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CC
LARUSLARUS
SQ 8 MSSQ 8 MS
Hardware GuideHardware Guide
GAS GAS CHROMATOGRACHROMATOGRAPHY PHY
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Clarus SQ 8 MSClarus SQ 8 MS
Hardware GuideHardware Guide
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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: info@perkinelmer.com
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.
Copyright InformationCopyright 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 © 2011 PerkinElmer, Inc.
TrademarksTrademarks
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 7 is a trademark of the Microsoft Corporation
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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
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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
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Contents
5
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
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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
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Warnings and
Safety Information
11
Page 10
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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.
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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
einer VerletzungVerletzung 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 tot verwondingenverwondingen van de gebruiker.
PP
Warning (Aviso)
Significa que a não observância da instrução referida poderá causar
um ferimentoferimento ao usuário.
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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
einen GeräteschadenGeräteschaden 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, om beschadiging 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.
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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: (800) 762-4000 or (203) 762-4000
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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.
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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
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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.
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Clarus SQ 8 MS Hardware Guide
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Figure 2 Figure 2 Rear View of Rear View of the Clarus SQ 8 the Clarus SQ 8 T.T.
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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.
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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.
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Warnings and Safety Information
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WARNINGWARNING
Lethal voltages are present at certain areas within the instrument.
Internal maintenance of the instrument should only be performed
by a PerkinElmer service engineer or similarly authorized and
trained person. When the instrument iWhen the instrument is connected to line s connected to line power,power,
opening the instrument covers iopening the instrument covers is likely to expose live pars likely to expose live parts. ts. EvenEven
when the power switch is off, high voltages can still be present.when the power switch is off, high voltages can still be present.
Capacitors inside the instrument may still be charged even Capacitors inside the instrument may still be charged even if theif the
instrument has been disconnected from all voltage sources.instrument has been disconnected from all voltage sources.
WARNINGWARNING
Connect the Clarus SQ 8 MS 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 WARNING
Customers should nevernever operate the Clarus SQ 8 MS with any
covers or parts removed. Only a trained PerkinElmer Service
Engineer or similarly trained and authorized person may need to
operate the Clarus SQ 8 MS with covers or parts removed as they
service it.
WARNINGWARNING
Do not Do not make adjustments, replacements or repairs to the Clarus
SQ 8 MS except as described in the supplied user manuals. Only a
PerkinElmer Service Engineer or similarly trained and authorized
person should be permitted to service the Clarus SQ 8 MS.
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Clarus SQ 8 MS Hardware Guide
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WARNING WARNING
For protection against fire hazard, only replace a fuse with a fuse
with the same type and rating. For example, a 10 amp fuse for
120 V and a 5 amp fuse for 240 V.
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 circuit ground to earth.
Use only three-prong outlets with common earth ground connections. For details, refer to
the descriptions in the
Clarus GC Installation Guide (P/N 09936590 or 09936779)
.
•
Servicing of electrical components within the mass spectrometer should be
performed
onlyonly
by a PerkinElmer Service Representative.
•
Servicing of the incoming AC power line components in your laboratory
should be performed
onlyonly
by a licensed electrician.
WARNING WARNING
Electrical shock hazard.To prevent electrical shock, disconnectTo prevent electrical shock, disconnect
the power cord from the AC outlet before servicing.the power cord from the AC outlet before servicing.
Under no circumstances should circuit boards be removed or inserted unless the
instrument is disconnected from line power.
Contamination
CAUTIONCAUTION
Never touch manifold components with your fingers. This will
introduce contaminants into the system.
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Warnings and Safety Information
21
CAUTIONCAUTION
To prevent Clarus SQ 8 MS contamination, always wear clean,
lint-free, powder-free nitrile, nylon, or PVC gloves before
touching, removing, or replacing parts on or in the vacuum
manifold assembly. These parts include the source, filament, prequads, analytical quads, and electron multiplier. Always hold the
EI or CI source by its handle. Never touch these parts with
ungloved (bare) fingers since this will introduce contaminants
into the system.
Decontamination
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.
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.
Follow the “Decontamination of Instrumentation and Associated Sub-assemblies”
procedure and complete the “Certificate of Decontamination.” The certificate is used
to certify the decontamination process was completed before equipment can be
returned to PerkinElmer. These documents are available on the PerkinElmer public
website:
Procedure:
http://las.perkinelmer.com/Content/technicalinfo/dts_instrumentdeconphttp://las.perkinelmer.com/Content/technicalinfo/dts_instrumentdeconp
rocedure.pdf rocedure.pdf
Certificate form:
http://las.perkinelmer.com/Content/technicalinfo/dts_perkinelmercertif http://las.perkinelmer.com/Content/technicalinfo/dts_perkinelmercertif
icationofdecontaminationform.pdf icationofdecontaminationform.pdf
If you do not have access to the internet and are located in the U.S., call toll free at
1-800-762-000 or (+1) 203-925-4602, 8:30 a.m. – 7 p.m. EST and speak to
Customer Support.
In Canada, call toll free at 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.
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Clarus SQ 8 MS Hardware Guide
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Compressed Gases
WARNINGWARNING
Explosive hazard. Explosive hazard. Cylinders (tanks) of compressed gases should
be handled with extreme care. Gas cylinders can be hazardous if
mishandled.
Avoid banging the valves and ensure that the correct valves and gauges are installed.
Gas cylinders should be stored (and placed) outside the laboratory and connected to
the instrument through specially cleaned copper tubing. Use care to prevent kinking
or stressing the gas tubing. For safety, cylinders should be firmly clamped in an
upright position.
WARNINGWARNING
Explosive hazard. Explosive hazard.
When using hydrogen, either as the
combustion gas for a flame ionization detector or as a carrier
gas, special care must be taken to avoid buildup of explosive
hydrogen/air mixtures either in the GC oven or the Clarus SQ 8
vacuum manifold.
Ensure that all hydrogen line couplings are leak-free and do not allow hydrogen to
vent within the oven.
Ventilation
WARNING WARNING
Hazardous vapors Hazardous vapors. When analyzing hazardous compounds, such
as pesticides, it is necessary to arrange for venting of the mass
spectrometer effluent from the fore pump exhaust into a fume
hood or charcoal trap.
In addition, adequate ventilation must be provided, particularly if a liquid nitrogen
or carbon dioxide sub-ambient accessory is in constant use. The area underneath the
bench (around the fore pump) should be well ventilated . An oil separation filter and
charcoal trap should be installed at the outlet of the fore pump exhaust to prevent
contamination if fume hood venting is unavailable.
