it aligns with the guide pin, gently insert the source
into the mass spectrometer, and secure it in place with the two black
thumbscrews. Tighten the black thumbscrews until they are fingertight.
Do not overtighten.
Access Ma ssClarus 60
Spec 0
tro me
ter
Door
Inner Source
Black
Thumbscrews Handle
Figure 22 Reinstalling the source
98
Maintenance
8. Carefully slide the column into the transfer line until the septum is flush to the
back of the column nut. To make a leak-free seal, use a ¼-inch wrench to
tighten the column nut ¼ turn past fingertight.
Injector
Slide Column
Septum flush to the back

of the column nut.
Flats for the 5/32-inch
(4 mm) on the transfer line 1/16-inch Column Nut
Figure 23 Repositioning the column in the source
Checking for Leaks

1. Start the carrier gas flow and leak-check the fittings for leaks.
To ensure maximum sensitivity, if this is a new column condition the

CAUTION column to its maximum accepted operating temperature, even if the
column manufacturer claims that it is preconditioned.
2. Start the vacuum by selecting Pump from the Options menu on the Tune
window. Monitor the vacuum and search for leaks if necessary.
Refer to the vacuum leak-checking procedure described in Leak Checking on
page 79.
3. Once you have verified that no leaks exist, set the transfer line temperature to
its original value and close the GC oven door to heat the column.
99
Refilling the Reference Gas Vial

It is time to refill the reference gas vial when you lose reference gas peaks intensity
and you do not see a liquid in the reference gas vial, or any time the mass
spectrometer is vented, and the liquid in the vial level appears low.
NOTE: You should check liquid level in the reference gas vial any time you need to remove
the mass spectrometer cover and vent the instrument. Using a tool such as a dental
mirror will help you observe the liquid level in the Reference Gas Vial.
Items Required
• Lint-free, powder-free PVC or polypropylene gloves (Part No. N621-2495).
• Pasteur Pipette or 50 µL syringe.
• Heptacosa (FC43) (Part No. N621-2407).
To refill the reference gas vial, follow this procedure:
Make sure to vent the instrument and turn the power off.
WARNING
1. Ensure that the solenoid have been switched off.
100
Maintenance
2. With the power off, unplug the source connector for more room to work. Use a
5/32 inch Allen wrench to remove the two allen nuts from the handle. See
following photo.
Source Connector
Allen Nuts
3. With the handle off remove the reference gas vial assembly and bracket out.
See the following figure.
101
Figure 24 Removing the reference gas vial from the mass spectrometer
The toxicity of the FC-43 calibrant is uncertain. Take appropriate

precautions to avoid getting the calibrant on your skin or in your eyes.
WARNING
4. Loosen the knurled fitting behind the gas vial by ½ turn, and pull out the vial.
A black O-ring may remain in the fitting.
5. Using a pipette or syringe, add 25 to 50 µL but no more than 50 µL of

Heptacosa (FC43). See the following figure. Fill the bulb.
Never add more than 50 µL.
102
Maintenance
Gas Tight
Syringe
Reference
Gas Vial
Figure 25 Filling the reference gas vial

6. Re-insert the reference gas vial into the mass spectrometer. Make sure the O-ring
is still present and the tapered end of the ferrule faces the mass spectrometer.
7. Tighten the knurled nut with your fingers until fingertight.
8. Return the bracket to the proper position and use a 5/32 inch Allen wrench to
retighten the two Allen nuts to the bracket.
9. Replace the top cover and pump the system down to the proper vacuum.
10. From the Gas Menu select the Reference Gas Option from the drop down menu.
Leave the Reference Gas Valve open for 60 minutes with Operate off to pump to
pump out the gas from the bulb before tuning the mass spectrometer.
NOTE: On the Tune Page the Gas drop down the Pump Out Reference Gas choice no
longer works. If you try to have both the Reference Gas On and the Pump Out
Reference Gas options selected you will get an error message. To avoid an error
message make sure to only check Reference Gas On.
103
Inner Source Maintenance

Inner source maintenance consists of cleaning those components that contact ions.
For example,
• EI source: the ionization chamber, repeller, trap, ion exit plate, and ion entry
area.
• CI source: the ionization chamber, ion entry area, and ion exit plate.
Never clean the filament. If the filament is open, replace it by following

CAUTION the procedure in this chapter.
Items and Tools Required

• Ultrasonic bath.
• Aluminum foil or lint-free disposable cloth squares.
• Aluminum oxide powder.
• Wooden stick cotton swabs.
• 2 mm open-end wrench (for EI source).
• Tweezers.
• Powder-free, lint-free gloves (Part No. N621-2495).
• Small flat-blade screwdriver.
• Reagent Grade acetone.
• Reagent Grade methanol.
• De-ionized Water
• Clean 100 mL glass beaker.
• 6000 Grade Micro Mesh (Part No. N930-3420).
• 600 grit aluminum oxide in DI Water with a few drops of methanol to make a
paste
104
Maintenance
Removing the Inner Source

To remove the inner source, follow this procedure:
Before performing source maintenance, always prepare the mass

CAUTION spectrometer by following the instructions in Preparing Clarus 600/560
D MS for
Hardware Maintenance on page 85.
1. Prepare the mass spectrometer for maintenance as described in Preparing
2. Open the GC oven door and locate the Clarus MS transfer line.
3. Using a 9/16-inch wrench, loosen the ¼-inch nut on the transfer line.
4. Pull the inner transfer line tube back 25 mm (1 inch).
Transfer Line
Remove
Column
1/4-inch Nut
Figure 26 Pulling back the transfer line
105
5. Loosen the two thumbscrews on the inner source, grab it by its handle, pull it
out of the mass spectrometer and set it on a clean surface.
6. Close the mass spectrometer access door.
7. Put on a pair of powder-free, lint-free gloves (Part No. N621-2495).
Access
Door
Inner Source
Black
Thumbscrews Handle
Figure 27 Removing the inner source
EI Inner Source Maintenance

To gain access to the parts on the EI inner source that need cleaning, follow this
procedure.
NOTE: For this procedure use the Inner Source Rebuild Kit Part No. E640-0043.

CAUTION lint-free, powder-free gloves (Part No. N621-2495) while performing
this procedure.
106
Maintenance
Disassembling
1. Prepare a clean, uncluttered work area and place a square of aluminum foil
with the shiny side up. Obtain some clean, small containers (for example, small
beakers) to store the screws and small parts as you remove them.
2. Using a small flat-blade screwdriver, loosen the screw that secures the old
filament assembly to the source. Use tweezers to remove the screw and washer.
Pull out the filament assembly.
Defective
Filament
Assembly
Screw
(P/N E531-4043)
Washer
(P/N E533-1031)
Figure 28 Removing the filament assembly
107
3. Using a small flat-blade screwdriver, loosen and remove the four screws on the
ion chamber cover plate and remove the cover plate.
4. Using a 2 mm open-end wrench, loosen and remove the nut and washer that
secure the repeller. Then remove the repeller.
5. Using a 2 mm open-end wrench, loosen and remove the nut and washer that
secure the ion trap. Then remove the ion trap.
Clean this
area.
Trap
(P/N E640-1220)
Screw (4)
2 mmSpacer
(P/N E640-1222)
12 mm Spacer
(P/N E640-1221) Clean underside
of Ion Exit Plate. Clean this
(P/N E640-1213) area.
Repeller
(P/N E640-1219)
Clean these
areas.
2 mm Spacer
(P/N E640-1222)
12 mm Spacer
(P/N E640-1221)
6 mm Ceramic Spacer
(P/N E640-1224)
Trap Contact
(P/N E640-1217) 6 mm Ceramic Spacer
(P/N E640-1224)
Washer
Insulator
Nut (P/N E640-1218)
Viton O-Ring
(P/N E571-1061) Repeller Contact
(P/N E640-1216)
Washer
Nut
Figure 29 Removing the ion chamber cover plate and repeller
108
Maintenance
Cleaning
NOTE: You can do the following cleaning method of aluminum oxide paste or use the 6000
or 8000 grade micro mesh to polish the flat surfaces of the parts. For either
cleaning method, the final step you must sonicate the parts in an ultrasonic bath of
methanol for at least five minutes. Dry off the parts using lint-free tissue and/or
clean compressed Nitrogen gas to prevent solvents from drying on these parts and
leaving a residue
1. Mix together aluminum oxide and de-ionized water and a few drops of
methanol to make a watery paste.
2. Dip a wooden-stick cotton swab in the solution and clean the darkened areas on
the source. Work quickly to prevent the mixture from drying on the surface.
Place the cleaned components in de-ionized water prior to rinsing to prevent
drying.
Rinsing
1. Add 50 mL of acetone to a 100 mL beaker, insert the source assembly, repeller,
ion trap, ion chamber plate, and sonicate in an ultrasonic bath for ten minutes.
Do not allow the acetone and methanol to touch the O-ring on the
CAUTION source.
2. Carefully drain the acetone.

