Clarus 600/650 D MS Hardware Guide

Clarus 600/650 D MS Hardware Guide
Clarus 600/560 D MS
Hardware Guide
Release History
Part Number
09936768
Release
C
Publication Date
March 2008
Any comments about the documentation for this product should be addressed to:
User Assistance
PerkinElmer, Inc.
710 Bridgeport Avenue
Shelton, Connecticut 06484-4794
U.S.A.
Or emailed to: info@perkinelmer.com
Notices
The information contained in this document is subject to change without notice.
Except as specifically set forth in its terms and conditions of sale, PerkinElmer makes no
warranty of any kind with regard to this document, including, but not limited to, the
implied warranties of merchantability and fitness for a particular purpose.
PerkinElmer shall not be liable for errors contained herein for incidental consequential
damages in connection with furnishing, performance or use of this material.
Copyright Information
This document contains proprietary information that is protected by copyright.
All rights are reserved. No part of this publication may be reproduced in any form
whatsoever or translated into any language without the prior, written permission of
PerkinElmer, Inc.
Copyright © 2008 PerkinElmer, Inc.
Produced in the US.
Trademarks
Registered names, trademarks, etc. used in this document, even when not specifically marked
as such, are protected by law.
PerkinElmer is a registered trademark of PerkinElmer, Inc.
Clarus 600 is a trademark of PerkinElmer, Inc.
Swagelok is a registered trademark of the Crawford Fitting Company.
Teflon and Vespel are registered trademarks of E.I. duPont de Nemours and Company, Inc.
Microsoft is a registered trademark of the Microsoft Corporation.
Windows XP SP2 is a trademark of the Microsoft Corporation
Contents
Contents
Warnings and Safety Information .................................................... 7
Conventions Used in this Manual................................................................... 9
Customer Service................................................................................... 12
Electromagnetic Compatibility (EMC)......................................................... 13
Regulatory Information ......................................................................... 13
Electrical Symbols Used on ClarusMS ................................................. 14
Label Location and Content .................................................................. 15
Clarus MS Safety Practices .......................................................................... 18
Generic Warnings.................................................................................. 18
Moving the Clarus MS .......................................................................... 19
Decontamination and Cleaning..................................................................... 21
Decontamination.................................................................................... 21
Cleaning the Instrument ........................................................................ 21
Compressed Gases................................................................................. 22
Ventilation ............................................................................................. 22
Heated Zones ......................................................................................... 23
Using Hydrogen, Methane or Isobutane................................................ 24
Using Ammonia Gas ............................................................................. 24
Hazardous Chemicals ............................................................................ 24
Definitions in Warnings for Hazardous Chemicals ............................... 26
Temperature, Humidity and Environment .................................................... 27
Operating Conditions............................................................................. 27
Storage Conditions ................................................................................ 28
General Laboratory Safety............................................................................ 29
WEEE Instructions for PerkinElmer Products.............................................. 30
Pre-Installation Requirements ...................................................................... 31
Laboratory Space Requirements............................................................ 31
Environmental Requirements ................................................................ 32
Power Requirements.............................................................................. 33
Safety Requirements.............................................................................. 35
Computer and System Software Requirements ..................................... 37
PC Requirements ................................................................................... 37
Operating System .................................................................................. 37
Software................................................................................................. 38
Instrument Firmware Versions .............................................................. 38
3
Clarus 600/560 D MS Hardware Guide
Printers................................................................................................... 38
Pre-Installation Checklist.............................................................................. 39
Introduction ...................................................................................... 41
Preface .......................................................................................................... 43
System Overview................................................................................... 43
Summary of this Guide.......................................................................... 44
Related Documentation ......................................................................... 44
About Part Numbers Listed in this Manual ........................................... 45
About the Clarus 600/560 D System ............................................... 47
About the Clarus 600/560 D System ............................................................ 49
Clarus 600/560 D GC ................................................................................... 51
GC Interface (Transfer Line) ........................................................................ 53
Reference Gas Inlet....................................................................................... 54
Ion Optics Path ............................................................................................. 57
Vacuum System............................................................................................ 59
Rotary Pump.......................................................................................... 59
Vacuum Pump Options.......................................................................... 61
Diffusion Pump Operating States .......................................................... 62
Diffusion Pump Operating States Continued ........................................ 63
Turbomolecular Pump ........................................................................... 64
Diffusion Pump ..................................................................................... 64
