PerkinElmer Clarus SQ 8 MS Series Installation instructions

CCLARUSLARUSSQ 8 MSSQ 8 MSHardware GuideHardware Guide
GAS GAS CHROMATOGRACHROMATOGRAPHY PHY

Clarus SQ 8 MSClarus SQ 8 MS
Hardware GuideHardware Guide

Release HistoryRelease History
Part Part Number Number Release Release Publication Publication DateDate
09931017 A July 2011
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]
NoticesNotices
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 noExcept 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, thewarranty of any kind with regard to this document, including, but not limited to, the
implied warranties of merchantability and implied warranties of merchantability and fitness for a particular purpose.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.
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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 © 2011 PerkinElmer, Inc.
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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.
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Contents
3
Contents
Contents .......................................................................................................... 3
Warnings and Safety Warnings and Safety InformatInformation .................................................ion .................................................... 7... 7
Conventions Used in this Manual ................................................................... 9
Customer Service .......................................................................................... 12
Electromagnetic Compatibility (EMC) ......................................................... 13
Regulatory Information ......................................................................... 13
United States (FCC) .............................................................................. 13
Europe ................................................................................................... 13
Electrical Symbols Used on Clarus SQ 8 MS Series ............................. 14
Label Location and Content .................................................................. 15
Clarus MS Safety Practices .......................................................................... 18
Generic Warnings .................................................................................. 18
Moving the Clarus SQ 8 MS ................................................................. 18
Electrical High Voltage ......................................................................... 18
Contamination ....................................................................................... 20
Decontamination.................................................................................... 21
Compressed Gases ................................................................................. 22
Ventilation ............................................................................................. 22
Heated Zones ......................................................................................... 23
Using Hydrogen, Methane or Isobutane ................................................ 23
Using Ammonia Gas ............................................................................. 24
Hazardous Chemicals ................................................................................... 24
Definitions in Warning for Hazardous Chemicals ................................ 25
Temperature, Humidity, and Environment ................................................... 26
Operating Conditions............................................................................. 26
Storage Conditions ................................................................................ 26
General Laboratory Safety .................................................................... 27
Cleaning Requirements ......................................................................... 27
WEEE Instructions for PerkinElmer Products.............................................. 28
Pre-Installation Requirements ...................................................................... 29
Laboratory Space Requirements ............................................................ 29
Environmental Requirements ................................................................ 30
Power Requirements .............................................................................. 31
Gas Requirements .................................................................................. 32
Safety Requirements .............................................................................. 33
Computer and System Software Requirements ..................................... 34

Clarus SQ 8 MS Hardware Guide
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PC Requirements ................................................................................... 34
Operating System .................................................................................. 35
Software ................................................................................................. 35
Instrument Firmware Versions .............................................................. 35
Printer .................................................................................................... 35
Pre-Installation Checklist.............................................................................. 36
IntroducIntroduction .....................................tion ...................................................................................... 37................................................. 37
Preface .......................................................................................................... 39
System Overview................................................................................... 39
Summary of this Guide .......................................................................... 40
Related Documentation ......................................................................... 40
Supplies, Accessories and Replacement Parts ....................................... 41
About the Clarus GC/MS System ...............................About the Clarus GC/MS System ................................................... 43.................... 43
About the Clarus SQ 8 MS System .............................................................. 45
Clarus 580/680 Series GC ............................................................................ 47
GC Interface (Transfer Line) ........................................................................ 48
Reference Gas Inlet....................................................................................... 48
Ion Optics Path ............................................................................................. 49
Vacuum System ............................................................................................ 50
Rotary Pump .......................................................................................... 50
Vacuum Pump Options .......................................................................... 51
TurboMass Software ..................................................................................... 53
Top Level Screen ................................................................................... 53
Tune Page .............................................................................................. 54
Analytical Column ........................................................................................ 55
Pre-Operational Checklist ............................................................................. 56
MaintenanMaintenance .....................................................................................ce ...................................................................................... 57. 57
Overview ...................................................................................................... 59
Typical Overall Maintenance Schedule ........................................................ 61
Daily ...................................................................................................... 61
Weekly ................................................................................................... 61
Monthly ................................................................................................. 62
Every Six Months .................................................................................. 62
Yearly .................................................................................................... 62
Leak Checking .............................................................................................. 63
Tuning the Clarus MS ................................................................................... 66
Preparing Clarus MS for Hardware Maintenance ......................................... 68
Removing and Returning the Source ............................................................ 71