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Warnings and Safety Information
23
To ensure adequate cooling of the instrument electronics, do not obstruct the gap at
the base of the Clarus MS/Clarus GC, in the system (for example, the TurboMatrix
ATD or and if practical, leave a minimum 6-inch clearance between each instrument
Headspace). This does not include the Clarus MS/Clarus GC since they are
connected.
Heated Zones
WARNINGWARNING
Risk of burns. Risk of burns. Never touch a heated Clarus SQ 8 MS transfer
line or a GC injector cap with bare (unprotected) fingers.
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 Clarus SQ 8 manifold. Proper
cooling of the transfer line may take from 1/2 to 1 hour.
Using Hydrogen, Methane or Isobutane
WARNING WARNING
Explosive Hazard. 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.
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.
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Clarus SQ 8 MS Hardware Guide
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Using Ammonia Gas
WARNING WARNING
Hazardous gas vapors 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
charcoal trap.
Hazardous Chemicals
WARNING 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 Sheets (MSDS) supplied with the
solvents, chemicals, and pump oils.
Be aware that the chemicals that you use in conjunction with the Clarus SQ 8 may
be hazardous.
DO NOT DO NOT
store, handle, or work with any chemicals or hazardous
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.
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Warnings and Safety Information
25
WARNINGWARNING
When using toxic samples, the mechanical pump oil is toxic
waste.
WARNING 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 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.
Definitions in Warning for Hazardous Chemicals
Responsible bodyResponsible 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].
OperatorOperator. “Person operating equipment for its intended purpose.”
[per EM/IEC 61010-1].
OSHA:OSHA:
Occupational Safety and Health Administration (United States)
ACGIH:ACGIH: American Conference of Governmental Industrial Hygienists
COSHH:COSHH: Control of Substances Hazardous to Health (United Kingdom)
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Clarus SQ 8 MS Hardware Guide
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Temperature, Humidity, and Environment
Operating Conditions
CAUTIONCAUTION
The Clarus SQ 8 MS is designed for indoor use only.
CAUTIONCAUTION
Do not operate the mass spectrometer in a Cold Room or a refrigerated
area. Clarus SQ 8 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).
The Clarus SQ 8 MS will operate safely between 5°C and 40 °C (41 °F
and 104 °F).
If operating at ambient temperatures 10°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 -400 to 2000 m (-1,312 to 6,562 feet).
WARNING WARNING
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.
Pollution Degree
Clarus SQ 8 MS will operate safely in environments that contain non-conductive
foreign matter up to Pollution Degree 2 in EN/IEC 61010-1.
Storage Conditions
The mass spectrometer may be stored under the following conditions:
•
ambient temperature is -20 °°C to +60 °C (-4 to 140 °F)
Page 29
Warnings and Safety Information
27
•
ambient relative humidity is 20 to 80%, non-condensing
•
altitude in the range of -400 to 12,000 m (-1,312 to 39,370 feet).
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 eyewash fountain, spill cleanup equipment, etc.).
Cleaning Requirements
Exterior surfaces of the MS may be cleaned with a soft cloth, dampened with a mild
detergent and water solution. Do notnot use abrasive cleaners or solvents.
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 instrument.
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Clarus SQ 8 MS Hardware Guide
28
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.
Page 31
Warnings and Safety Information
29
Pre-Installation Requirements
Laboratory Space Requirements
Size WeightSize Weight
Clarus SQ 8 T, C, and SMS32 cm (13 in.) wide x 50 cm
(20 in.) high x 77 cm (30 in.) deep
46.8 kg (102 lb)
Clarus 580 GC 32 cm (13 in.) wide x 46 cm
(18 in.) high x 77 cm (30 in.) deep
48 kg (105 lb)
Forepump 30.5 cm (12 in.) wide x 44 cm (17.3
in.) high x 72 cm (28.4 in.) deep.
25.9 kg (57 lb)
Clarus 680 GC 99 cm (39 in.) wide x 53 cm
(21 in.) high x 82 cm (32 in.) deep
49 kg (108 lb)
Autosampler Tower 13 cm (5 in.) wide x 36 cm (14 in.)
high x 24 cm (9.5 in.) deep
4.5 kg (10 lb)
Physical Configuration Single unit for use on standard laboratory bench that can be
interfaced to a computer and printer.
Peripherals, Printers etc. Allow at least 94 cm (36 in.) on either side of the GC/MS
to accommodate additional equipment (for example, the
computer).
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Clarus SQ 8 MS Hardware Guide
30
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 SQ 8 T and C 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 SQ 8 S the AC power on/off
switch is on the back of the instrument.
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 Environment Install the GC/MS in an indoor laboratory environment that
is 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 SQ 8 C, SQ 8 T,
and SQ 8 S systems unless the turbomolecular pump is
water cooled, and between 10 °C and 35 °C (50 °F and 95
°F) for Clarus SQ 8 C, SQ 8 T, and SQ 8 S systems with
water cooling.
Page 33
Warnings and Safety Information
31
Power Requirements
Power Consumption Clarus MS: 1000 VA (volt-amps)
Clarus GC: 2400 VA (volt-amps)
Add 100 VA for the computer and 108 VA for a printer.
Power Consumption
(with optional oven
heater)
See below listing for the Clarus 580/680. Add 100 VA for the
computer and 108 VA for the printer.
Power Specification 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:
Clarus MS:
120 VAC ±10 % @ 50/60 Hz ±1 % 1000 VA maximum
230 VAC ±10 % @ 50/60 Hz ±1 % 1000 VA maximum
Clarus GC:
For GC with slow heating rate as standard;
120 VAC ± 10% @ 50/60 Hz ± 1% @ 20 Amps, 2400 VA
maximum
230 VAC ± 10% @ 50/60 Hz ± 1% @ 10 Amps, 2400 VA
maximum
For GC with optional oven heater for fast heating rate;
220 VAC ± 5% @ 50/60 Hz ± 1% @ 15 Amps, 3120 VA
maximum
230 VAC ± 5% @ 50/60 Hz ± 1% @ 16 Amps, 3120 VA
maximum
240 VAC ± 5% @ 50/60 Hz ± 1% @ 13 or 16 Amps, 3120
VA max
Instruments and peripherals should not be connected to
circuits with large inductive or large and frequent loads (for
example, large motors, discharge lamps, photocopy systems,
radio transmitters, etc.).
Page 34
Clarus SQ 8 MS Hardware Guide
32
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
equipments, such as computers and printers, should be
connected per their specifications.
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.
CAUTIONCAUTION
For all gases delivered to the mass spectrometer, always use
copper tubing that is free of grease, oil, and organic material. If in
doubt about the condition of your tubing, clean it before use.
Carrier Gases
GC/MS Carrier
Gases:
Helium
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.