Vacuum Gauge ...................................................................................... 67
TurboMass Software..................................................................................... 68
Top Level Screen................................................................................... 68
Tune Page .............................................................................................. 69
Analytical Column........................................................................................ 70
Pre-Operational Checklist............................................................................. 71
Maintenance ...................................................................................... 73
Overview ...................................................................................................... 75
Typical Overall Maintenance Schedule........................................................ 77
Daily ...................................................................................................... 77
Weekly................................................................................................... 77
Monthly ................................................................................................. 78
Every Six Months .................................................................................. 78
Yearly .................................................................................................... 78
4
Contents
Leak Checking .............................................................................................. 79
Tuning Clarus 600/560 D MS....................................................................... 82
Preparing Clarus 600/560 D MS for Hardware Maintenance...................... 85
Changing a Column ...................................................................................... 88
Tools and Items Required...................................................................... 88
Removing a Column.............................................................................. 88
Connecting the New Column to the Split/Splitless Injector.................. 91
Connecting a New Column to Clarus 600 MS ...................................... 94
Refilling the Reference Gas Vial ................................................................ 100
Items Required .................................................................................... 100
Inner Source Maintenance .......................................................................... 104
Removing the Inner Source ................................................................. 105
EI Inner Source Maintenance .............................................................. 106
CI Inner Source Maintenance .............................................................. 113
Reinstalling the Source........................................................................ 119
Replacing a Filament .................................................................................. 121
Items and Tools Required.................................................................... 121
Replacing the Head Amplifier .................................................................... 126
Mass Analyzer Maintenance....................................................................... 128
Items and Tools Required.................................................................... 128
Cleaning Materials............................................................................... 129
Removing the Ion Optics Assembly.................................................... 129
Replacing an Outer Source Thermocouple.......................................... 139
Removing the Outer Source from the Ion Optics ................................ 141
Replacing Outer Source Heaters ......................................................... 142
Replacing the Quadrupole Heater........................................................ 144
Cleaning the Outer Source Lens.......................................................... 146
Reassembling the Ion Optics Assembly .............................................. 149
Reassembling the Clarus 600/560 D MS............................................. 152
Vacuum System Maintenance .................................................................... 154
Maintanenace of the Turbomolecular and Diffusion Pump ................ 154
Checking the Forepump Oil Level ...................................................... 154
Adding Oil to the Forepump Reservoir ............................................... 156
Decontaminating the Oil...................................................................... 156
Replacing the Oil................................................................................. 156
Inline Gas Purifiers ..................................................................................... 159
Changing from EI to CI Mode.................................................................... 160
Connecting the CI Gas......................................................................... 160
5
Clarus 600/560 D MS Hardware Guide
Changing to CI .................................................................................... 162
Leak Checking..................................................................................... 163
Setting-Up CI ...................................................................................... 165
Troubleshooting .............................................................................. 175
Overview .................................................................................................... 177
Spare Components............................................................................... 178
Logical Troubleshooting Steps............................................................ 178
Troubleshooting Chart ................................................................................ 180
Chromatography Related..................................................................... 191
Spectral Related................................................................................... 195
Communications Related..................................................................... 197
Forepump Related ............................................................................... 198
Message Dialogs......................................................................................... 201
Replacement Parts ...................................................................................... 207
Index ................................................................................................ 209
6
Warnings and
Safety Information
1
Warnings and Safety Information
Conventions Used in this Manual
Normal text is used to provide information and instructions.
Bold text refers to text that is displayed on the touch screen.
All eight digit numbers are PerkinElmer part numbers unless stated otherwise.
Notes, warnings and cautions
Three terms, in the following standard formats, are also used to highlight special
circumstances and warnings.
NOTE: A note indicates additional, significant information that is provided with some
procedures.
Terminology
Throughout the manual, the term ‘mass spectrometer’ or MS specifically refers to
the Clarus MS; while for ‘GC’ Clarus GC is implied.