3. Add 50 mL of methanol to another 100 mL beaker, insert the source assembly,
repeller, ion trap, ion chamber plate, and sonicate in an ultrasonic bath for at
least ten minutes.
4. Carefully drain the methanol.
109
Source Assembly
50 mL sonocation solution
in 100 mL Beaker
Figure 30 Rinsing the aluminum oxide from the source
5. Dry off the repeller, ion trap, source assembly and ion chamber plate using lint-
free tissue and/or clean compressed Nitrogen gas to prevent solvents from
drying on these parts and leaving a residue.
6. Take the parts amd wrap them in a clean, lint-free cloth and bake them in the
GC oven at about 80 ºC for about fifteen minutes.
Reassembling
1. Insert the ion trap and repeller through the spacer and insulator. Then insert it
into the source.
110
Maintenance
Ion Trap Repeller

(P/N E640-1220) (P/N E640-1219)
2 mm Spacer 2 mm Spacer
(P/N E640-1222) (P/N E640-1222)
12 mm Spacer 12 mm Spacer
(P/N E640-1221) (P/N E640-1221)
Figure 31 Inserting the ion trap and repeller into the inner source
2. Invert the source and insert a crumpled laboratory wipe into the repeller and
ion trap.
3. Using tweezers, install the remaining ceramic pieces, spacers and nut first on
the ion trap and then on the repeller.
4. Tighten each nut with a 2 mm open-end wrench.
111
5. Replace the filament assembly.
Nut
(P/N E532-1018)
Washer
(P/N E533-1013)
Nut
(P/N E532-1018)
Trap Contact Washer
(P/N E640-1217) (P/N E533-1013)
6 mm Ceramic Spacer Repeller Contact

(P/N E640-1224) (P/N E640-1216)
Locator
and Clarus 560 D (P/N E640-1218)
6 mm Ceramic Spacer
(P/N E640-1224)
Post removed to show

parts assembly path
Laboratory Wipe crumpled and inserted

into the ion chamber and trap areas.
Figure 32 Installing the ceramics, contacts, washers and nuts on the repeller
and ion trap
112
Maintenance
Ensure filament coil

aligns with hole.
Rhenium
Filament Assembly
(P/N N6470012)
Screw
Washer
Contacts
Figure 33 Replacing the filament assembly
CI Inner Source Maintenance

The supplied CI inner source assembly can be used for both negative CI and positive
CI. The maintenance procedures for the CI source are very similar to those of the EI;
however, the CI does not have a repeller or ion trap. It does have a smaller exit
aperture to ensure that the sample ions properly react with the CI gas.

CAUTION lint-free, powder-free gloves (Part No. N621-2495) while performing
this procedure.
To gain access to the parts on the CI inner source that need cleaning, follow this
procedure.
113
Disassembling
1. Prepare a clean, uncluttered work area and place a square of aluminum foil
with the shiny side up. Obtain some small containers (for example, small
beakers) to store the screws and small parts as you remove them.
2. Using a small flat-blade screwdriver, loosen the screw that secures the old
Pull out the filament assembly.
Defective
Filament
Assembly
Screw
(P/N E531-4043)
Washer
(P/N E533-1031)
Figure 34 Removing the filament assembly
3. Using a small flat-blade screwdriver, loosen and remove the four screws on the
ion chamber cover plate and ion aperture plate, then remove the plates.
114
Maintenance
Screw (1 of 4)
Underside of the Ion Exit

Plate (P/N E640-1213) shown.
Clean the underside

of the CI Ion Exit Plate
(P/N E640-1214).
Clean these
areas.
Figure 35 Removing the ion chamber and aperture plates and cleaning the
areas shown
Cleaning
NOTE: You can do the following cleaning method of aluminum oxide paste or use the 6000
or 8000 grade micro mesh to polish the flat surfaces of the parts. For either
cleaning method, the final step you must sonicate the parts in an ultrasonic bath of
methanol for at least five minutes. Dry off the parts using lint-free tissue and/or
clean compressed Nitrogen gas to prevent solvents from drying on these parts and
leaving a residue
115
1. Mix together aluminum oxide and de-ionized water and a few drops of
methanol to make a watery paste.
2. Dip a wooden-stick cotton swab in the solution and scrub the darkened areas on
Rinsing and Reassembling
1. Add 50 mL of acetone to a 100 mL beaker, insert the source assembly, ion

aperture plate, ion chamber plate, and sonicate in an ultrasonic bath for ten
minutes.
Do not allow the acetone and methanol to touch the O-ring on the
CAUTION source.
2. Carefully drain the acetone.

3. Add 50 mL of methanol to another 100 mL beaker, insert the source assembly,
ion aperture plate, ion chamber plate, and sonicate in an ultrasonic bath for at
least ten minutes.
4. Carefully drain the methanol.
Source Assembly
50 mL sonocation solution
in 100 mL Beaker
Figure 36 Rinsing the aluminum oxide from the source
116
Maintenance
5. Dry off source assembly and plates using lint-free tissue and/or clean
compressed Nitrogen gas to prevent solvents from drying on these parts and
leaving a residue.
6. Take the parts amd wrap them in a clean, lint-free cloth and bake them in the
GC oven at about 80 ºC for about fifteen minutes.
7. Reassemble the ion aperture plate and ion chamber plate on the source.
8. Replace the filament assembly.
Screw (1 of 4)
Underside of the Ion Exit

Plate (P/N E640-1213) shown.
Clean the underside

of the CI Ion Exit Plate
(P/N E640-1214).
Clean these
areas.
Figure 37 Reassembling the CI inner source
117
Ensure filament coil

aligns with hole.
Rhenium
Filament Assembly
(P/N N6470012)
Screw
Washer
Contacts
Figure 38 Replacing the filament assembly
118
Maintenance
Reinstalling the Source

1. Position the source so it aligns with the guide pin, gently insert the source into
the mass spectrometer, and secure it in place with the two black thumbscrews.
Tighten the black thumbscrews until they are fingertight. Do not overtighten
the thumbscrews.
Access
Door
Inner Source
Black
Thumbscrews Handle
Figure 39 Reinstalling the source in the mass spectrometer
2. Insert the inner transfer line tube back in the outer transfer line.
3. Tighten the ¼ inch transfer line nut fingertight.

To make a leak-free seal use a 9/16 inch wrench to tighten the ¼ inch nut an
additional 1/8 turn. Tighten it enough to make a leak-free seal but do not
overtighten the nut.
119
Transfer Line
Replace
Column
1/4-inch Transfer
Line Nut
Figure 40 Reconnecting the transfer line
Checking for Leaks
1. Start the carrier gas flowing and leak-check the fittings for leaks.
2. Start the vacuum by selecting Pump/Vacuum System On from the Options

menu on the Tune window. Monitor the vacuum and search for leaks if
necessary. Refer to the leak checking procedure described in Leak Checking on
page 79.
3. Once you have verified that no leaks exist, set the transfer line temperature to
its original value, and close the GC oven door to heat the column.
120
Maintenance
Replacing a Filament
Make sure you are wearing powder-free PVC gloves (Part No. N621-
CAUTION 2495), and that you wipe each part with a methanol dampened
Kimwipe.

• Filament assembly (Part No. E6400209).
• Tweezers.
• 0.8 mm hex wrench.
• Methanol.
• Powder-free, lint-free gloves (Part No. N621-2495).
• Aluminum foil or lint-free disposable cloth squares.
To replace a filament, follow this procedure.
1. Prepare a clean, uncluttered work area and place a square of aluminum foil with
the shiny side up.
2. Remove the EI source by following the procedure Removing the Inner Source as
described on page 105.
To ensure that the mass spectrometer remains contamination free,

CAUTION make sure you are wearing powder-free, lint-free gloves (Part No.
N621-2495), and that all tools have been cleaned with a methanol-
dampened laboratory wipe.
3. Using a small flat-blade screwdriver, loosen the screw that secures the defective
4. Pull out the defective filament assembly.
121
Defective
Filament
Assembly
Screw
(P/N E531-4043)
Washer
(P/N E533-1031)
Figure 41 Removing the defective filament assembly
5. Using a 0.8 mm hex wrench, loosen the two screws that secure the contacts to
the filament assembly leads. Remove the two contacts.
122
Maintenance
0.8 mm
Hex Wrench
Contacts
Defective Filiment
Assembly
Figure 42 Removing contacts from the defective filament assembly
6. Position the new filament assembly with the filament side up.
7. Insert the contacts on the new filament assembly leads so that they are flush with
the white ceramic and positioned with the hex screw side facing up.
8. Secure the contacts to the filament assembly by tightening the hex screws with a
0.8 mm hex wrench. Tighten firmly but do not overtighten.
123
1. Insert Contacts
New Filament Assembly

(P/N E647-0012)
Contacts (2)
(P/N E640-1215)
2. Secure Contacts
0.8 mm
Hex Wrench
Figure 43 Installing contacts on the new filament assembly
9. Position the new filament assembly so that it faces the source and the white
ceramic rests on the tab.
10. Ensure that the filament coil is aligned with the entrance hole on the inner source
assembly.
124
Maintenance
11. Using a small flat-blade screwdriver, secure the filament assembly in place with
the screw and washer that you previously removed.
Ensure that the filament coil
aligns with the entrance hole.
Filament Coil
New Filament
Tab Assembly
Screw
Washer
Contacts
Tab positioned between contacts.
Figure 44 Installing a new filament assembly on the source
12. Install the source assembly back into the mass spectrometer by following the
procedure described in Reinstalling the Source on page 119.
125
Replacing the Head Amplifier
To replace the Photomultiplier head amplifier (Part Number E649-9032), follow this
procedure and refer to Figure 45:
The mass spectrometer contains high voltage. To prevent the risk of

shock, unplug the line cord from the AC outlet and wait at least one
minute before opening or removing any instrument cover or panel.
WARNING
1. Vent the vacuum from the mass spectrometer.
2. Turn off the mass spectrometer.
3. Unplug the AC line cords from the AC outlets.
4. Remove the four screws securing the rear panel and remove the rear panel.
5. Remove the two screws on the left side of the top panel and remove the top
panel.
6. Remove the head amplifier board cover.
7. Remove the cable connector to the board.
8. Pull off head amplifier board, removing the screw with the ground wire on it.
9. Install a new board, making sure that you do not over-tighten the screw with
the ground wire.
NOTE: Pins on the photomultiplier are key for proper alignment.
10. Replace the photomultiplier head amplifier board cover, cable connector,
replace the panels, turn on the mass spectrometer, and pump-down the system
to the proper vacuum.
126
Maintenance
11. Go to the Head Amplifier electronic adjustment procedure.
Detail of Photomultiplier
Tube Pin Connections
Note keying position of

short pin when plugging
the Photomultiplier Tube
into the Head Amplifier
Board
Head Amplifier Board

(P/N E640-9032)
Cover
Ground Cable
Nut
Lock
Washer
Figure 45 Replacing the head amplifier
127
Mass Analyzer Maintenance

The analyzer element of any high performance quadrupole mass spectrometer is, of
necessity, a finely machined assembly that has been precisely aligned using
specialized equipment. Under no circumstances should you ever disassemble the
main mass analyzer assembly.
The mass spectrometer is fitted with prequads that act as a prefilter assembly
designed to protect the analytical quads by intercepting the majority of any
contamination. As a consequence, the analytical quads should never, under normal
working conditions, require cleaning. Occasionally, it may be necessary to remove
the prefilter rods for cleaning. The need to clean these rods is usually indicated by
poor peak shape or loss of resolution, although other more likely causes, such as
source contamination, should be eliminated first.

