PerkinElmer Clarus SQ 8 MS Series Installation instructions

CLARUS SQ 8 MS
Hardware Guide
GAS CHROMATOGRAPHY

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Clarus SQ 8 MS
Hardware Guide

Release History
Part Number
Release
Publication Date
09931017
C
October 2017
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.
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 © 2017 PerkinElmer, Inc.
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.
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Contents
Warnings and Safety Information ....................................................7
Conventions Used in this Manual...................................................................9
Customer Service..........................................................................................12
Electromagnetic Compatibility (EMC).........................................................13
Europe ...................................................................................................13
South Korea...........................................................................................13
United States (FCC)......................................................................................14
Electrical Symbols Used on Clarus SQ 8 MS Series.............................15
Label Location and Content ..................................................................16
Clarus MS Safety Practices ..........................................................................19
Generic Warnings..................................................................................19
Moving the Clarus SQ 8 MS ................................................................. 19
Electrical High Voltage.........................................................................20
Contamination .......................................................................................24
Decontamination...........................................................................................25
Cleaning the Instrument ........................................................................25
General Laboratory Safety.....................................................................26
Compressed Gases.................................................................................26
Ventilation.............................................................................................27
Heated Zones.........................................................................................28
Using Hydrogen, Methane or Isobutane................................................28
Using Ammonia Gas .............................................................................29
Hazardous Chemicals ...................................................................................30
Definitions in Warning for Hazardous Chemicals.................................32
Temperature, Humidity, and Environment...................................................33
Operating Conditions.............................................................................33
Storage Conditions ................................................................................35
General Laboratory Safety.....................................................................35
Cleaning Requirements .........................................................................35
WEEE Instructions for PerkinElmer Products..............................................36
Pre-Installation Requirements ......................................................................37
Laboratory Space Requirements............................................................37
Environmental Requirements................................................................38
Power Requirements..............................................................................39
Gas Requirements..................................................................................40
Safety Requirements..............................................................................41

Pre-Installation Checklist..............................................................................43
Introduction ......................................................................................45
Preface..........................................................................................................47
System Overview...................................................................................47
Summary of this Guide..........................................................................48
Related Documentation.........................................................................48
Supplies, Accessories and Replacement Parts.......................................49
About the Clarus GC/MS System ...................................................51
About the Clarus SQ 8 MS System ..............................................................53
Clarus 580/680 Series GC ............................................................................55
GC Interface (Transfer Line)........................................................................56
Reference Gas Inlet.......................................................................................56
Ion Optics Path .............................................................................................57
Vacuum System............................................................................................58
Rotary Pump..........................................................................................58
Vacuum Pump Options..........................................................................59
TurboMass Software.....................................................................................61
Top Level Screen...................................................................................61
Tune Page..............................................................................................61
Analytical Column........................................................................................63
Pre-Operational Checklist.............................................................................64
Maintenance......................................................................................65
Overview ......................................................................................................68
Typical Overall Maintenance Schedule........................................................71
Daily......................................................................................................71
Weekly...................................................................................................71
Monthly.................................................................................................72
Every Six Months..................................................................................72
Yearly....................................................................................................72
Leak Checking..............................................................................................73
Tuning the Clarus MS...................................................................................76
Preparing Clarus MS for Hardware Maintenance.........................................78
Removing and Returning the Source............................................................82
Removing the Source ............................................................................82
Returning the Source.............................................................................86
Changing a Column......................................................................................88
Tools and Items Required:.....................................................................88
Physical Measurement Outside the SQ 8MS.........................................90

Alignment Using the 10 mm Positioning Gauge Tool ..........................93
Optical Column Alignment Using the Optional Plug Handle
and Sight................................................................................................95
Refilling the Reference Gas Vial..................................................................99
Items Required.......................................................................................99
Replacing a Filament..................................................................................102
Items and Tools Required....................................................................102
Source Maintenance....................................................................................107
Mass Analyzer Maintenance (PerkinElmer Service Representative Only) 112
Items and Tools Required....................................................................112
Cleaning Materials...............................................................................113
Removing and Returning the Ion Optics Assembly............................114
Replacing the Electron Multiplier ..............................................................124
Cleaning the Prequads ................................................................................125
Changing to CI ....................................................................................135
Leak Checking.....................................................................................136
Setting-Up CI.......................................................................................138
Troubleshooting..............................................................................145
Overview ....................................................................................................147
Spare Components...............................................................................148
Logical Troubleshooting Steps............................................................148
Troubleshooting Chart................................................................................150
Chromatography Related.....................................................................161
Spectral Related...................................................................................165
Communications Related.....................................................................167
Forepump Related ...............................................................................168
Message Dialogs.........................................................................................171
Index ................................................................................................175

Warnings and
Safety Information
1

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.
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.