A number 1A (200 ft3) gas cylinder should be used for all carrier
gases with a high-purity, stainless-steel diaphram, 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 99.95%.
Page 35
Warnings and Safety Information
33
Ammonia
Methane
Isobutane
The gas delivery pressure required is 15 psi (103 kPa) to the
bulkhead fitting (1/8 in. Swagelok) on the mass spectrometer.
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 trap.
A high-purity, stainless-steel diaphragm, two-stage regulator is
required for methane and isobutane with a final delivery pressure of
15 psi (103 kPa). Clean tubing must be used. It must be solventwashed 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.
Safety Requirements
Gas Delivery
Lines
Copper tubing that is free of grease, oil and organic
material must always be used with the Clarus 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.
Page 36
Clarus SQ 8 MS Hardware Guide
34
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.
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 7 are changed. Consult the latest Product Description
List for current requirements.
NOTE: 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 already
have been configured.
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:
•
Lenovo ThinkCentre® M58p
•
3.0 GHz Intel® Core 2 Duo Processor
•
4 GB of Random Access Memory (RAM)
Page 37
Warnings and Safety Information
35
•
Integrated video, Intel® GMA4500
•
Hard disk with 2.0 GB free space
•
1 RS-232 port
•
2 RJ-45 10/100Base-T ports
•
Lenovo USB Keyboard and Lenovo USB optical mouse with scroll
Operating System
Windows 7 Professional
Software
TurboMass Software.
Instrument Firmware Versions
Internal dotLINK
Printer
HP LaserJet P4014 Printer Series (CB506A)
NOTE: NOTE: Using any printers other than the one recommended above may not
correctly display the Communiqué reports.
Page 38
Clarus SQ 8 MS Hardware Guide
36
Pre-Installation Checklist
MODEL:
__________________________
DATE:
_____________________
CUSTOMER: __________________________________
SPO#: __________________________________
Requirements Requirements OK OK Needs Needs Prior Prior To To InstallationInstallation
Customer Responsibility
Lab Space Requirements
Power Requirements
Gas Requirements
Environmental
Requirements
Safety Requirements
Preparation of Samples
(Customer Responsibility)
Computer Configuration
Customer Experience
Page 39
Introduction
22
Page 40
Page 41
Introduction
39
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 7 computer.
System Overview
The system consists of:
•
Clarus GC
•
Clarus MS
•
Computer
•
TurboMass Software
•
Foreline Pump
Page 42
Introduction
40
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 SQ 8 MS 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 ST8 family of manuals includes the following:
•
Clarus GC/MS Tutorial
(part number 09931018): The tutorial provides a step-
by-step guide to performing a number of tasks using the instruments and
software.
•
TurboMass Software User’s Guide
(part number 09931016): A comprehensive
manual describing the functionality of each part of the TurboMass software. It
describes the keys and fields on each screen.
Page 43
Warnings and Safety Information
41
•
Clarus SQ 8 MS Hardware Manual
(part number 09931017): 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.
Supplies, Accessories and Replacement Parts
Supplies, accessories, and replacement parts can be ordered directly from
PerkinElmer using the eight-digit part numbers provided in this manual. To place an
order for supplies and many replacement parts, request a free catalog, or ask for
information visit our website.
www.perkinelmer.com/supplies
The most up-to-date information on part numbers, product brochures, spare parts
and application notes are located in the PerkinElmer website.
• If you are located
within
the U.S., call toll-free: (800) 762-4000, Monday Friday, 8:30 a.m. to 7 p.m. EST. Your order will be shipped promptly, usually
within 24 hours.
• If you are located
outside the U.S.
, call your PerkinElmer sales office.
Page 44
Clarus SQ 8 MS Hardware Guide
42
Page 45
About the
Clarus GC/MS System
33
Page 46
Page 47
About the Clarus SQ 8 MS System
45
About the Clarus SQ 8 MS System
The Clarus SQ 8 mass spectrometers (MS) are compact benchtop instruments that
produce positive identification and quantitation of compounds separated by the
Clarus 580 and 680 series gas chromatographs, respectively. Even if the compounds
coelute, the mass spectrometer can still positively identify and quantitate each
compound based on spectral data. Clarus SQ 8 C MS is designed to include both
Electron Impact (EI) ionization as well as chemical ionization (CI). The Clarus SQ 8
S and SQ 8 T MS are electron impact (EI) only.
Figure 4 Figure 4 Clarus SQ 8 Clarus SQ 8 MS with Clarus MS with Clarus 680 GC.680 GC.
The Clarus MS system is controlled by a PC using TurboMass Software. The
application runs in a Microsoft Windows 7 Professional 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 09931016), supplied
with the system.
Page 48
Clarus SQ 8 MS Hardware Guide
46
Figure 5 Figure 5 Clarus SQ Clarus SQ 8 Mass 8 Mass Spectrometer.Spectrometer.
A high-performance, research-grade analytical quadrupole mass analyzer with a
quadrupole prefilter assembly transmits only those ions having your selected massto-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 detected by the electron multiplier detector system.
Page 49
About the Clarus GC/MS System
47
Clarus 580/680 Series GC
The Clarus 580/680 Series 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 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 6 Figure 6 Clarus 68Clarus 680 GC.0 GC.
The Programmed Pneumatic Control (PPC) Version of the The Programmed Pneumatic Control (PPC) Version of the Clarus 580/680 SeriesClarus 580/680 Series
GC 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.
The Clarus 500/600 Series 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
Page 50
Clarus SQ 8 MS Hardware Guide
48
autosampler can run up to 15 injections per vial from as many as 108 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.
GC Interface (Transfer Line)
The detector end of a capillary GC column in the Clarus 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
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.
Figure 7 Figure 7 The transfer The transfer line.line.
Reference Gas Inlet
The MS 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. The reference gas vial is located toward the front of the instrument
underneath the top cover andnotnot visible on the front panel.
Page 51
About the Clarus GC/MS System
49
Ion Optics Path
Ion SourceIon Source
The Clarus MS ion source consists of a removable ion source. The
Clarus SQ 8 C also supports a CI source. 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 AnalyzerMass 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 Under no circumstancescircumstances
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.
DetectorDetector
The detector consists of a series of focusing lenses, a 270 ⁰ turn and a
high voltage conversion dynode. The ions hit the high voltage
conversion dynode and are converted to electrons. The electrons are
directed into a series of diecrete dynodes with amplify the signal.
Finally the signal is collected and transferred to the Data system.
ElectronicsElectronics
The Clarus MS electronics consist of an Ethernet port in the PC, an
embedded processor & digital I/O board, analog board (GC/MS),
backplane board, head amplifier, and high voltage and low voltage
power supply boards. The embedded processor controls all aspects of
instrument and data acquisition.