CAUTION
Caution
We use the term CAUTION to inform you about situations that could
result in serious damage to the instrument or other equipment. Details
about these circumstances are in a box like this one.
9
Clarus 600/560 D MS Hardware Guide
D
DK
E
Caution (Achtung)
Bedeutet, daß die genannte Anleitung genau befolgt werden muß, um
einen Geräteschaden zu vermeiden.
Caution (Bemærk)
Dette betyder, at den nævnte vejledning skal overholdes nøje for at
undgå en beskadigelse af apparatet.
Caution (Advertencia)
Utilizamos el término CAUTION (ADVERTENCIA) para advertir
sobre situaciones que pueden provocar averías graves en este equipo o
en otros. En recuadros éste se proporciona información sobre este tipo
de circunstancias.
F
Caution (Attention)
Nous utilisons le terme CAUTION (ATTENTION) pour signaler les
situations susceptibles de provoquer de graves détériorations de
l'instrument ou d'autre matériel. Les détails sur ces circonstances
figurent dans un encadré semblable à celui-ci.
I
Caution (Attenzione)
Con il termine CAUTION (ATTENZIONE) vengono segnalate
situazioni che potrebbero arrecare gravi danni allo strumento o ad
altra apparecchiatura. Troverete informazioni su tali circostanze in un
riquadro come questo.
NL
P
Caution (Opgelet)
Betekent dat de genoemde handleiding nauwkeurig moet worden
opgevolgd, om beschadiging van het instrument te voorkomen.
Caution (Atenção)
Significa que a instrução referida tem de ser respeitada para evitar a
danificação do aparelho.
Warning
We use the term WARNING to inform you about situations that could
result in personal injury to yourself or other persons. Details about
these circumstances are in a box like this one.
WARNING
10
Warnings and Safety Information
D
Warning (Warnung)
Bedeutet, daß es bei Nichtbeachten der genannten Anweisung zu einer
Verletzung des Benutzers kommen kann
DK
Warning (Advarsel)
Betyder, at brugeren kan blive kvæstet, hvis anvisningen ikke
overholdes.
Warning (Peligro)
Utilizamos el término WARNING (PELIGRO) para informarle sobre
situaciones que pueden provocar daños personales a usted o a otras
personas. En los recuadros como éste se proporciona información
sobre este tipo de circunstancias.
E
F
Warning (Danger)
Nous utilisons la formule WARNING (DANGER) pour avertir des
situations pouvant occasionner des dommages corporels à l'utilisateur
ou à d'autres personnes. Les détails sur ces circonstances sont données
dans un encadré semblable à celui-ci.
I
Warning (Pericolo)
Con il termine WARNING (PERICOLO) vengono segnalate situazioni
che potrebbero provocare incidenti alle persone. Troverete
informazioni su tali circostanze in un riquadro come questo.
NL
P
Warning (Waarschuwing)
Betekent dat, wanneer de genoemde aanwijzing niet in acht wordt
genomen, dit kan leiden tot verwondingen van de gebruiker.
Warning (Aviso)
Significa que a não observância da instrução referida poderá causar
um ferimento ao usuário.
11
Clarus 600/560 D MS Hardware Guide
Customer Service
This instrument is manufactured by:
PerkinElmer Inc.
710 Bridgeport Avenue
Shelton, Connecticut 06484-4794
U.S.A.
Tel: 1 (800) 762-4000
Internet: http://www.perkinelmer.com
12
Warnings and Safety Information
Electromagnetic Compatibility (EMC)
Regulatory Information
United States (FCC)
This equipment has been tested and found to comply with the limits for a Class A
digital device, pursuant to part 15 of the FCC Rules. These limits are designed to
provide reasonable protection against harmful interference when the equipment is
operated in a commercial environment. This equipment generates, uses, and can
radiate radio frequency energy and, if not installed and used in accordance with
the instruction manual, may cause harmful interference to radio communications.
Operation of this equipment in a residential area is likely to cause harmful
interference in which user will be required to correct the interference at his own
expense.
NOTE: Changes or modifications not expressly approved by PerkinElmer could cause the
instrument to violate FCC (U.S. Federal Communications Commission) emission
regulations, and because of this violation could void the user’s authority to operate
this equipment.