• 4 mm hex wrench.
• 5 mm hex wrench.
• Deionized Water
paste
• Long flat-blade screwdriver.
• Aluminum foil.
• Acetone.
• Methanol.
• Tweezers.
128
Maintenance
Cleaning Materials
When cleaning internal components it is important to maintain the quality of the
surface finish. Deep scratches or pits can cause loss of performance. Where no
specific cleaning procedure is provided, you should use fine abrasives to remove dirt
from metal components. Recommended abrasives are:
paste
After cleaning with abrasives, it is necessary to wash all metal components in

suitable solvents to remove all traces of grease, oil and, if micro-mesh is used,
rubber. The recommended procedure is to swill or sonicate the components in a
clean beaker of methanol for at least ten minutes and subsequently to blot them dry
with lint-free tissue. Recommended solvents are:
After the components are reassembled, they should be blown with oil-free nitrogen
to remove dust particles.
Removing the Ion Optics Assembly

To remove the EI inner source, follow this procedure:
Before performing source maintenance, always prepare the mass

CAUTION spectrometer by following the instructions in Preparing Clarus 600/560
D MS for
1. Prepare the mass spectrometer for maintenance as described in Preparing

2. Open the GC oven door and locate the mass spectrometer transfer line.
3. Using a 9/16-inch wrench, loosen the ¼-inch nut on the transfer line.
129
Risk of burns. Never touch a heated mass spectrometer transfer line or

a GC injector cap with unprotected (bare) fingers.
WARNING
4. Pull the inner transfer line tube back 25 mm (1 inch).
Transfer Line
Remove
Column
1/4-inch Nut
Figure 46 Pulling back the transfer line
5. Loosen the two thumbscrews on the inner source, grab it by its handle, gently
pull it out of the mass spectrometer, and set it on a clean surface.
130
Maintenance
6. Close the mass spectrometer access door.
Access
Door
Inner Source
Black
Thumbscrews Handle
Figure 47 Removing the inner source
Removing the Mass Spectrometer Cover Panels
The mass spectrometer contains high voltage. To prevent the risk of

shock, unplug the line cord from the AC outlet and wait at least one
minute before opening or removing any instrument cover or panel.
WARNING
1. Turn off the Clarus GC and Clarus MS.

2. Unplug the AC line cords from the AC outlets.
3. Remove the four screws securing the rear panel, remove the rear panel, and lay it
on the bench. If necessary, disconnect the fan wires.
4. When reconnecting the fan wires, make sure the fan blows the air into the mass
spectrometer.
131
5. Remove the two screws on the left side of the top panel and remove the top panel.
NOTE:
The rear panel vent fan should NOT be removed
from the instrument. It is removed in this illustration
only to clearly show how to access the PMT Access
Panel. ONLY remove the PMT Access Panel.
Screws (4)
Figure 48 Removing the mass spectrometer panels
132
Maintenance
Removing the Photomultiplier Tube
1. Unplug the cable from the head amplifier board.
2. Using a long flat-blade screwdriver, loosen the two captured screws securing
the photomultiplier tube (PMT) amplifier cover, and remove the cover.
PMT Amp
Cover
Lock
Screw
NOTE:
Figure 49 Removing the PMT amplifier cover
3. Using a 4 mm hex wrench, remove the screw securing the PMT amplifier
board-grounding strap.
4. Carefully remove the amplifier board from the PMT by pulling it straight back.
133
5. Using a 4 mm hex wrench, remove the screws securing the PMT flange to the
vacuum chamber.
6. Put on a pair of powder-free, lint-free gloves.
7. Carefully remove the PMT. Cover it with a laboratory wipe and place it in a
safe, dark place.
8. Insert a crumpled laboratory wipe into the PMT hole in the vacuum chamber to
prevent particulates from entering the vacuum chamber.

(P/N E640-9032)
Cover
Ground Cable
Nut
Lock
NOTE: Washer
Figure 50 Removing the head amplifier board and the PMT
134
Maintenance
Removing the Ion Optics Assembly
Make sure to vent the instrument and turn the power off and
unplug the mass spectrometer from the AC power source.
WARNING
1. Disconnect the cables connected to the ion optics assembly and place them to
the side so they will not interfere with the removal of the ion optics assembly.
See the following figure.
2. Disconnect the Reference and CI gas lines from the top of the ion optics
assembly. See the following figure.
REAR VIEW
Ion Optics Assembly

Phosphor
Dynode
Source
Reference Gas
CI Gas
RF Generator
Location of Reference Cable
Gas Vial Assembly
Handle Fan Plug
Figure 51 Disconnecting cables and tubing from the ion optics assembly
135
3. With the power off , unplug the source connector for more room to work. Use a
5/32 inch Allen wrench to remove the two allen nuts from the handle. See
following photo.
Source Connector
Allen Nuts
4. With the handle off remove the reference gas vial assembly and bracket out and
move it out to the side of the instrument. See the following photo.
136
Maintenance
5. Remove the four hex head bolts loosely holding the ion optics assembly to the
vacuum chamber. See the following figure.
6. Grabbing the ion optics assembly by the two handles, carefully lift the ion
optics assembly straight up and away. See the following figure.
Hexagon
Fan Plug Head Bolt (4)
Handle
Handle
Guide Pins
Figure 52 Lifting the ion optics assembly from the vacuum manifold
137
7. Place the ion optics assembly on a clean work surface, with the RF box down
and the mass analyzer facing up (see Figure 3).
8. Cover the open vacuum chamber with aluminum foil to prevent particulates
from contaminating the chamber.
Outer Source Prequads
Assembly
of Ion Optics
Assembly
Analytical Quads
Figure 53 Positioning the ion optics for maintenance
Cleaning the Prequads

When operating under normal circumstances, you may not have to remove the
prequads from the ion optics assembly. To clean the prequads, follow this
procedure.
1. Using a very fine abrasive paper (8000 grade) gently clean the ion burns off of
the prefilters.
138
Maintenance
2. Wipe the prequads with a methanol dampened laboratory wipe.

3. Blow dry with helium or dry nitrogen.
Replacing an Outer Source Thermocouple

• Thermocouple (Part No. E640-0213).
• Small adjustable wrench.
To replace the thermocouple, follow this procedure and refer to the following figure:

CAUTION lint-free, powder-free gloves while performing this procedure.
1. Using a small flat-blade screwdriver, remove the screw and the thermocouple.
2. Loosen and remove the nut.
3. Remove all wires from the contact pins.
4. Pull all the wires down through the feed connector
5. Thread the new wires up through the feed connector and connect all the wires
on the contact pins. Tighten the nuts.
6. Secure the new thermocouple with the screw.
139
1.
Remove the
screw securing
thermocouple (1)
(P/N E640-0213)
2.
Loosen and
Remove Nut
Feed
Connector
3.
Remove all wires
from contact pins
(10)
4.
Pull all wires down
through feed connector
5.
Thread all new wires
up through feed connector and
connect wires on contact pins
6.
Tighten
Nut
7.
Secure the
replacement
thermocouple
with the screw.
Figure 54 Replacing the thermocouple
140
Maintenance
Removing the Outer Source from the Ion Optics

To remove the outer source from the ion optics, follow this procedure (use Outer
Source Rebuild Kit, Part No.E640-0042):
1. Position the ion optics assembly as shown.
Outer Source Assembly
of Ion Optics
Assembly
2. Detach wires and tubes from outer source assembly as required.

Remove tubes
Remove screw Disconnect wires
3. Remove the two screws securing

outer source to the ion optics.
4. Place the outer source assembly
on a clean work surface.
Screw (1 of 2)
(one each side)
Figure 55 Removing the outer source from the ion optics assembly
141
Replacing Outer Source Heaters

• Two Cartridge heaters (Part No. E640-0202).
• Tweezers.
To replace the outer source heaters, follow this procedure:

1. Position the outer source base plate on a clean work area so that the clamp plate
faces up.
2. Using a flat blade screwdriver, loosen the three screws that connect to the three
pillars.
The four ceramic rods (Part Number E640-1319) are very fragile. Use
CAUTION extreme care when removing the support plate and lens.
3. Carefully lift the clamp plate (Part Number E640-1322) straight up and put it
aside.
4. Carefully lift and remove the contact support plate from the four ceramic rods.
5. Remove the pillar.
6. Unplug the outer source heaters from the quadrupole heater.
7. Using a flat-blade screwdriver, loosen the outer source heater setscrews.
8. Slide the old heaters out of the outer source block and insert the new heaters
(Part Number E640-0202).
9. Tighten the setscrews 1/8 turn past fingertight.
Do not overtighten the setscrews.
10. Connect the heater wires together and plug the quadrupole heater wire into the
remaining connector.
11. Reassemble the outer source.
142
Maintenance
Screw (1 of 3)
(P/N E531-4016)
Clamp Plate
(P/N E640-1322)
Contact Support Plate

(P/N E640-1229)
Pillar
(P/N E640-1320)
Heater
Locking
Screws
Source Heaters
(P/N E640-0265)
Figure 56 Replacing heaters in the outer source
143
Replacing the Quadrupole Heater

The quadrupole heater is connected in series with the two outer source heaters.
• Cartridge heater (Part No. E640-0202).