Contents
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Removing the Source ............................................................................ 71
Returning the Source ............................................................................. 74
Changing a Column ...................................................................................... 75
Tools and Items Required: ..................................................................... 75
Physical Measurement Outside the SQ 8MS ......................................... 76
Alignment Using the 10 mm Positioning Gauge Tool .......................... 79
Optical Column Alignment Using the Optional Plug Handle
and Sight ............................................................................................. 81
Refilling the Reference Gas Vial .................................................................. 85
Items Required ...................................................................................... 85
Replacing a Filament .................................................................................... 88
Items and Tools Required ...................................................................... 88
EI Source Maintenance .......................................................................... 91
Mass Analyzer Maintenance (Advanced Users Only) .................................. 95
Items and Tools Required ...................................................................... 95
Cleaning Materials................................................................................. 95
Removing and Returning the Ion Optics Assembly .............................. 96
Replacing the Electron Multiplier .............................................................. 106
Cleaning the Prequads ................................................................................ 107
Vacuum System Maintenance .................................................................... 109
Maintanenace of the Turbomolecular Pump ....................................... 109
Checking the Forepump Oil Level ...................................................... 109
Adding Oil to the Forepump Reservoir ............................................... 110
Decontaminating the Oil ...................................................................... 110
Replacing the Oil ................................................................................. 111
Inline Gas Purifiers ..................................................................................... 113
Changing from EI to CI Mode .................................................................... 114
Connecting the CI Gas......................................................................... 114
Changing to CI .................................................................................... 116
Leak Checking ..................................................................................... 117
Setting-Up CI ...................................................................................... 118
TroublesTroubleshooting .............................................................................. hooting .............................................................................. 125125
Overview .................................................................................................... 127
Spare Components ............................................................................... 128
Logical Troubleshooting Steps ............................................................ 128
Troubleshooting Chart ................................................................................ 130
Chromatography Related ..................................................................... 141
Spectral Related ................................................................................... 145

Clarus SQ 8 MS Hardware Guide
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Communications Related ..................................................................... 147
Forepump Related ............................................................................... 148
Message Dialogs ......................................................................................... 151
Index ..............................................................................Index ................................................................................................ 15.................. 1555
Index ........................................................................................................... 157

Warnings and
Safety Information11

Warnings and Safety Information
9
Conventions Used in this Manual
Terminology
Throughout the manual, the term ‘mass spectrometer’ or MS specifically refers to
the Clarus SQ 8 series, while for ‘GC’ Clarus 580/680 is implied.
Normal text is used to provide information and instructions.
BoldBold 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: NOTE: A note indicates additional, significant information that is provided with some
procedures.

Clarus SQ 8 MS Hardware Guide
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WARNINGWARNING We use the term WARNING to inform you about situations that could
result in personal injurypersonal injury to yourself or other persons. Details about
these circumstances are in a box like this one.
DD Warning (Warnung)
Bedeutet, daß es bei Nichtbeachten der genannten Anweisung zu
einerVerletzungVerletzung des Benutzers kommen kann.
DKDK Warning (Advarsel)
Betyder, at brugeren kan blive kvæstetkvæstet, hvis anvisningen ikke
overholdes.
EE Warning (Peligro)
Utilizamos el término WARNINGWARNING (PELIGRO) para informarle sobre
situaciones que pueden provocar daños personalesdaños personales a usted o a otras
personas. En los recuadros como éste se proporciona información
sobre este tipo de circunstancias.
FF Warning (Danger)
Nous utilisons la formule WARNINGWARNING (DANGER) pour avertir des
situations pouvant occasionner des dommages corporelsdommages corporels à
l'utilisateur ou à d'autres personnes. Les détails sur ces circonstances
sont données dans un encadré semblable à celui-ci.
II Warning (Pericolo)
Con il termine WARNINGWARNING (PERICOLO) vengono segnalate situazioni
che potrebbero provocare incidenti alle personeincidenti alle persone. Troverete
informazioni su tali circostanze in un riquadro come questo.
NLNL Warning (Waarschuwing)
Betekent dat, wanneer de genoemde aanwijzing niet in acht wordt
genomen, dit kan leiden totverwondingenverwondingen van de gebruiker.
PP Warning (Aviso)
Significa que a não observância da instrução referida poderá causar
umferimentoferimento ao usuário.