Page 52
Clarus SQ 8 MS Hardware Guide
50
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 is inside the instrument.
Rotary Pump
The Clarus MS has a 3 m3/hr computer controlled mechanical pump. The
turbomolecular 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.
0
l
l
l
0
Mass Sp ectromete r Mass Sp ectromete r
Conn ection PortConnec tion Port
Exhaust Por tE xhaust Por t
Oil Fill er Pl ugOil F iller Plug
Drai n PlugDrai n Plug
Oil LevelOil Level
Indi cator In dicato r
Gas Ball astGas Bal last
Swit chSwitch
On/Off On/Off
Swit chSwitch
Mode Sele ctionMo de Selec tion
Swit chSwitch
MaxMax
MinMin
Voltage Sele ction Swi tchVo ltage Sel ection Sw itch
(on the sid e)( on the side)
Figure 8 Figure 8 The rotary The rotary (fore) pump.(fore) 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.
Connect the rotary pump exhaust to a line vented to the atmosphere outside the
laboratory or use an appropriate exhaust line filter.
Page 53
About the Clarus GC/MS System
51
CAUTIONCAUTION
The AC line cord for the rotary vane pump must be plugged into the
designated receptacle on the back of the Clarus MS. The pump is
controlled by the TurboMass software.
Connecting the vacuum hose to the exhaust connection of the rotary
pump will severely contaminate the Clarus MS.
Vacuum Pump Options
The Clarus SQ 8 MS offers two different vacuum pump capacities.
Turbomolecular pumps are high-speed turbines which transport the sample and
carrier gas molecules away from the mass spectrometer.
•
Clarus SQ 8 S - The 75 L/sec turbomolecular pump supports Electron
Ionization operation (EI) and has optional water cooling.
•
Clarus SQ 8 T – All of the functions and options of the SQ 8 S with a 255
L/sec turbomolecular pump for higher column flow rates, pump-down time
under three minutes, and lower detection limits
•
Clarus SQ 8 C - All of the functions and options of the SQ 8 T with positive
and negative Chemical Ionization (CI) operation.
Pumping Down a Turbomolecular Pump Vacuum System
Select Pump/VacuuPump/Vacuum System m System OnOn from the OptionsOptions menu on the Tune page.
The menu name will change from Pump/VacuuPump/Vacuum System m System OnOn to
Vent/Vacuum System Off Vent/Vacuum System Off
, and the system will begin its pump-down
sequence. Once OPERATEOPERATE is enabled, it remains enabled unless the
Vent/Vacuum System Off Vent/Vacuum System Off command is given.
Venting the Turbomolecular Pump Vacuum System
1. Cool the source and inlet to below 100 °C.
2. Select Vent/Vacuum System Off Vent/Vacuum System Off from the OptionsOptions menu on the Tune
page, and confirm that you want to vent the system.
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Clarus SQ 8 MS Hardware Guide
52
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 pump will operate at somewhat higher pressures,
typically below 4x10-5 Torr.
Page 55
About the Clarus GC/MS System
53
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.
Page 56
Clarus 600 GC-MS User’s Guide
54
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.
Page 57
About the Clarus GC/MS System
55
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.
Page 58
Clarus SQ 8 MS Hardware Guide
56
Pre-Operational Checklist
This checklist provides you with a list of items to check to make sure everything is
in working order before you begin to use Clarus.
Item OKItem 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?
Page 59
Maintenance
44
Page 60
Page 61
Overview
WARNINGWARNING
High electrical voltage is High electrical voltage is present inside the mass specpresent inside the mass spectrometer.trometer. 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.
WARNINGWARNING
Disconnect AC power cord from outlet before removing any cover or
parts. Do
notnot
operate the instrument with any covers or parts removed.
WARNINGWARNING
Do not not attempt to make adjustments, replacements or repairs to this
instrument except as described in the accompanying user
documentation.
NOTE: NOTE: This equipment requires no specified inspection or preventive maintenance to ensure
the continuous functioning of its safety features.
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.
Page 62
Clarus SQ 8 MS Hardware Guide
60
•
Use tweezers and pliers whenever possible.
•
If nylon or cotton gloves are used, prevent leaving fibers in sensitive areas.
NEVER 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.
WARNINGWARNING
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.
Page 63
Maintenance
61
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.
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Clarus SQ 8 MS Hardware Guide
62
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 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.
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Maintenance
63
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
StartStart
button at the
bottom left of the screen and select TurboMassTurboMass under the
Programs/TurboMass/TurboMass
path, or double-click on the TurboMass icon if
it is on your Windows desktop.
The initial TurboMass window is displayed.
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64
4.
Display the TunePage dialog by clicking .
The TunePage dialog is displayed.
5.
Make sure the Tune parameters are similar to the values displayed.
NOTE: NOTE:
The inlet and source temperatures should be less than 100°C only when venting the
system.
6. Click Press for OperatePress for Operate next to the red indicator box.
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Maintenance
65
The indicator box color changes to green and the name of the button changes
to Press for Standby.
7. Select PumpPump from the OptionsOptions menu.
This starts the forepump and the turbomolecular pump. 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 StandbyPress 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.
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66
Tuning the Clarus 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 displayed in the top right-center 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 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.
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Maintenance
67
To display the Tune page:
1. While displaying TurboMass sample list screen click .
The TunePage displays.
2. Turn on the filament and high voltages by clicking Press for OperatePress 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)UltraTune/Custom (AutoTune) from the OptionsOptions menu, then click
StartStart
.
You will hear a click when the reference gas solenoid valve opens and
AutoTune begins. Upon completion, the message AutoTune completedAutoTune completed
successfullysuccessfully is displayed.
4. Click OKOK.
5.
Select
Reference Gas OnReference Gas On
from the
GasGas
menu to remove the check mark (),
or click to set it in the
upup
position.
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68
6. Save this new TuneTune of the instrument by selecting Save AsSave As from the File
menu and entering a name for this tune in the File nameFile name field.
A way to keep track of the tunes is to use dates for the file names.
7. Click SaveSave.
Your mass spectrometer is now Tuned. To ensure proper operation, check the
mass calibration.
Preparing Clarus 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 TuneTune window.
2.
If the Press for StandbyPress for Standby button is green (indicating an operating instrument),
switch it off by clicking on it.
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Maintenance
69
Cool the Transfer Line, GC Column Oven, and the Source
WARNINGWARNING
The transfer line, GC oven, and source are HOT 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.
1. On the left side of the Tune page enter 2020 in the Inlet Line TemperatureInlet Line Temperature to
cool the GC Interface (transfer line).