To replace the quadrupole heater, follow this procedure:
1. Unplug the quadrupole heater wire from the outer source heater wires.
2. Loosen the setscrew that secures the quadrupole heater to the standoff.
3. Slide the heater out, discard it, and slide the new heater into the standoff.
4. Secure the heater in place by tightening the setscrew 1/8 turn past fingertight.
Do not overtighten the setscrew.
5. Plug the quadrupole heater wire into the outer source heater wire connector.
144
Maintenance

of Ion Optics
Assembly
Cartridge Heater Setscrew
To outer source
Quadrupole cartridge heater (other side)
Cartridge Heater
(P/N E640-0266)
Purple wire
To outer source
cartridge heater (this side)
Quadrupole Cartridge
Heater Connections
Figure 57 Removing the quadrupole heater
145
Cleaning the Outer Source Lens

• 600 grit aluminum oxide.

• Tweezers.
• Methanol.
• Laboratory wipes.
• Acetone.
To clean the outer source, follow this procedure:
1. Position the outer source on a clean work area so that the side with the support
plate is facing up.
2. Using a flat-blade screwdriver, loosen the three screws that connect to the three
pillars.
3. Carefully lift the support plate straight up and put it aside.
4. Carefully remove the Lens 2, then Lens 1 focus plates.
146
Maintenance
Cleaning
1. Mix together aluminum oxide and methanol to make a watery paste.
2. Dip a wooden-stick cotton swab in the solution and clean the darkened areas on
3. Remove the residual aluminum oxide by sonication in a beaker of methanol for
ten minutes.
4. Blow dry with helium or dry nitrogen.
5. Reassemble the outer source.
147
3 x 10 Screw (1)
(P/N E531-4017)
3 x 6 Screw (1 of 2)
(P/N E531-4016)
Support Plate
(P/N E640-1321)
2mm Ceramic Spacer

(1 of 4)
(P/N E640-1222)
Lens 2 Focus Plate

(P/N E640-1235)
5mm Ceramic Spacer Clean these areas.

(1 of 4)
(P/N E640-1325)
Lens 1 Focus Plate
(P/N E640-1307)
Ceramic Rod Pillar (1 of 3)

(1 of 4) (P/N E640-1320)
(P/N E640-1319)
Figure 58 Removing the lenses from the outer source for cleaning
148
Maintenance
Reassembling the Ion Optics Assembly

The following drawing is an exploded view of the outer source showing all parts
with their part numbers.
3 x 6 Screw (1 of 3 top)
(P/N E531-4016) Clamp Plate
(P/N E640-1322)
Wavy Washer
(1 of 8)
(P/N E533-5005)
Typical Contact Attachment
2mm Ceramic Spacer
(1 of 4) Stainless Steel Spring Contact Screw (1 of 7)
(P/N E640-1222) (P/N E640-1389) (P/N E531-4044)
Copper Spring Contact
Ceramic Rod (P/N E640-1230)
(1 of 4) Stainless Steel Spring Contact
(P/N E640-1319) Contact Terminal
(1 of 3) (P/N E640-1390) (1 of 3)
Copper Spring Contact (P/N E640-1328)
(1 of 3) (P/N E640-1231)
Pillar (1 of 3) Copper Spring
(P/N E640-1320) Contact
(P/N E640-1232)
12mm Metal Spacer
(1 of 4) Contact Support Plate Stainless Steel Spring
(P/N E640-1324) (P/N E640-1229) Contact
(P/N E640-1391)
Outer Ion Block
(without magnet) Magnet
(P/N E640-1233) 4mm Ceramic
(P/N E640-1227) Insulating Spacer
Magnet Cap (P/N E640-1317)
7.7mm Metal Spacer (P/N E640-1226)
(1 of 4)
(P/N E640-1323)
Lens 1 Focus Plate 2mm Ceramic
2mm Ceramic Spacer (P/N E640-1307) Insulating Spacer
(1 of 4) (P/N E640-1222)
(P/N E640-1222)
Washer
5mm Ceramic Spacer Lens 2 Focus Plate (P/N E533-1013)
(1 of 4) (P/N E640-1235)
(P/N E640-1325)
Nut
(P/N E532-1018)
2mm Ceramic Spacer

(1 of 4)
(P/N E640-1222) Support Plate
(P/N E640-1321)
3 x 6 Screw (1 of 2 bottom)
(P/N E531-4016)
3 x 10 Screw (1)
(P/N E531-4017)
Earth Plate
(P/N E640-1326)
Figure 59 Exploded view of the outer source
149
1. Place the assembled outer source on the ion optics assembly and secure it in
place with the two screws.
2. Reattach the tubing to the outer source.
1. Place the assembled outer source on the ion optics

assembly and secure it in place with the two screws.
Ion Optics Outer Source
Screws (2)
(one each side)
2. Reattach the tubes to the outer source assembly.

Reattach tubes
Figure 60 Reinstalling the outer source

3. Using a flat-blade screwdriver, reconnect the thermocouple to the outer source.
150
Maintenance
4. Reconnect the wires to the outer source as shown in the following illustration.
of Ion Optics
Assembly
To outer source Contact Support Plate

Quadrapole Cartridge Heater cartridge heater (other side) (See Detail)
Thermocouple Wires
Ground
(green/yellow wire)
Purple wire
To outer source
cartridge heater (this side)
Lens 2 Focus Plate Orange wire Lens 1 Focus Plate
(green wire) (gray wire)
Wiring Connections
to the Contact Trap (yellow wire)
Support Plate
(View from Front)
Contact Ring
Part No.
N6470055
Repeller
(white wire)
(black wire) (red wire)
Filament
Figure 61 Reconnecting the wires to the outer source
151
Reassembling the Clarus 600/560 D MS

To reassemble the mass spectrometer, follow this procedure:
1. Remove the aluminum foil covering the vacuum manifold.
2. Hold the ion optics assembly by its handles and align the guide pins with the
holes in the vacuum manifold.
3. Gently lower the ion optics assembly until it is seated on the vacuum manifold.
4. Replace the four screws and tighten fingertight.
5. Remove the laboratory wipe from the PMT hole and reinstall the PMT
assembly. Observe the orientation of the PMT tube as shown in the detail.
6. Insert the end of the head amplifier ground wire through one of the screws for
the PMT assembly. Insert this screw into the hole in the 2 o’clock position and
insert the other screw in the other hole. Tighten both screws fingertight. Using
a 4 mm hex wrench, tighten both screws ¼ turn past fingertight.
7. Plug the head amplifier board onto the pins on the PMT.
152
Maintenance
Detail of Photomultiplier
Tube Pin Connections
Note keying position of

short pin when plugging
the Photomultiplier Tube
into the Head Amplifier
Board

(P/N E640-9032)
Cover
Ground Cable
Nut
Lock
Washer
Figure 62 Reinstalling the PMT

8. Reinstall the PMT head amplifier cover and secure it in place with the two
captured screws.
9. Replug all the cables and reconnect the tubing.
10. Reinstall the top and rear panels.
11. Reinstall the source.
153
Vacuum System Maintenance
Vacuum system maintenance consists of the following:

• Checking the forepump to ensure the oil is at the proper level.
• Adding oil to the forepump reservoir.
• Replacing forepump oil.
• Replacing foreline trap pellets.
Complete pump instructions are in the instruction manual supplied with the pump.
Maintanenace of the Turbomolecular and Diffusion

Pump
You should never service the turbomolecular and diffusion pumps. Call your
PerkinElmer Service Representative for the maintenance and any problems you may
have with these pumps.
Checking the Forepump Oil Level

1. Locate the oil level indicator window on the forepump.
154
Maintenance
Voltage Selection
Switch Under Cover
Handle
TurboMass
Connection Port
Oil Filler Plug
Exhaust Port
Max
On/Off Min
Switch
Gas Ballast
Switch
Mode Selection
Switch Drain Plug
Oil Level
Indicator
Figure 63 Location of the forepump oil viewing window
2. Determine if the oil level is between the Max Oil Level and Min Oil Level
marks next to the window.
• If the oil level is closer to the Min Oil Level mark, add oil. Use Edwards 45 oil
(Part No. 0992-3492, 1 liter).
• If it is near the scheduled six-month service, drain and refill the pump with
clean oil.
• If the oil is contaminated (indicated by a darkened color), try gas ballasting and
if that does not help, drain and refill the pump with clean oil.
155
Adding Oil to the Forepump Reservoir
Vent the mass spectrometer before opening the plug to add oil.
CAUTION
1. Unscrew and remove one of the filler plugs on the top of the pump.
2. Locate the bottle of pump oil supplied with the pump and add oil until it
reaches the MAX mark on the top of the sight glass. Do not overfill.
3. Replace the oil filler plug by tightening it until it is fingertight. Do not
overtighten the oil filler plug.
4. After restarting the pump and allowing it to run for a few minutes, recheck the
oil level. If the oil level is below the MAX mark, repeat the above procedure by
adding more oil until it reaches the MAX mark.
Decontaminating the Oil

The pump oil should be clear. If the oil is cloudy or discolored, it is contaminated
with residual sample vapors.
1. Observe the oil in the oil sight glass.

2. Turn the mode selector fully counterclockwise to select the High Throughput
mode and set the gas ballast control to the low flow (position I).
3. Run the pump until the oil appears clear.
Replacing the Oil

1. Warm the oil by running the pump for at least 10 minutes, and then switch off
the vacuum system.
2. Unplug the pump from the AC outlet and disconnect it from your vacuum
system.
3. Remove one of the oil filler plugs.
156
Maintenance
Filler Plug
Max Oil Level
Min Oil Level
Drain Plug
2 Liter
Drain Container
Figure 64 Draining forepump oil
157
4. Place the pump on a table. Place a drain container under the drain plug. Raise
the end of the pump opposite the drain plug by putting a block under it.
If you were running toxic samples, the oil is contaminated as toxic

waste. Handle and dispose of waste oil appropriately.
WARNING
5. Remove the drain plug and allow the oil to drain into the container.
If the pump oil was contaminated, pour clean oil into the filler hole and allow it
to drain until the oil appears clear.
6. Replace the drain plug, remove the block and reconnect the vacuum system.
7. Add oil until it reaches the MAX mark on the top of the sight glass.
Do not overfill.
8. Replace the oil filler plug by tightening it until it is fingertight.

