PerkinElmer Clarus 600/560 D MS Installation instructions

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: [e-mail]
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
3
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

Clarus 600/560 D MS Hardware Guide
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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

Contents
5
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

Clarus 600/560 D MS Hardware Guide
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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

Warnings and
Safety Information 1

Warnings and Safety Information
9
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
Caution
We use the term CAUTION to inform you about situations that could
result in serious damage to the instrument or other equipment. Details
about these circumstances are in a box like this one.

Clarus 600/560 D MS Hardware Guide
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Caution (Achtung)
Bedeutet, daß die genannte Anleitung genau befolgt werden muß, um
einen Geräteschaden zu vermeiden.
Caution (Bemærk)
Dette betyder, at den nævnte vejledning skal overholdes nøje for at
undgå en beskadigelse af apparatet.
Caution (Advertencia)
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.
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.
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.
Caution (Opgelet)
Betekent dat de genoemde handleiding nauwkeurig moet worden
opgevolgd, om beschadiging van het instrument te voorkomen.
Caution (Atenção)
Significa que a instrução referida tem de ser respeitada para evitar a
danificação do aparelho.
WARNING
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.
D
DK
E
F
I
NL
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Warnings and Safety Information
11
Warning (Warnung)
Bedeutet, daß es bei Nichtbeachten der genannten Anweisung zu einer
Verletzung des Benutzers kommen kann
Warning (Advarsel)
Betyder, at brugeren kan blive kvæstet, hvis anvisningen ikke
overholdes.
Warning (Peligro)
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.
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.
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.
Warning (Waarschuwing)
Betekent dat, wanneer de genoemde aanwijzing niet in acht wordt
genomen, dit kan leiden tot verwondingen van de gebruiker.
Warning (Aviso)
Significa que a não observância da instrução referida poderá causar
um ferimento ao usuário.
D
DK
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Clarus 600/560 D MS Hardware Guide
12
Customer Service
This instrument is manufactured by:
PerkinElmer Inc.
710 Bridgeport Avenue
Shelton, Connecticut 06484-4794
U.S.A.
Tel: [phone]
Internet: http://www.perkinelmer.com

Warnings and Safety Information
13
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.
CAUTION
The Clarus MS contains protective circuitry. Contact PerkinElmer
Service before performing any AC line tests.

Clarus 600 GC-MS Hardware Guide
14
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.

Warnings and Safety Information
15
Label Location and Content
Clarus 600
Mass Spectrometer
Figure 1 Front View of Clarus 600 MS Front View of Clarus 560 D
Clarus600
MassSpectrometer

Clarus 600/560 D MS Hardware Guide
16
ROTARY PUMP
POWER IN
Air
PC
Ethernet
Connection
Intakes
Processor
Reset
Switch
Air
Exhaust
Air
Vents
Mass Spectrometer
Mass Spectrometer
GC
Interface
120 VAC ~ 50/60Hz
230 VAC ~ 50/60Hz
MAX POWER 1000 VA
EN 55011-Class A, Group 1
Caution
Do not restrict air intake or exhaust
!
!
Warning
120 VAC ~ 50/60Hz
230 VAC ~ 50/60Hz
MAX POWER 1000 VA
EN 55011-Class A, Group 1
This unit contains protective circuitry.
Contact PerkinElmer qualified service
personnel before performing any
AC line tests
!
Caution
S1
ETHERNET
Disconnect AC power cord from oulet
before removing any cover or parts.
Do not operate the instrument with any
cover or parts removed.
Warning
Warning
This unit contains protective circuitry.
Contact PerkinElmer qualified service
personnel before performing any
AC line tests.
Caution
Do not restrict air intake orexhaust.
Caution
FCC Compliance
This device complies with Part 15 of the FCC Rules.
Operation is subject to the following two conditions:
1) this device may not cause harmful interference, and
2) this device must accept any interference received,
includi ng interference that may cause undesired
operation.
Disconnect A C power cord from oule t
before removingany cover orparts.
Do not operate the instrument with any
cover or parts removed.
Warning
WATER
IN WATER
OUT
N
VENT
2
NH
CH
CI GAS
3
4
410
CH
15 psi
(103 kPa)
MAX
5 psi
(35 kPa)
MAX
50 psi
(345 kPa)
MAX
Figure 2a Rear View of the Clarus 600 MS

Warnings and Safety Information
17
ROTARY PU MP
POWER IN
Air
PC
Ethernet
Connection
Intakes
Processor
Reset
Switch
Air
Exhaust
Air
Vents
PerkinElmer
Nxxx xxxx
Xxxxxxx
precisely.
Shelto n, CT 06484 USA
PartNo.
Serial No.
Clarus 560 D
MassSpectrometer
GC
Interface
120 VAC ~ 50/60Hz
230 VAC ~ 50/60Hz
MAX POWER 1000 VA
EN 55011-Class A, Group 1
Caution
!
!
!
Caution
S1
FCC Compliance
This device complies with Part 15 of the FCC Rules.
Operation is subject to the following two conditions:
1) this device may not cause harmful interference, and
2) this device mustaccept any interferencereceived,
including interference that may cause undesired
operation.
Disconnect AC power cord from oulet
before removing any cover orparts.
Do not operate the instrument with any
cover or parts removed.
Warning
REMOVEVENT LINE BLANKINGCAP
AT INSTALLATION.
Warning
This unit contains protective circuitry.
ContactPerkinElmer qualified service
personnel before performing any
AC line tests.
Caution
Do not restrictair intakeor exhaust.
Caution
FCC Compliance
Warning
2
On/Off Switch
Figure 2b Rear View of the Clarus 560 D MS

Clarus 600/560 D MS Hardware Guide
18
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.
WARNING
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.
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
the continuous functioning of its safety features.

Warnings and Safety Information
19
Moving the Clarus MS
WARNING
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
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.
WARNING
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
ground conductor, inside or outside the mass spectrometer, or
disconnection of the protective ground terminal may impair the
protection provided by the mass spectrometer.
WARNING
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
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

Clarus 600/560 D MS Hardware Guide
20
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.
WARNING
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.
Under no circumstances should circuit boards be removed or inserted unless the
instrument is disconnected from line power.