CAUTIONCAUTION
If the Clarus GC is off, then the PPC control is off and no gas is
flowing through the system.
2. Open the GC oven door to cool the column oven.
3. On the TuneTune page, set the source temperature by entering 2020 in the SourceSource
TempTemp field.
4. Allow the transfer line, column oven, and source to cool before touching them.
WARNINGWARNING
Remember, the transfer line was heated and it may take at least
10 to 20 minutes to cool.
CAUTIONCAUTION
Avoid venting to air whenever possible. This eliminates the
introduction of oxygen and water vapor into the mass
spectrometer. The Clarus MS should be vented with UHP
nitrogen (99.9995%). Helium should not not be used. To properly
connect a source of dry nitrogen to the instrument order the
manifold venting kit (Part No. N6470045).
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70
Vent the System
1.
Once both the Inlet Line and Source temperatures have dropped below 100 °C,
select
Vent/Vacuum System Off Vent/Vacuum System Off
from the
OptionsOptions
menu.
2.
The Vent Pump dialog appears. All pumps are turned off.
3. Click OKOK.
4. Observe the Vacuum Pressure Gauges status on the Tune window.
5.
The gauge goes to
ZEROZERO
after the turbopump reaches 50 % speed and the vent
valve is opened.
NOTE: NOTE:
Mass Spectrometer venting may take several minutes depending on the helium flow
and/or vent gas flow into the manifold.
6. The system is now vented to atmosphere (or optional dry gas).
Turn off the GC Carrier Gas
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.
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Maintenance
71
Removing and Returning the Source
CAUTIONCAUTION
To prevent contamination of the mass spectrometer, always wear clean,
lint-free, powder-free nitrile, nylon, or PVC gloves before touching,
removing or replacing parts. Hold the source by its handle only. Never
touch these parts with ungloved (bare) fingers, as this will introduce
contaminants into the system.
Removing the Source
To remove the source, follow this procedure:
1.
Prepare the mass spectrometer for maintenance as described in Preparing the
Clarus MS for Hardware Maintenance on page 68.
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.
WARNINGWARNING
Risk of burns. Risk of burns. Never touch a heated mass spectrometer transfer line or
a GC injector cap with unprotected (bare) fingers.
4.
Pull the inner transfer line tube back 25 mm (1 inch).
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72
1/4-inch Nut1/4-inch Nut
ColumnColumn
Inner Trans fer TubeInner Trans fer Tube
Pul l Bac kPul l Bac k
Figure 9Figure 9 Pulling back the inner transfer tube.Pulling back the inner transfer tube.
5. Open the Clarus SQ 8 MS access door.
6.
Hold the source by the edge and rotate it counter clockwise.
Figure 10 Figure 10 Rotating Rotating the sourthe source.ce.
7. Carefully pull out the source.
Access DoorAccess Door
SourceSource
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Maintenance
73
Figure 11 Figure 11 Removing Removing the source.the source.
8.
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.
Figure 12 Figure 12 The source placed in The source placed in an upright position.an upright position.
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Clarus SQ 8 MS Hardware Guide
74
Returning the Source
CAUTIONCAUTION
To prevent contamination of the mass spectrometer, always wear clean,
lint-free, powder-free nitrile, nylon, or PVC gloves before touching,
removing or replacing parts. Hold the source by its handle only. Never
touch these parts with ungloved (bare) fingers, as this will introduce
contaminants into the system.
1. Carefully hold the source by its edges.
2.
Align the red dot on the source handle with the red dot on the instrument panel
and rotate the source clockwise until it locks into position.
Figure 13 Figure 13 Lining up Lining up the red the red dots.dots.
3.
Push the inner transfer line tube back.
4. Using a 9/16-inch wrench, tighten the ¼-inch nut on the transfer line.
5.
Close the Clarus SQ 8 MS access door.
Red dotsRed dots
alignedaligned
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Maintenance
75
Changing a Column
This procedure outlines the steps required to properly position the end of the column in
the Source and connect the column to the MS Transfer Line tube fitting inside the GC
oven.
CAUTIONCAUTION
To prevent contamination of the mass spectrometer, always wear clean,
lint-free, powder-free nitrile, nylon, or PVC gloves when handling the
part of the capillary column that will be inserted into the MS Transfer
Line. Never touch these parts with ungloved (bare) fingers, as this will
introduce contaminants into the system.
Tools and Items Required:
NOTE: NOTE: Do not not use a 100% Graphite ferrule to connect the column since it is a porous
material that will allow air to diffuse into the MS system and prevent a high vacuum
from being attained inside the system.
•
9/16 inch wrench
•
1/4 inch wrench
•
5 mm wrench
•
One 1/16 inch Column Nut
•
One Graphite/Vespel ferrule appropriately sized for the capillary column i.d.
that you will be using. (</= 0.25 mm i.d. columns require a 0.4 mm i.d. ferrule
and >/= 0.32 mm i.d columns require a 0.5 mm i.d. ferrule.)
•
Optional Plug Handle and Sight (P/N N6480380)
NOTE: NOTE: Please read the following guidelines in entirety prior to attempting the procedure for
the first time. Following these guidelines at all times when performing this procedure
will ensure that contaminants entering your MS system will be minimized, vacuum
leaks will be minimized and detector response (sensitivity) will be maximized.
NOTE: NOTE: The placement of the outlet end of the column relative to its position inside the source
is a critical parameter for maximizing peak responses in your application. Follow this
procedure closely to ensure that you achieve the correct column placement inside the
source. Failure to do so may result in less than optimal detector response of target
compounds in your analysis.
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Clarus SQ 8 MS Hardware Guide
76
CAUTIONCAUTION
Prior to removing the source from the Clarus SQ 8 MS instrument (for example,
to change a filament or clean the source), the column must be pulled back from
its placement inside the source. This is conveniently achieved by loosening the
large nut on the Transfer Line tube assembly so that the entire Transfer Line
tube assembly can be pulled back from the source. It is not necessary to loosen
the column nut as this may disrupt its proper positioning inside the source after
the source is reinstalled. The source will not be able to be removed or
reinstalled if the Transfer Line tube assembly is not pulled back first.
There are three different recommended techniques that may be used to position and
connect the capillary column. Each of the three techniques is outlined in the following
procedure. Use the technique that you are most comfortable with.
The three different techniques are:
1.
Physical measurement outside the SQ 8MS
2. Alignment using the 10 mm gauge tool (supplied with the SQ 8 MS
instrument)
3.
Optical Column Alignment Using the Optional Plug Handle and Sight (P/N
N6480380)
Physical Measurement Outside the SQ 8MS
CAUTIONCAUTION
To prevent contamination of the mass spectrometer, always wear clean,
lint-free, powder-free nitrile, nylon, or PVC gloves when handling the
part of the capillary column that will be inserted into the MS Transfer
Line. Never touch these parts with ungloved (bare) fingers, as this will
introduce contaminants into the system.