Do not overtighten the oil filler plug.
9. After restarting the pump and allowing it to run for a few minutes, recheck the
oil level. If the oil level is below the MAX mark, repeat the above procedure by
adding more oil until it reaches the MAX mark.
158
Maintenance
Inline Gas Purifiers
The inline gas purifier lets you change the trap without introducing contaminants
into your system. This eliminates the need to flush the system. The trap contains
oxygen, moisture and hydrogen adsorbents and is packed and purged under helium.
Color changes in the glass indicating trap will indicated when filter needs to be
replaced.
The click on connector fitting has a spring loaded needle valve, which seals when
the trap is removed and only opens when the new trap is connected and locked into
position. When the click on connectors are installed into the gas line here is no need
to loosen or tighten any fittings, the new trap will just click in.
Replacement Traps
Description Part No.

Indicating Glass Triple Gas specific (He) N09306107
Oxygen/Moisture/Hydrocarbons
Oxygen/Moisture/Hydrocarbons with 1/8” Brass Connector (2)
Oxygen/Moisture/Hydrocarbons with 1/8” Steel Connector (2)
Click On Connectors
Description Part No.

1/8” Brass Connector (2) N09306119
1/8” Steel Connector (2) N09306120
Stain steel Connector (for connecting two click on traps) N09306121
Refer to the installation instructions that accompany your new in line gas purifier
trap for detailed installation and operating instructions.
159
Changing from EI to CI Mode
Changing modes consists of the following:
• Connecting the CI gas.
• Changing the source and instrument control mode.
• Leak-checking.
• Setting-up CI.
Connecting the CI Gas
Hazardous gas vapors. When using ammonia gas when running in the
chemical ionization (CI) mode, it is necessary to vent the mass
spectrometer effluent from the forepump exhaust into a fume hood or
outside the building.
WARNING
Explosive Hazard. If the hydrogen is turned on without a column

attached to the injector and/or detector fittings inside the oven, the gas
could diffuse into the oven creating the possibility of an explosion.
If the mass spectrometer is not under vacuum, hydrogen, can fill the
vacuum chamber thereby creating an explosive hazard.
WARNING To avoid possible injury, do not turn on the hydrogen, unless a column
is attached, all joints have been leak-tested, and the mass spectrometer
is under vacuum with the forepump exhaust properly vented to a fume
hood.
160
Maintenance
Recommended Gases
Reagent gases used in chemical ionization (CI) are methane with a minimum purity
of 99.999%, isobutene with a minimum purity of 99.98% and ammonia with a
minimum purity of 99.998%. Carrier gas tubing should be ultra-clean.
Methane and isobutene require a gas delivery pressure of 15 psi (104 kPa) to the
bulkhead fitting on the back of the mass spectrometer. A two-stage stainless steel
diaphragm, high purity regulator is. A single-stage stainless steel diaphragm, high
purity, rated for corrosive service is required for ammonia. Clean tubing must be
used. It must be solvent-washed and nitrogen-dried. The bulkhead connector at the
rear of the instrument is a 1/8 inch Swagelok fitting.
To prepare Clarus 600 MS for CI:
NOTE: Make sure to purge the CI line before you attach it to the rear of the mass
spectrometer.
1. Obtain the CI gas cylinder for your analysis.
2. Connect the gas line to the CI Gas connector on the rear of the mass
spectrometer.
3. Ensure that the mass spectrometer is at the proper vacuum level.
4. Turn on the CI gas and set the delivery pressure to 15 psi (104 kPa).
5. Leak-check all connections.
161
ROTARY PUMP
Rotary
Warning Pump
Power
POWER IN
NH 3
CH4
C 4H 10 N2 WATER WATER Power In
CI GAS VENT IN OUT
15 psi
(103 kPa)
5 psi
(35 kPa)
50 psi
(345 kPa) Warning
MAX MAX MAX Labels
Vacuum
Line
Figure 65 CI Gas connection on the rear panel of the mass spectrometer
Changing to CI
To change from the EI to the CI mode:
1. Remove the EI inner source by following the procedure described in earlier in

this chapter, Removing the Inner Source.
2. Install the CI source by following the procedure described in on page 105.

Properly cover and protect the EI source and put it in a safe place.
3. Select CI+ from the Ion Mode menu.

The CI+ window appears.
162
Maintenance
4. Select Pump from the Options menu.

This starts the forepump and the turbomolecular pump.
5. In the Vacuum Pressure Gauges area of the window, observe the Pirani gauge
time line and the Penning gauge time line. Wait about 5 minutes until the
vacuum gauge achieves about 2.5 x 10-5.
Leak Checking
Before running in the CI mode, confirm that the column is properly installed and the
system is leak-free. The best way to check this is by running CI without the reagent
gas.
163
To leak-check the system:

1. Display the Tune page.
2. Select CI+ from the Ion Mode menu.
164
Maintenance
3. Click Press for Operate and observe the air/water masses.
The CI source running in the CI mode without reagent gas to produce an EI

emission similar to the EI mode but with reduced sensitivity. You will leak-check
your system this way.
If mass 28 is larger than mass 18, you have a leak. Determine the source of the leak
and correct it. For example, leak-check all fittings and connections.
Setting-Up CI
After verifying that no leaks exist, you can proceed to set up the CI mode for an
analysis.
165
Setting the Parameter Values

1. Display the following CI window:
2. Set the values as shown above.

The following table describes the CI parameters to check:
Parameter: CI+ Values and Comments:

Electron energy 30 eV
Emission Should be below 200 µA, although 200 to 300 µA is acceptable.
(Above 200 mA may cause hydrocarbon “cracking” patterns with
methane and isobutane.) Emission measures the real emission current,
i.e. the source current from the source block, there is no trap "source
current" in CI.
Lens 1 and 2 The tuning of these lenses may be different from the optimum values set
for EI, since the source pressure is much higher in CI.
Multiplier 200V to 600V
Ion Energy Approx. 1. Similar to EI.
Source temperature 150 ºC
166
Maintenance
Adjust the Reagent Gas for CI+

When running in the CI+ mode with reagent gas off, the resulting EI spectra have
about 10x lower sensitivity than with the EI source.
If using methane reagent gas, the reagent ions at m/z 17 (CH5+) and 29 (C2H5+)
should be of approximately equal intensity. Maximize the m/z 29 intensity. With
m/z 29 maximized, the ion at m/z 16 should be about 1% of the m/z 17 peak height.
(Higher indicates a leak at the transfer line/inner source connection.) Operate
slightly to the low-pressure side of the maximum to minimize gas load on the MS.
(The vacuum gauge pressure will be 1.5x10-4 to 5x10-4 Torr.)
If using ammonia reagent gas, reagent ions at m/z 18 (NH4+) and 35 [(NH3)2H+]
should be present and the ions at m/z 35 should be optimized.
If using isobutane reagent gas, the reagent ions at m/z 43 (C3H7+) and 57 (C4H9+)
should be tuned in the approximate ratio of 1:2.
The following example uses methane reagent gas.
NOTE: The CI gas adjustment knob controls a delicate needle valve. To avoid damaging the
needle valve, do not overtighten it. Always use the CI gas button on the screen to
turn off the CI gas.
167
Access Door
Inner Source
Black Knurled Knobs
Figure 66 CI reagent gas needle valve adjustment knob
1. Carefully turn the delicate CI Gas adjustment knob fully clockwise until you
feel it stop.
2. Select CI Gas On from the Gas menu. A check mark appears next to the
option.
NOTE: Always turn on the CI gas before Operate to avoid a pressure surge hitting the
filament.
168
Maintenance
3. Click Press for Operate and monitor the Penning gauge as you adjust the CI
gas. Observe that mass 16 initially grows larger. As pressure increases in the
ion chamber of CI source, the mass 29 peak will begin to grow. Keep the
pressure below 5 e-4 Torr.
4. When using methane gas, carefully turn the CI adjustment knob

counterclockwise until m/z 16 is low or non-existent, and m/z 29 is maximized.
As you turn the knob, reduce the multiplier voltage to keep the peaks on scale.
A typical multiplier value is 235.
m/z 17 and 29 will typically be 80 – 100%.
5. Continue to turn the knob counterclockwise. Observe that the pressure

increases and mass 41 will start to grow. Stop when mass 29 is at 100%.
169
6. Turn the knob to maximize the intensity of mass 29. Also verify that mass 16 is
small (< 1.0% of the height of the peak at mass 17).
If mass 16 does not appear as a small peak, STOP. You probably have a gas
leak at the transfer line/inner source connection. Locate and correct the leak.
7. After you have maximized the peak, slightly decrease the reagent gas by
turning the knob clockwise 1/8 turn.
170
Maintenance
8. Tuning may be optimized on the m/z 69, 219, 414, and 652 ions of the
heptacosa reference gas.
9. Click Press for Standby to turn off Operate, followed by the CI gas.
You are now ready to run your CI+ analysis.
171
Adjust the Reagent Gas for CI-
1. Open the CI gas inlet by selecting CI Gas from the Gas menu. Wait at least 10
seconds before clicking Press for Operate.
Parameter: CI− value and comments:

Electron Energy 30 to 70 eV
(This parameter should be optimized.)
Emission 200 to 300 μA is acceptable

(Emission measures the real emission current, i.e. the
source current from the source block, there is no separate
measurement of source current in CI.)
Lens 1 and 2 The tuning of these lenses may be different

from the optimum values set for EI, since the
source pressure is much higher in CI.
Multiplier 200V to 600V
Source temperature 150 °C is standard. Higher temperatures keep
the source cleaner, but may increase
fragmentation.
For example, down a little from EI to minimize
fragmentation. 120 °C is the practical lower limit.
Ion Energy Approx. 1 or 2
2. Optimize the amount of reagent gas flowing into the source by using two
heptacosa ions, m/z 452 and 633, which usually produce relative intensities of
65 – 85% and 95% respectively.
Heptacosa can be used to calibrate the m/z range for negative ion CI analyses.
172
Maintenance
3. Maximize the peak intensities, then slightly decrease the reagent gas by turning
the knob clockwise 1/8 turn.
Optimize the tuning parameters for maximum intensity.
4. Save the Tune page parameters by selecting Save As…from the File menu.
5. Select Calibrate Instrument from the Tune page Calibration menu.
6. Select heptaneg.ref from the drop-down menu.
Make sure the “Use Air Refs” check box is not selected.
CAUTION
173
7. Click the Start button to display the following dialog box.
8. Click Acquisition Parameters and enter the following values.
9. Click OK to begin calibration.