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.
DWarning (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.
EWarning (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.
FWarning (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.
IWarning (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.
PWarning (Aviso)
Significa que a não observância da instrução referida poderá causar
um ferimento ao usuário.

Warnings and Safety Information
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.
DCaution (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.
ECaution (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.
FCaution (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.
ICaution (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.
PCaution (Atenção)
Significa que a instrução referida tem de ser respeitada para evitar a
danificação do aparelho.

Customer Service
Company Name and Address:
PerkinElmer
710 Bridgeport Avenue
Shelton, Connecticut 06484-4794 USA
Tel: [phone] or [phone]

Warnings and Safety Information
Electromagnetic Compatibility (EMC)
Europe
All information concerning EMC standards is in the Declaration of Conformity, and
these standards may change as the European Union adds new requirements.
PerkinElmer instruments have been designed and manufactured, having regard to
the state of the art, to ensure that:
•the electromagnetic disturbance generated does not exceed the level above
which radio and telecommunications equipment or other equipment cannot
operate as intended;
•it has a level of immunity to the electromagnetic disturbance to be expected in
its intended use which allows it to operate without unacceptable degradation of
its intended use.
South Korea
This device complies with MSIP (Ministry 0f Science, ICT, and Future Planning)
EMC Registration requirements. This instrument is registered as a Class A
instrument for business use only. Product seller and user should notice that this
equipment is not for house hold use.

United States (FCC)
This equipment has been tested and found to comply with the limits for a Class B
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 may cause harmful interference in which
user will be required to correct the interference at their 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.
CAUTION
ATTENTION
The Clarus SQ 8 contains protective circuitry. Contact
PerkinElmer Service before performing any AC line tests.
Le Clarus SQ 8 contient des circuits de protection. Contactez le
service PerkinElmer avant d'effectuer des tests de ligne AC.

Warnings and Safety Information
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.
Avertissement: Risque de choc électrique
Warning: Hot surface.
Avertissement: Surface chaude.
Warning: Refer to accompanying documents.
Avertissement: Se référer aux documents d'accompagnement
Vacuum

Label Location and Content
Figure 1 Front View of Clarus SQ 8 T.

Warnings and Safety Information
Figure 2 Rear View of the Clarus SQ 8 T.
Attention
Ne limitez pas l'admission ou
l'échappement d'air.
Avertissement
RETIRER LE CAPUCHON EN
BLANCHE DE VENT LINE À
L'INSTALLATION.
Attention
Cette unité contient les circuits protecteurs.
Contactez le personnel de service qualifié de
PerkinElmer avant d'exécuter n'importe quelle
ligne essais à C.A.
Avertissement
La continuité du circuit de mise à
la terre est indispensable au
fonctionnement en toute sécurité
de l'équipement. Ne faites jamais
fonctionner l'équipement lorsque
le conducteur de mise à la terre
est déconnecté.
Avertissement
Démontez la corde de
courant alternatif du
débouché avant d'enlever
toute la couverture ou
pièces. N'actionnez pas
l'instrument avec aucune
couverture ou pièces
enlevées.

Figure 3 Rear View of the Clarus SQ 8 S compatible with the Clarus 580 GC
and Clarus 680 GC.
Attention
Ne limitez pas l'admission ou
l'échappement d'air.
Avertissement
Démontez la corde de courant
alternatif du débouché avant
d'enlever toute la couverture
ou pièces. N'actionnez pas
l'instrument avec aucune
couverture ou pièces enlevées.
Avertissement
RETIRER LE CAPUCHON EN
BLANCHE DE VENT LINE À
L'INSTALLATION.
Attention
Cette unité contient les circuits protecteurs.
Contactez le personnel de service qualifié de
PerkinElmer avant d'exécuter n'importe quelle
ligne essais à C.A.
Avertissement
La continuité du circuit de mise à la terre est indispensable au fonctionnement en
toute sécurité de l'équipement. Ne faites jamais fonctionner l'équipement lorsque le
conducteur de mise à la terre est déconnecté.