1. Slide an injector septum over the outlet end of the capillary column to use it as
a positioning indicator aid.
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Maintenance
77
Figure 14 Figure 14 Location of septum Location of septum on capillary column.on capillary column.
2. Slide a 1/16 inch column nut over the outlet end of the column.
3. With the tapered end facing towards the column nut, slide a graphite/vespel
ferrule over the outlet end of the column.
4. Using the edge of a wafer scribe, score the outside surface of the column
perpendicular to its length approximately 2 inches from the end and carefully
break it off and discard the cut off piece of column. Jagged or angled cuts should
be avoided. See
Figure 15
for examples of good cuts and bad cuts.
Figure 15Figure 15 Good cuts and bad cutsGood cuts and bad cuts
5. Use a lint-free wipe pre-soaked with a small amount of methanol to wipe the
outside of the column a few times to remove surface contamination.
6. Place the column onto a clean, lint-free surface on the bench top. Measure exactly
34.434.4
cm from the outlet end of the column to the front side of the septum.
7. Confirm that the Source is fully installed in the instrument. If it is not, install
the source into the instrument. See Removing and Returning the Source
on page 71.
Bad CutsBad Cuts
Good CutGood Cut
SeptumSeptum
Graphite/VGraphite/Vespel espel FerruleFerrule
Column NutColumn Nut
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Clarus SQ 8 MS Hardware Guide
78
8. Insert the column into the MS Transfer Line tube and carefully slide it
partially
toward the source. Be careful not to move the septum.
9. With the column
partially
inserted, engage the threaded column nut onto the
Transfer Line tube fitting until it is just finger-tight.
10. Slide the column into the Transfer Line tube until the septum is aligned at a
distance exactly 10 mm away from the end of the column nut. See
Figure 16
.
Figure 16 Figure 16 Measuring from the outlet of the column to the froMeasuring from the outlet of the column to the front of the septum.nt of the septum.
11. Using the 5 mm and 1/4 inch crescent wrenches, tighten the column nut until
the ferrule is crimped onto the column. See Figure 17.
Figure 17 Figure 17 Tightening the Tightening the column nut.column nut.
metric
10
20 30 40 50 60
70
8
Slide the column back until theSlide the column back until the
septum is 10 mm f rom nut.septum is 10 mm from nut.
1/16-inch Column Nut1/16-inch Column Nut
SeptumSeptum ColumnColumn
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Maintenance
79
12. The column is now installed the MS may be pumped down. Confirm that the
proper vacuum level is reached (on the TurboMass software Tune Page).
13. After initially heating the GC oven through one or two analysis cycles, the
column nut may loosen. Re-tighten the column nut. After re-tightening, the
column nut should not loosen any more.
Alignment Using the 10 mm Positioning Gauge Tool
CAUTIONCAUTION
To prevent contamination of the mass spectrometer, always wear clean,
lint-free, powder-free nitrile, nylon, or PVC gloves when handling the
part of the capillary column that will be inserted into the MS Transfer
Line. Never touch these parts with ungloved (bare) fingers, as this will
introduce contaminants into the system.
NOTE: NOTE: The 10 mm positioning gauge tool is supplied with the instrument.
1. Slide an injector septum over the outlet end of the capillary column to use it as a
positioning indicator aid. Slide the septum approximately 40 mm up the column.
2. Slide a 1/16 inch column nut over the outlet end of the column.
3.
With the tapered end facing towards the column nut, slide a graphite/vespel
ferrule over the outlet end of the column. See Figure 14.
4. Using the edge of a wafer scribe, score the outside surface of the column
perpendicular to its length approximately 2 inches from the end and carefully
break it off and discard the cut off piece of column. Jagged or angled cuts
should be avoided. See Figure 15for examples of good cuts and bad cuts.
5.
Use a lint-free wipe pre-soaked with a small amount of methanol to wipe the
outside of the column a few times to remove surface contamination.
6. Confirm that the Source is fully installed in the instrument. If it is not, install the
source into the instrument. See
Removing and Returning the Source
on page 71.
7. Insert the column into the MS Transfer Line tube and carefully slide it toward
the source.
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Clarus SQ 8 MS Hardware Guide
80
8. With the column partially inserted, engage the threaded column nut onto the
Transfer Line tube fitting until it is finger-tight.
9.
Carefully continue inserting the column into the Transfer Line tube until it hits
the far side of the source. Be careful to avoid forcefully jamming the column
into the side of the source. Doing so may damage the cleanly cut end of the
column resulting in poor chromatography.
10. With the column positioned as described in Step 9, slide the septum toward the
column nut until it touches the nut.
11.
Pull the column back 10 mm. Then use the 10 mm positioning tool (Gauge) to
set the column nut at this position by placing the slot in the 10 mm Gauge over
the column between the nut and the septum. At this point be careful to avoid
moving the septum from its position on the column. See Figure 18.
Figure 18 Figure 18 The 10 mm poThe 10 mm positioning tool (Gsitioning tool (Gauge) in place.auge) in place.
12. Using the 5 mm and 1/4 inch crescent wrenches, tighten the column nut until
the ferrule is crimped onto the column making sure that the 10 mm spacing is
retained between the end of the column nut and the septum.
13. Remove the 10 mm Gauge.
The column is now installed and the MS may be pumped down. Confirm that the
proper vacuum level is reached (on the TurboMass software Tune Page).
14. After initially heating the GC oven through one or two analysis cycles, the
column nut may loosen. Re-tighten the column nut. After re-tightening, the
column nut should not loosen any more.
Page 83
Maintenance
81
Optical Column Alignment Using the Optional Plug Handle
and Sight
CAUTIONCAUTION
To prevent contamination of the mass spectrometer, always wear clean,
lint-free, powder-free nitrile, nylon, or PVC gloves when handling the
part of the capillary column that will be inserted into the MS Transfer
Line. Never touch these parts with ungloved (bare) fingers, as this will
introduce contaminants into the system.
1. Loosen the large nut on the Transfer Line tube assembly using the 9/16 inch
wrench and pull back the Transfer Line tube approximately 1 to 2 inches.
2.
Remove the source from the Clarus SQ 8 MS instrument. See
Removing and
Returning the Source
on page 71.
3.
Insert the optional Plug Handle and Sight (Part No N6480380). Make sure to
line up the red dots on the plug and instrument.
4. Turn the plug clockwise until the line on the plug and the lock symbol line up.
Figure 19 Figure 19 Inserting the Inserting the Plug Handle Plug Handle and Sight.and Sight.