You are now ready to run CI analysis.
174
Troubleshooting 5
176
Overview
The following sources of problems can occur in gas chromatography and mass
spectrometry:
• The operator: When the operator is new to chromatography/mass

spectrometry and/or a new instrument, problems can be introduced during the
learning curve. Once the operator becomes familiar with both the technique
and the instrument, this problem source diminishes greatly.
• The sample: Unlike clean standards, real world samples such as

environmental samples can introduce problems because they are difficult to
handle, have complicated matrices, contain unknown constituents, etc.
• The column: The column is most often the major factor contributing to poor
analyses. The more a column is used, the greater the possibility of
contamination, loss of substrate, etc. Columns do not last forever and should be
changed when results become suspect.
• The gas flow system: Gas leaks are a major concern in gas chromatography
and can lead to many problems.
• The vacuum system: Vacuum leaks are a major concern in mass spectrometry
and can lead to many problems.
• Ion Optics: Over time, the ion optics can become contaminated. This results in
reduced sensitivity and difficult or impossible tuning.
• The electronics: The problem must be identified as either chromatographic or

hardware. Electronics used in the system can malfunction.
• Data handling: Today, most chromatographers rely on sophisticated data

handling systems to integrate their results. Some problems can be related to the
incorrect data handling parameter settings or hardware problems with the
computer.
Spare Components
The following list contains items you should have on hand to help solve problems.
• New syringes: a syringe can break, become plugged or begin leaking. Always
have spare syringes available.
• Duplicate columns: a column does not last forever; always have a duplicate
column on hand in the event that your separation begins to degrade. Also,
capillary columns can be damaged if oxygen is introduced at high
temperatures. A duplicate column will allow you to determine if the column is
the cause of the problem.
• Septa: this is the one area of the gas chromatograph that requires routine
maintenance. Always have spare septa available.
• Leak detector: the gas flow system can be a problem as fittings wear with age
and can begin to leak. You should have a thermal conductivity leak detector to
help find and fix leaks.
• Injector liners: are made of glass or fused silica and can be easily broken when
removed. You should keep a supply of spare liners on hand. Please remember
that you cannot run satisfactory analyses without an injector liner.
Logical Troubleshooting Steps

There are some simple steps that you should take when trying to locate a problem.
Use the following guide to troubleshoot your system.
1. Note the symptoms - define the problem. Compare your runs with good
analysis, that is, with the results normally obtained.
2. Systematically eliminate possible causes.
The first rule here is, "What did you change last?" Many times a problem
arises when a change is made to the system, such as changing a gas tank,
column, septum or glass liner. If the problem occurred after such a change,
then the change is the most likely cause of the problem.
Change the simplest thing first. For example, if you suspect a gas leak, the
easiest change to make is the GC septum instead of replumbing the internal
pneumatics.
178
Change only one parameter at a time and check for its effect. If you change
three items at once and your problem goes away, you may not know which of
the three moves or combination of moves corrected the problem. This way, if
the problem happens again, you will know exactly what corrective action to
take.
179
Troubleshooting Chart
Problem Probable Cause Solution
Mass Spectrometer will AC line cord not plugged into Plug the Mass
not turn on (no indication an AC outlet. Spectrometer AC line cord
of power to the into an AC outlet.
instrument).
No AC power to the outlet. Check the outlet.
Fuse blown. Call a PerkinElmer service

engineer.
Mass Spectrometer is on Forepump is not plugged into Plug the forepump line
but the forepump is not the AC outlet on the rear of cord into the mass
running. the mass spectrometer. spectrometer.
Forepump is not operating Make sure the forepump is

correctly ( mass spectrometer switched on.
does not pump down).
Blown fuse in Mass Call a PerkinElmer service

Spectrometer. engineer.
180
The ultimate pressure is Is the cooling inadequate? Check the cooling-air flow and
poor. correct if possible.
Check the cooling-air duct for

obstructions and correct as
necessary.
If the cooling air flow is fine

and there are no obstructions
contact your PerkinElmer
service representatives.
Is the backing pressure Check for a leak in the backing

high? pipeline and poor backing
pump performance. Correct as
necessary.
The pump is very noisy or Is the noise irregular and If so, a bearing may be
there is excessive vibration getting progressively defective. Contact your
or both. worse? PerkinElmer service
representative.
Is the pump making a If so, the rotor may be out of

constant high pitched balance. Contact your
noise? PerkinElmer service
representative.
181
Turbo pump will not Pump malfunction. Call a PerkinElmer service

accelerate engineer.
Pump controller Call a PerkinElmer service

malfunction. engineer.
GC is not properly Set the proper GC

configured. configuration for your site.
Vacuum light continues to Large leak. Locate vacuum leak and

blink. correct.
Foreline trap has Replace filter.

excessive moisture.
Rotary pump set to gas Switch the gas ballasting off.

ballast.
Rotary pump requires oil Change oil.

change.
High mass spectra appears Bad tune. Run AutoTune.

as a large blotch, or loss of
high mass spectra.
Drastic change in mass peak Bad tune. Run AutoTune.

shape for no apparent
reason.
No spectra, or large blotch. Bad tune. Run AutoTune.
182
No spectra, or very little Bad tune. Run AutoTune.

spectra at the low mass end.
No spectra, not even noise at Loose electrometer cable. Reset the cable.
a high PMT voltage.
Defective electrometer Call a PerkinElmer service

board. engineer.
No filament current. Defective filament. Replace the filament.
Wavering baseline (by Defective outer source Replace the temperature

several hundred counts). temperature sensor or a sensor.
defective electrometer.
Call a PerkinElmer service

engineer.
183
Poor or inadequate Leaking injector septum. Replace the septum.

sensitivity.
Leak from injector Tighten/replace ferrules.

ferrules.
Foreign material in the Clean the injector.

injector.
Peak splitting. Prevent double injections.
Dry the outside of the injector

needle.
Replace the injector septum.
Injector and column are Install a silanized injector

more active toward liner, or silanize the current
acid/base compounds. injector liner.
Check or replace the injector

packing material, such as
quartz wool.
Cut off the first 30 cm of the

column and rerun the test mix.
If the results do not improve
replace the column.
184
Solvent tailing. Inadequate splitter flow. Increase the splitter flow.
Column not properly Reinstall the column in the

installed in the injector. injector.
Loss of high end compounds. Temperature setting too Increase the injector, column
low on the injector, oven or transfer line
column oven or transfer temperature to allow the less
line. volatile compounds of the
sample to reach the mass
spectrometer.
Peaks at masses 28 (nitrogen) Leaks in or around Tighten the fittings and

and 32 AMU (oxygen) are in a vacuum or column connection points to the high
ratio of < 4 to 1, and the peak at fittings. vacuum system.
mass 28 is larger than the peak
Set the injector split flow to
at mass 18.
50:1.
Peaks at masses 14 and 16 are Leaks or improper tuning. Tighten the fittings and
larger than the peak at mass 28. connection points to the high
vacuum system.
Set the injector split flow to
50:1.
Run AutoTune.
185
Poor sensitivity (correct Column is improperly Reinstall the column and

amount of sample is reaching positioned in the ion check the cut at the end
the mass spectrometer). source. that fits in the source.
Improper tuning, or a Check the tuning. Increase

dirty or defective ion the PMT voltage.
source.
Shut down the system,

remove the inner source,
clean or replace lenses in
the outer source, and
install a new filament.
Loss of resolution (especially Dirty prequadrupole rods. Clean the prequadrupole

at high mass). rods.
Mass assignment drifts. Large temperature Stabilize the lab

fluctuations in the temperature, or isolate the
laboratory. GC/MS system from large
temperature fluctuations.
Mass assignment incorrect. Run mass calibration.
Skewed spectra. Improper scan speed (too Increase the scan speed.
slow for the narrow peaks
produced by capillary
columns).
Unusually high repeller Repeller dirty. Clean repeller.

voltage.
186
Unusually high emission Ion volume dirty. Clean the inner source.
setting.
Prefilters dirty. Clean the prefilters.
Poor tuning. Retune.
Tuning peaks show Poor tuning. Retune.

precursors (forward slope
shoulders).
Dirty prefilter. Clean prefilters.
Dirty source. Clean source.
Particulates on analyzer Clean the particulates of the rods

rods. with a methanol-dampened lab
wipe.
Blow the particulates off the rods

with helium or dry nitrogen.
Defective or damaged Call a PerkinElmer service

analyzer. engineer.
No reference peak. Reference gas off. Turn on the reference gas.
Empty reference vial. Visually check and refill.
Faulty solenoid. Listen for click when

activating/deactivating the valve.
187
Inconsistent peak widths. Poor tubing. Retune.
Ground loop from GC and Unify supplies.