Warnings and Safety Information
11
CAUTIONCAUTION We use the term CAUTION to inform you about situations that could
result in serious damageserious damage to the instrumentto the instrument or other equipment. Details
about these circumstances are in a box like this one.
DD Caution (Achtung)
Bedeutet, daß die genannte Anleitung genau befolgt werden muß, um
einenGeräteschadenGeräteschaden zu vermeiden.
DKDK Caution (Bemærk)
Dette betyder, at den nævnte vejledning skal overholdes nøje for at
undgå en beskadigelse af apparatetbeskadigelse af apparatet.
EE Caution (Advertencia)
Utilizamos el término CAUTIONCAUTION (ADVERTENCIA) para advertir sobre
situaciones que pueden provocar averías gravesaverías graves en este equipoen este equipo o en
otros. En recuadros éste se proporciona información sobre este tipo de
circunstancias.
FF Caution (Attention)
Nous utilisons le terme CAUTIONCAUTION (ATTENTION) pour signaler les
situations susceptibles de provoquer degraves détériorationsgraves détériorations dede
l'instrumentl'instrument ou d'autre matériel. Les détails sur ces circonstances
figurent dans un encadré semblable à celui-ci.
II Caution (Attenzione)
Con il termine CAUTION CAUTION (ATTENZIONE) vengono segnalate situazioni
che potrebbero arrecare gravi dannigravi danni allo strumentoallo strumento o ad altra
apparecchiatura. Troverete informazioni su tali circostanze in un riquadro
come questo.
NLNL Caution (Opgelet)
Betekent dat de genoemde handleiding nauwkeurig moet worden
opgevolgd, ombeschadiging van het instrumentbeschadiging van het instrument te voorkomen.
PP Caution (Atenção)
Significa que a instrução referida tem de ser respeitada para evitar a
danificação do aparelhodanificação do aparelho.

Clarus SQ 8 MS Hardware Guide
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Customer Service
Company Name and Address:
PerkinElmer
710 Bridgeport Avenue
Shelton, Connecticut 06484-4794 USA
Tel: [phone] or [phone]

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 their own
expense.
NOTE: 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.
CAUTIONCAUTION The Clarus SQ 8 contains protective circuitry. Contact
PerkinElmer Service before performing any AC line tests.

Clarus SQ 8 MS Hardware Guide
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Electrical Symbols Used on Clarus SQ 8 MS Series
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.
Warning: Refer to accompanying documents.
Vacuum

Warnings and Safety Information
15
Label Location and Content
Figure 1 Front View of Clarus SQ 8 T.Figure 1 Front View of Clarus SQ 8 T.

Clarus SQ 8 MS Hardware Guide
16 Figure 2 Figure 2 Rear View of Rear View of the Clarus SQ 8 the Clarus SQ 8 T.T.

Warnings and Safety Information
17
Figure 3 Figure 3 Rear View of the Clarus SQ 8 S compaRear View of the Clarus SQ 8 S compatible with the Clarus 580 GCtible with the Clarus 580 GC
and Clarus 680 GC.and Clarus 680 GC.

Clarus SQ 8 MS Hardware Guide
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Clarus MS Safety Practices
NOTE: NOTE: This equipment requires no specified inspection or preventive maintenance to ensure
the continuous functioning of its safety features.
The Clarus SQ 8 Mass Spectrometer should be used in accordance with the instructions
provided in the hardware and software user’s guides and tutorial supplied with the
instrument. If used otherwise, the protection provided by the instrument may be impaired.
Generic Warnings
Before installing or operating a Clarus SQ 8 MS, read the following topics concerning
hazards and potential hazards. Ensure that anyone involved with installation and/or
operation of a Clarus SQ 8 MS is knowledgeable in both general safety practices for
the laboratory and safety practices for the mass spectrometer. Get advice from your
safety engineer, industrial hygienist, environmental engineer, or safety manager before
you install or use this instrument.
Moving the Clarus SQ 8 MS
WARNING WARNING
The Clarus SQ 8 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.
Electrical High Voltage
WARNINGWARNING
High voltage. High voltage. The Clarus SQ 8 MS 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 panel.