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Clarus SQ 8 MS Hardware Guide
82
5.
Re-insert the Transfer Line tube assembly and tighten the large nut.
6.
Slide a 1/16 inch column nut over the outlet end of the column.
7.
With the tapered end facing towards the column nut, slide a graphite/vespel
ferrule over the outlet end of the column. See Figure 14.
8.
Using a wafer scribe, score the outside surface of the column approximately 2
inches from the end and carefully break it off and discard the cut off piece of
column.
9. Use a lint-free wipe pre-soaked with a small amount of methanol to wipe the
outside of the column a few times to remove surface contamination.
10. Insert the column into the MS Transfer Line tube and carefully slide it toward
the source.
Figure 20 Figure 20 Inserting the Inserting the transfer line.transfer line.
11.
With the column partially inserted, engage the threaded column nut onto the
Transfer Line tube fitting until it is finger-tight.
ColumnColumn
Page 85
Maintenance
83
12.
Carefully continue inserting the column into the Transfer Line tube until it
becomes visible inside the Plug Handle and Sight. Be careful to avoid inserting
the column so far that it hits the far side of the MS vacuum chamber.
13.
Position the outlet end of the column so it aligns with the edge of the engraved
circle on the tip of the Plug Handle and Sight.
The correct position of the column is reached when it is aligned with the edge
of the circle (in other words, at the "3 o'clock" position).
Figure 21 Figure 21 Viewing the CViewing the Column through the Plug Holumn through the Plug Handle and Sight.andle and Sight.
14.
Using the 5 mm and 1/4 inch crescent wrenches, tighten the column nut until
the ferrule is crimped onto the column. Be careful to avoid moving the column
from the set position. Confirm by gently tugging back the column. It should not
move from the set position. Verify that the column placement is correct by
visually inspecting its position on the circle inside the Plug Handle and Sight.
CircleCircle
Column at 3Column at 3
o’clock positiono’clock position
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Clarus SQ 8 MS Hardware Guide
84
15. Loosen the large ¼ inch nut on the Transfer Line tube assembly using the 9/16
inch wrench and pull back the Transfer Line tube approximately 1 to 2 inches.
See Figure 9.
16. Turn the Plug Handle and Sight counterclockwise to the unlock symbol on the
instrument and remove it from the Clarus SQ 8 MS instrument.
17. Insert the source. See
Removing and Returning the Source
on page 71.
18.
Re-insert the Transfer Line tube assembly and tighten the large nut.
19. The column is now installed and the MS is ready to be pumped down. Confirm
that the proper vacuum level is reached (on the TurboMass software Tune
Page).
20. After initially heating the GC oven through one or two analysis cycles, the
column nut may loosen. Re-tighten the column nut. After re-tightening, the
column nut should not loosen any more.
Page 87
Maintenance
85
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: 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 nitrile, nylon, or PVC gloves.
•
Pasteur Pipette or 50 µL syringe.
•
Heptacosa (FC43) (Part No. N6212407).
To refill the reference gas vial, follow this procedure:
WARNINGWARNING
Make sure to vent the instrument and turn the power off.
1.
Ensure that the solenoid has been switched off.
2.
Locate the reference gas vial under the top cover of the instrument.
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86
Figure 22 Figure 22 Reference gas Reference gas vial and knuvial and knurled fitting.rled fitting.
WARNINGWARNING
The toxicity of the FC-43 calibrant is uncertain. Take appropriate
precautions to avoid getting the calibrant on your skin or in your eyes.
3. Loosen the knurled fitting by ½ turn, and pull out the vial.
A black O-ring may remain in the fitting.
4. 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.
NeverNever add more than 50 µL.
Knurled FittingKnurled Fitting
Reference Gas VialReference Gas Vial
Page 89
Maintenance
87
ReferenceReference
Gas VialGas Vial
50 µL max50 µL max
Gas TightGas Tight
SyringeSyringe
Figure 23 Figure 23 Filling the Filling the reference gas vireference gas vial.al.
5. Re-insert the reference gas vial into the knurled fitting.
Make sure the O-ring is still present and the tapered end of the ferrule faces the
mass spectrometer.
6. Tighten the knurled fitting with your fingers until fingertight.
7.
Replace the top cover and pump the system down to the proper vacuum.
8. 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: NOTE:On the Tune Page the Gas drop down the select Reference Gas On Reference Gas On.
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Clarus SQ 8 MS Hardware Guide
88
Replacing a Filament
This procedure is the same for both an EI or CI source.
CAUTIONCAUTION
Make sure you are wearing lint-free, powder-free nitrile, nylon, or
PVC gloves, and that you wipe each part with a methanol
dampened Kimwipe.
Items and Tools Required
•
Filament assembly (Part No. E6470012).
•
Methanol.
•
Lint-free, powder-free nitrile, nylon, or PVC gloves.
•
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 source by following the procedure Removing and Returning the
Source on page 71.
3.
Orient the source so that the filament faces you, then locate the filament
retaining clip that holds it in place.
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Maintenance
89
Figure 24 Figure 24 Moving the ceramMoving the ceramic insulating connector ic insulating connector assembly down.assembly down.
CAUTIONCAUTION
To ensure that the mass spectrometer remains contamination free,
make sure you are wearing lint-free, powder-free nitrile, nylon, or PVC
gloves, and that all tools have been cleaned with a methanol-dampened
laboratory wipe.
4.
Using your thumb and forefinger, push down the ceramic insulating connector
assembly to release it from the filament leads, trap lead, and repeller lead.
5. Press down on the retaining clip to release it from the locked position and
swing it down.
6. The defective filament assembly will fall out of place, so carefully hold or
catch it with your other hand.
Move the CeramicMove the Ceramic
Insulating ConnectorInsulating Connector
Assembly DownAssembly Down
FilamentFilament
FilamentFilament
Retaining ClipRetaining Clip
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90
Figure 25 Figure 25 Removing the defecRemoving the defective filament assemtive filament assembly.bly.
7. Position the new filament assembly with the filament side up.
8.
Position the new filament assembly with the coiled filament wire facing and
centered in the orifice in the ion volume and the white ceramic rests on the tab.
9.
Insert the Filament retaining clip into the slot in the block to hold it in place.
10.
Align the four male gold leads (Trap, Repeller and Filament) with the four gold
female connectors in the ceramic insulating connector assembly.
11.
Carefully move the connector assembly upwards to fully encapsulate the four
gold leads. You should be able to feel it “click” into position around the leads
and close to the underside of the block.
12. Install the source assembly back into the mass spectrometer by following the
procedure Removing and Returning the Sourceon page 71.