MS on different power
supplies.
Peaks shifted from their Poor calibration. Perform mass calibration.

nominal mass position.
Tuned peaks are too narrow. Over-resolved tuning. Retune.
Tuned peaks are too wide. Under-resolved tuning. Retune.
Big peaks observed at m/z Air leak developed. Check column

18, 28, 32. connections.
Change carrier gas tank. Fit oxygen scrubber.
Moisture from recent Bake out source

source clean/column overnight.
change.
No ion beam but the filament Large air leak. See procedure for leak-
status OK. checking.
Detector voltage too low. Increase PMT value.
Electronics failure. Call a PerkinElmer

service engineer.
Poor sensitivity. Beam Column improperly Check and reinstall the

instability/peaks breaking up. installed. column if necessary.
188
Piece of column broken off in Remove the inner source,

the ion chamber. check for and remove piece of
column.
Source filament is bent. Check and replace filament if

necessary.
RF generator malfunction. Call a PerkinElmer service

engineer.
Analyzer drive electronics Call a PerkinElmer service

malfunction. engineer.
Total Ion Chromatogram Dirty source. Clean the source.

too high.
Contamination from poor Set source and transfer line to

handling technique. 250 ºC and maintain this
temperature overnight.
Stationary phase of column Change column.

de-polymerizing (bleeding).
Air leak. Find the leak and fix it.
Poor quality carrier gas. Replace the carrier gas tank.
Carrier gas filter is ineffective Replace the carrier gas filter.

and needs replacing.
No noise on mass Detector multiplier voltage too Increase the multiplier

chromatogram. low. voltage.
189
Excessive noise. Dirty source. Clean the source.
GC and MS on separate power Connect GC and MS together

supplies. with the ground strap.
PMT voltage too high. Run AutoTune.
Data acquisition thresholds set too Raise the thresholds.

low.
Instrument won’t calibrate Poor AutoTune/Manual tune. Retune.

(after retuning and
recalibrating).
Contaminated ion source. Clean the ion source. Set the

source temperature to 250 ºC and
maintain this temperature
overnight.
Source too hot/cool. Set the correct source

temperature.
Air leak. Find the leak and fix it.
Wrong calibration reference file Select the correct file.

selected.
Incorrect calibration calculation Set the calibration parameters to

parameters. the default values.
No calibration gas. Refill the calibration gas vial.
Incorrect electron energy. Reset to 70 eV.
190
Chromatography Related
Inconsistent retention Injector septum leak. Replace the septum.

time.
Carrier gas manifold leak. Locate and fix the leak.
Rising Total Ion Column bleed. Disconnect the column from

Chromatogram baseline. the mass spectrometer and
condition the column.
Vacuum leak. Locate and fix the leak.
Discreet high intensity Column bleed. Disconnect the column from

contaminant peaks. the mass spectrometer and
condition the column.
Injector septum bleed. Replace the septum and/or

glass liner.
Tailing peaks (sloping on Improperly installed column. Check the column and
RHS). reinstall if necessary.
Injector too cool. Raise the injector

temperature.
Interface temperature too cool. Raise the interface

temperature.
Inadequate carrier gas flow. Set proper flow.
191
Dirty injector liner. Clean or replace.
Column has active sites. Equilibrate or replace.
Chromatographic peaks Injector too cool. Raise injector temperature.

too wide.
Sample overloading the Use a split injection or a smaller

column. sample.
Incorrect GC oven program. Enter a new oven program.
Discrimination of relative Poor resolution or improper Retune.

peak intensities. tuning.
Unstable filament. Replace filament.
Poor calibration. Recalibrate.
Air leaks at detector. Check He/Air ratio.
Peaks are flat-topped. Signal strength exceeds Reduce PMT voltage.

dynamic range of detector.
Sample is too strong. Dilute or split.
High baseline. Dirty sample. Prepare and filter a new sample.
Air leak at injector. Locate and fix the air leak.
Contaminated carrier gas. Replace the gas tank.
192
Slowly falling baseline Split valve left closed during Open the split valve.
(from a high initial value). acquisition.
Inadequate purge flow rate. Increase flow rate.
Poor off for too long. Reduce purge time.
Low sensitivity. Dirty source. Clean the source.
Poor column performance. Replace column.
Dirty injector. Replace injector liner.
Source temperature not Set the proper source

optimized. temperature.
Detector voltage set too low. Increase PMT voltage.
Tune not set correctly. Run AutoTune.
Poor filament alignment. Realign or replace filament.
Incorrect column position in Reposition the column.

the source.
193
Poor reproducibility. Dirty source. Remove and clean the source.
Defective injector liner. Replace injector liner.
Defective syringe. Replace syringe.
Old or damaged filament. Examine and replace

filament.
Poor calibration. Recalibrate.
Air leak. Locate and fix.
Active sites in column/liner. Replace column/liner.
Intermittent source heater Call a PerkinElmer service

failure. engineer.
Poor S/N on test standards. See low sensitivity causes

above.
Incorrect GC/MS method Use the correct method.
Accidental split injection. Set the proper split.
Detector voltage set too low. Increase PMT voltage.
Column flow rate too high. Reset the column flow rate.
194
Spectral Related
Noisy spectra. Dirty source. Remove and clean the source.
Peak detection threshold set too low. Raise the thresholds.
PMT voltage set too high. Lower the PMT voltage.
Spectrum distortion. Scanning too fast or slow. Reset the scan rate.
Incorrect Isotope ratios. Poor calibration. Recalibrate.
Incorrect tune. Retune.
Defective filament. Replace filament.
Air leak. Find and fix.
Missing Isotopes in Bad calibration. Recalibrate.

spectrum.
Dirty source. Clean source.
Sample too weak. Use a higher sample

concentration.
Peak detection thresholds set too Lower the thresholds.

high.
PMT voltage set too low. Raise the PMT voltage.
195
Contamination. Locate the contamination and

eliminate it.
Co-eluting components. Change your sample

preparation or
chromatography.
Incorrect column alignment. Reinstall the column.
Section of a mass range Corruption of data file. Reacquire data.

missing from a
spectrum.
Scanning too fast. Reduce the rate.
Hard disk has too much Defrag the hard drive.

fragmentation.
Hard disk full. Remove unnecessary files.
Molecular Ion too Source temperature too high. Reduce the source
weak. temperature.
196
Communications Related
Will not boot MS. PC (computer) to MS cable Check and reset the cable.
has a loose connection.
Transient in power supply Reboot the PC (computer).

has halted communications.
Will not control GC. RS 232 communications Check and restart the mass
cable loose connections. spectrometer.
Power failure/transient
surge to GC or
autosampler.
GC electronic malfunction. Call a PerkinElmer service

engineer.
Communication cable GC electronics Call a PerkinElmer service

intermittent contact. malfunction. engineer.
Crashes when starting an Software corrupted. Reload software.

acquisition.
Rotary pump malfunction. Call a PerkinElmer service

engineer.
197
Forepump Related
Pump does not start. Forepump switched off. Switch on the pump.
Blown fuse. Call a PerkinElmer service

engineer.
Electrical supply voltage Determine the correct voltages,

does not match that of the and correct. Check the voltage
pump motor. switch at the pump.
The outlet filter is Find and unblock.

blocked.
Pump has failed to reach Pressure measurement or A contaminated Pirani gauge

vacuum. gauge head gives an can indicate a pressure several
incorrect indication of times higher that the actual.
pressure. Replace if necessary.
Pump contains the wrong Drain and refill with the

type of oil. correct oil - Edwards
Ultragrade 19 Oil. Consult
your Edwards Pump
instruction manual.
Mode selector and/or gas Check and set to correct

ballast control are position.
incorrectly set.
High oil level. Drain to the high oil level

mark.
Low oil level. Check and fill to correct level.
198
Contaminated oil. Drain and refill with new oil.
Vacuum fitting dirty or Check and replace if

damaged. necessary.
Noisy Pump. Motor fan cover damaged. Call a PerkinElmer service

engineer.
Worn motor bearings. Call a PerkinElmer service

engineer.
Oil contaminated with solid Determine cause and replace

particles. oil.
Oil saturated from CI Drain and refill with clean oil.

analysis.
199
External oil leak. Outer shaft seal worn or Call a PerkinElmer service
damaged. engineer.
Oil box gaskets deteriorated. Call a PerkinElmer service

engineer.
Oil leak from gas ballast Call a PerkinElmer service

control. engineer.
Oil leak from drain plug. Tighten the drain plug or

replace.
Oil leak from sight glass. Tighten sight glass screws or

call a PerkinElmer service
engineer.
200
Message Dialogs
When operating the instrument message dialog boxes will sometimes appear. The
following table is the Icon Key followed by tables that show the Message Title, icon,
dialog message and recommended action.
Icon Key
Icon Meaning
Press this icon to close the

message.
Press this informational icon

to get more details on the
message.
201
Message Title Icon Message Action

There is a problem with the Press OK to close the
Diffusion pump
diffusion pump. Either the message.
failure
diffusion pump fan has failed or
the pump has over heated. Check the cooling-air flow
Please look in the Hardware and correct if possible.
Guide for additional instruction.
necessary.

System not at The system has not reached the Press Yes if you wish to
pressure proper operating pressure. The continue.
filament could be damaged by
Press No if you wish to stop.
Caution starting the system now. Do you
wish to continue? See the Maintenance chapter
in this Hardware Guide for
the procedure to replace a
filament.
Safe to vent The vacuum system is off and Press OK to close the
the system can now be vented. message.
The GC carrier gas should be
turned off.
202
Message Icon Message Action
Title
Diffusion There is a problem with the diffusion Press OK to close the

Pump pump. Either the diffusion pump fan message.
failure has failed or the pump has over heated.
Check the cooling-air flow and
Please look in the Hardware Guide for
correct if possible.
additional instruction.
necessary.