FilamentFilament
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Maintenance
91
Source Maintenance
NOTE: NOTE:
Before beginning this procedure, you may want to have on hand the following source
component kits; Rebuild Kit Part No. N6480080 and N6480081.
CAUTIONCAUTION
To ensure that the mass spectrometer remains contamination free, wear
lint-free, powder-free nitrile, nylon, or PVC gloves while performing
this procedure.
Disassembling
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 small parts as you remove them.
1. Remove the source by following the procedure Removing and Returning the
Source on page 71.
2. Orient the source so that the filament faces you, then locate the filament
retaining clip that holds it in place.
Figure 26 Figure 26 Removing Removing the Filamthe Filament.ent.
3.
Using your thumb and forefinger, push down the ceramic insulating connector
assembly to release it from the filament leads, trap lead, and repeller lead.
4. Press down on the retaining clip to release it from the locked position.
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Clarus SQ 8 MS Hardware Guide
92
5. The filament assembly will fall out of place, so carefully hold or catch it with
your other hand.
CAUTIONCAUTION
As you remove the source parts, note their placement and position in
the source so that you can reassemble the source correctly. There is
only ONE way to replace the parts in the source. The following
illustrations should help you with the parts orientation and position.
6.
Turn Lens 3 counterclockwise until it disengages from the locking pin.
Figure 27 Figure 27 Removing Lens Removing Lens 3 from the 3 from the source.source.
7.
Remove the parts from the source.
Figure 28 Figure 28 Removing the sRemoving the source parts for cleaning.ource parts for cleaning.
Lens 3Lens 3
Locking PinLocking Pin
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Maintenance
93
Cleaning
NOTE: NOTE:
You can do the following cleaning method of aluminum oxide paste to polish the flat
surfaces of the parts. For either cleaning method, the final step you must 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 or a foam-pad swab in the solution and clean
the darkened areas on the source. Work quickly to prevent the mixture from
drying on the surface.
3.
Place the cleaned components in de-ionized water prior to rinsing to prevent
drying.
Rinsing
1.
Add 50 mL of methanol to a 100 mL beaker, insert the source parts, and
sonicate them in an ultrasonic bath for at least ten minutes.
2. Carefully drain the methanol.
3.
Add 50 mL of acetone to the 100 mL beaker, insert the source parts, and
sonicate in an ultrasonic bath for ten minutes.
CAUTIONCAUTION
Do not allow the methanol and acetone to touch the O-ring on the
source.
4.
Carefully drain the acetone.
5.
Dry off the source parts using lint-free tissue and/or clean compressed nitrogen
gas to prevent solvents from drying on these parts and leaving a residue.
If you did not use acetone to rinse the parts, wrap them in a clean, lint-free
cloth and bake them in the GC oven at about 80 ºC for about fifteen minutes.
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94
Reassembling
1.
Replace the source parts into the source as shown below.
Remember to insertRemember to insert
the parts into the source only as positioned below.the parts into the source only as positioned below.
You may want to insert the trap insulator and trap before you insert the
repeller.
Figure 29 Figure 29 Replacing Replacing the source the source parts.parts.
2. Align the Lens 3 grabbers with the pin on the source, then turn Lens 3
clockwise to lock it in place. See Figure 27.
3. Position the filament assembly with the coiled filament wire facing and
centered in the orifice in the ion volume and the white ceramic rests on the tab.
4. Insert the Filament retaining clip into the slot in the block to hold it in place.
5. Align the four male gold leads (Trap, Repeller and Filament) with the four
gold female connectors in the ceramic insulating connector assembly.
6. Carefully move the connector assembly upwards to fully encapsulate the four
gold leads. You should be able to feel it “click” into position around the leads
and close to the underside of the block.
7. Install the source assembly back into the mass spectrometer by following the
procedure Removing and Returning the Source on page 71.
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Maintenance
95
Mass Analyzer Maintenance (Advanced Users Only)
WARNINGWARNING
This procedure is intended foradvanced users onlyadvanced users only that have been
properly trained.
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 circumstancesUnder 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.
Items and Tools Required
•
4 mm hex wrench
•
5 mm hex wrench
•
Lint-free, powder-free nitrile, nylon, or PVC gloves
•
Aluminum foil
•
Small flat-blade screwdriver
•
Long flat-blade screwdriver
•
Tweezers
Cleaning Materials
•
Wooden stick cotton swabs
•
Deionized Water
•
6000 Grade Micro Mesh (Part No. N9303420)
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Clarus SQ 8 MS Hardware Guide
96
•
8000 Grade Micro Mesh (Part No. N9303421)
•
600 grit aluminum oxide in DI Water with a few drops of methanol to make a
paste
•
Acetone
•
Methanol
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:
•
6000 Grade Micro Mesh (Part No. N9303420).
•
8000 Grade Micro Mesh (Part No. N9303421).
•
600 grit aluminum oxide in DI Water with a few drops of methanol to make a 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 and Returning the Ion Optics Assembly
CAUTIONCAUTION
To prevent contamination of the mass spectrometer, always wear clean,
lint-free, powder-free nitrile, nylon, or PVC gloves before touching,
removing or replacing parts. Hold the source by its handle only. Never
touch these parts with ungloved (bare) fingers, as this will introduce
contaminants into the system.
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Maintenance
97
WARNINGWARNING
Make sure to vent the instrument and turn the power off and
unplug the mass spectrometer from the AC power source.
The mass spectrometer contains high voltage. To prevent the risk
of shock, unplug the line cord from the AC outlet and wait at leastwait at least
one minuteone minute before opening or removing any instrument cover or
panel.
Tools Required:
•
Medium sized Philips screwdriver
•
5 mm Allen Key
1. Power down and vent the Clarus SQ 8 MS.
2.
Remove the source. See
Removing and Returning the Source
on page 71.
3.
Use the medium sized Philips screwdriver to remove the two screws on the left
access panel. See the following figure.
Figure 30 Removing the cover screws.Figure 30 Removing the cover screws.
4.
Remove the left access panel and place in a secure location.
5.
Lift off the top cover by manipulating the slots on the right-hand side of the
cover off the metal tabs on the instrument. See the following figure.
ScrewsScrews
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Clarus SQ 8 MS Hardware Guide
98
Figure 31 Removing the top cover.Figure 31 Removing the top cover.
6.
Place the top cover in a safe location.
7. Loosen the two screws holding the plastic extensions in the front cover in place.
8.
Tilt the front cover towards you slightly to provide clearance for removing the
lid. It is not necessary to remove the front cover completely from the
instrument.
Top CoverTop Cover
Top Cover Slot (2)Top Cover Slot (2)
Metal Tab on Chassis (2)Metal Tab on Chassis (2)
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