Vacuum The backing pump could not reach the Press OK to close the
Leak necessary vacuum level to start the message.
Detected diffusion pump. There could be a
problem with a vacuum leak, the Check the system for any leaks
backing pump or the vacuum gauge. and correct. If the problem
The backing pump will be turned off. continues contact your
Make sure that the vent valve is closed PerkinElmer service
before restarting the backing pump. representatives.
203
Message Icon Message Action

Title
Vacuum There is a problem with the vacuum Press OK to close the

Gauge gauge. message.
Failure
Restart the system, if
you still have this failure
message contact your
PerkinElmer service
representatives.
Pump Press OK to close the

The vacuum system is off and the
failure- message.
system can now be vented. The carrier
Safe to Vent
gas should be turned off. Check the cooling-air
flow and correct if
There is a problem with the diffusion
possible.
pump. Either the diffusion pump fan
has failed or the pump has over heated.
Check the cooling-air
duct for obstructions and
correct as necessary.
If the cooling air flow is

fine and there are no
obstructions contact
your PerkinElmer
204
Vacuum Leak- Press OK to close the

The vacuum system is off and the
Safe to Vent message.
system can now be vented. The
carrier gas should be turned off
Check the system for
A Vacuum Leak has been any leaks and correct. If
detected. Please look in the the problem continues
Hardware Guide for additional contact your
instruction. PerkinElmer service
representatives.
Vacuum Gauge The vacuum system is off and the Press OK to close the
Failure-Safe to system can now be vented. The message.
Vent carrier gas should be turned off.
To replace the vacuum
There is a problem with the gauge contact your
vacuum gauge. Please look in the PerkinElmer service
Hardware Guide for additional representatives.
instruction.
Exit TurboMass- The vacuum system is in the Press OK to close the

Vacuum System process of the pumping down the message.
pumping down spectrometer. Exiting TurboMass
at this time may prevent a
successful pump down.
Exit TurboMass- The vacuum system is in the Press OK to close the

Vacuum System process of shutting down. Exiting message.
pumping down TurboMass at this time may
prevent a successful completion of
this task.
205
Backing Pump is
The system is not in an operating If the transfer line or the
on
state. A diffusion pump failure, a source temperatures are
vacuum leak or a vacuum gauge above 100C, please wait
failure could have occurred. until they have cooled
before pressing OK.
If the transfer line or the source
Pressing the OK button
temperatures are above 100C, please
will turn off the backing
wait until they have cooled before
pump.
pressing OK.
Pressing the OK button will turn off
the backing pump.
The backing pump could not reach
Problem with Press OK to close the
the necessary vacuum level to start
Vacuum message.
the diffusion pump.
There could be a problem with a
vacuum leak, the backing pump or
the vacuum gauge.
The backing pump will be turned off.
Make sure that the vent valve is
closed before restarting the backing
pump.
206
Replacement Parts
Contact PerkinElmer for Columns, Supplies, Accessories, and Replacement Parts.
Supplies, accessories and replacement parts can be ordered directly from

PerkinElmer's catalog service. PerkinElmer offers a full selection of high-quality
chromatography data handling products and gas chromatography supplies and
columns through the Gas Chromatography Supplies Catalog and the Gas
Chromatography Column Catalog.
To place an order for supplies and many replacement parts, request a free catalog, or
ask for information:
Telephone:
• U.S. only: Call toll free 1-888-PE-CHROM, 8 a.m. to 8 p.m. EST. Your order
will be shipped promptly, usually within 24 hours.
• Worldwide: Call your local PerkinElmer sales or service office or call

PerkinElmer, Shelton, CT USA 1-203-925-4600.
e-mail: [email protected]
207
208
Index
Index
Index
EI Inner Source maintenance, 106

EI to CI mode changing, 160
A Electricity, safety practices, 20
Aluminum oxide, 109, 116 Environmental requirements, 32
C F
Caution, 9, 86 Filament
Changing a column, 88 replacing, 121
Checklist
pre-installation, 39 G
pre-operational, 71
Chemicals Gases, 36
definitions of warnings, 26
hazardous, 24
CI
H
leak checking, 163 Hardware
setting parameter values, 166 maintenance, 85
setting up, 165 Heated surfaces, warnings, 23
CI Inner Source, 113 Heaters
disassembling, 114 quad, replacing, 144
maintenance, 113 source, replacing, 142
rinsing and reassembling, 116
Cleaning the Instrument, 21
Column, 70 I
leak checking, 99 Inline Gas Purifiers, 159
selection, 70 Inner Source, 104
Compressed gases, safety practices, 22 maintenance, 104
Computer requirements, 37 removing, 105
Introduction to TurboMass, 49
D Ion optics assembly
removing, 129, 135
Diffusion Pump, 61 Ion source, 57
pumping down, 64
L
E
Labels
EI Inner Source, 106 WEEE Instructions, 30
cleaning, 109, 115 Leak checking, 79
disassembling, 107 CI, 163
reassembling, 110
rinsing, 109
211
M Power requirements, 33
Pre-installation checklist, 39
Maintenance, 75 Pre-operational checklist, 71
cable removal, 135
cleaning the prequads, 138
EI inner source, 106
R
inner source, 104 Reference Gas Inlet, 54
leak-checking, 79 Refilling the reference gas vial, 100
mass analyzer, 128 Removing a column, 88
outer source Removing the photomultiplier tube, 133
wire connections, 151
outer source, cleaning, 146
outer source, detail view, 149 S
overview, 75 Safety practices
PMT tube removal, 133 ammonia gas, 24
preparing for, 85 compressed gases, 22
reassembling TurboMass, 152 electricity, 20
removing the cover panels, 131 environmental requirements, 32
replacing an outer source themocouple, 139 general laboratory safety, 29
replacing the quadrupole heater, 144 generic warnings, 18
schedule, 77 heated zones, 23
source heaters, 142 hydrogen, methane, isobutane, 24
tuning, 82 overview, 18
vacuum system, 154 pollution degree, 27
oil, 154 requirements, 35
venting the system, 87 space, 31
Mass analyzer storage, 28
maintenance, 128 ventilation, 23
Software, 68
O top level screen, 68
Tune page, 69
Operating conditions, 27 Source, 119
Outer source reinstalling, 119
cleaning, 146 Space requirements, 31
detail view, 149 Spare components, 178
Overview Storage, 28
Clarus 600/560D GC, 51 Supplies, accessories, replacement parts, 45
ion source, 57 system requirements, 37
maintenance, 75
reference gas inlet, 54
troubleshooting, 177 T
Transfer line
P cooling, 86
Traps
Photomultiplier Tube (PMT) click on connectors, 159
removing, 133 replacement, 159
Pollution degree, 27
212
Index
Troubleshooting, 177 Vacuum Gauge, 67

chart, 180 Vacuum system, 59
overview, 177 options, 61
spare components, 178 rotary pump, 59
Tune page, 69 Vacuum System
Tuning, 82 diffusion pump, 61, 64
TurboMass turbomolcular pump venting, 64
system requirements, 37 turbomolecular pump, 61
TurboMass Software, 68 Ventilation, safety practices, 23
Turbomolcular Pump Venting, 87
venting, 64
Turbomolecular Pump, 61
W
V Warnings, 10, 18
hazardous chemicals, 26
Vacuum Controls, 61
213

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Clarus 600/560 D MS

Part Number Release Publication Date

Or emailed to: [email protected]

Copyright © 2008 PerkinElmer, Inc.

PerkinElmer is a registered trademark of PerkinElmer, Inc.

Warnings and Safety Information .................................................... 7

About the Clarus 600/560 D System ............................................... 47

Leak Checking .............................................................................................. 79

Changing to CI .................................................................................... 162

Troubleshooting .............................................................................. 175

Index ................................................................................................ 209

Conventions Used in this Manual

Normal text is used to provide information and instructions.

Bold text refers to text that is displayed on the touch screen.

Notes, warnings and cautions

Throughout the manual, the term ‘mass spectrometer’ or MS specifically refers to

Tel: 1 (800) 762-4000

Electromagnetic Compatibility (EMC)

All information concerning EMC standards is in the Declaration of Conformity, and

The Clarus MS contains protective circuitry. Contact PerkinElmer

Electrical Symbols Used on ClarusMS

Protective conductor terminal. Ground.

Off position of the main power switch.

On position of the main power switch.

Warning: Risk of electric shock.

Warning: Hot surface.

Caution, risk of danger

Label Location and Content

Figure 1 Front View of Clarus 600 MS Front View of Clarus 560 D

Warning including interference that may cause undesired

Do not operate the instrument with any

Warning Warning POWER IN

120 VAC ~ 50/60Hz

Figure 2a Rear View of the Clarus 600 MS

Figure 2b Rear View of the Clarus 560 D MS

Clarus MS Safety Practices

NOTE: This equipment requires no specified inspection or preventive maintenance to ensure

Do not attempt to make adjustments, replacements or repairs to this

Explosive Atmosphere. This instrument is not designed for operation in an

This equipment requires no specified inspection or preventive maintenance to ensure

Moving the Clarus MS

Depending on the Clarus 600 MS GC pump option selected, the

Connect the mass spectrometer to an AC line power outlet that has a

Do not make adjustments, replacements or repairs to the mass

Electrical shock hazard. To prevent electrical shock, disconnect the

Disconnect AC power cord from outlet before removing any cover or

Under no circumstances should circuit boards be removed or inserted unless the

Decontamination and Cleaning

Before using any cleaning or decontamination methods except those specified by

The customer’s responsible body is required to follow the "Equipment

In Canada, call toll free 800-561-4646 and speak to Customer Support.

Cleaning the Instrument

Compressed Gases. High pressure gas cylinders can be dangerous if

Explosive hazard. When using hydrogen, methane or isobutane, special

Hazardous vapors. When analyzing hazardous compounds, such as

Toxic Gases-Fume Ventilation System. Without adequate ventilation

Adequate ventilation must be provided, particularly if a liquid nitrogen or carbon

Risk of burns. Never touch a heated mass spectrometer transfer line or

Using Hydrogen, Methane or Isobutane

MODEL: ______ DATE: _