Europe
All information concerning EMC standards is in the Declaration of Conformity, and
these standards may change as the European Union adds new requirements.
CAUTION
The Clarus MS contains protective circuitry. Contact PerkinElmer
Service before performing any AC line tests.
13
Clarus 600 GC-MS Hardware Guide
Electrical Symbols Used on ClarusMS
Alternating current.
Protective conductor terminal. Ground.
Off position of the main power switch.
On position of the main power switch.
Warning: Risk of electric shock.
Warning: Hot surface.
Caution, risk of danger
Documentation must be consulted to determine the nature of the
potential hazard and any actions which have to be taken.
14
Warnings and Safety Information
Label Location and Content
Clarus 600
Mass Spectrometer
Figure 1 Front View of Clarus 600 MS
Clarus 600
Mass Spectrom eter
Front View of Clarus 560 D
15
Clarus 600/560 D MS Hardware Guide
Mass Spectrometer
Air
Vents
GC
Interface
PC
Ethernet
Connection
Mass Spectrometer
ETHERNET
FCC Compliance
S1
This device complies with Part 15 of the FCC Rules.
Operation is subject to the following two conditions:
1) this device may not cause harmful interference, and
2) this device must accept any interference received,
including interference that may cause undesired
operation.
Warning
Processor
Reset
Switch
Warning
Disconnect AC power cord from oulet
before removing any cover or parts.
Do not operate the instrument with any
cover or parts removed.
Disconnect AC power cord from oulet
before removing any cover or parts.
Do not operate the instrument with any
cover or parts removed.
!
Caution
Do not re strict air intake or exhaus t
Air
Intakes
Caution
Do not restrict air intake or exhaust.
Air
Exhaust
ROTARY PUMP
Warning
!
NH 3
CH 4
C 4H 10
CI GAS
POWER IN
Warning
N2
VENT
15 psi
5 psi
(103 kPa) (35 kPa)
MAX
MAX
WATER
IN
50 psi
(345 kPa)
MAX
120 VAC ~ 50/60Hz
230 VAC ~ 50/60Hz
MAX POWER 1000 VA
EN 55011-Class A, Group 1
WATER
OUT
!
Caution
This unit contains protective circuitry.
Contact PerkinElmer qualified service
personnel before performing any
AC line tests
120 VAC ~ 50/60Hz
230 VAC ~ 50/60Hz
MAX POWER 1000 VA
EN 55011-Class A, Group 1
Caution
This unit contains protective circuitry.
Contact PerkinElmer qualified service
personnel before performing any
AC line tests.
Figure 2a Rear View of the Clarus 600 MS
16
Warnings and Safety Information
PerkinElmer
precisely.
Shelton, CT 06484 USA
Clarus 560 D
Mass Spectrometer
Air
Vents
GC
Interface
Part No. Nx xx xxx x
PC
Ethernet
Connection
Serial No. Xxx xx xx
FCC Compliance
This devi ce compli es with Part 15 of the FCC Rules.
Operation is subject to the follow ing tw o conditions:
1) this device may not cause harmful interference, and
2) this device must accept any interference r eceived,
including interference that may cause undesi red
operation.
FCC Compliance
S1
Warning
Processor
Reset
Switch
Warning
Disc onnect AC power cord from oulet
before removing any c over or parts .
Do not opera te the instrument with any
cover or parts removed.
!
Caution
Air
Intakes
Caution
D o not r estrict air in take o r exhaust.
Air
Exhaust
ROTA RY PU MP
Warning
REMOVE VENT LINE BLANKING CAP
AT INSTALLATION.
POWER IN
!
2
!
120 VAC ~ 50/60Hz
230 VAC ~ 50/60Hz
MAX POWER 1000 VA
EN 55011-Class A, Group 1
On/Off Switch
Caution
Caution
This unit contains protective circuitry.
Contact PerkinElmer qualified service
personnel before performing any
AC line tests.
Figure 2b Rear View of the Clarus 560 D MS
17
Clarus 600/560 D MS Hardware Guide
Clarus MS Safety Practices
NOTE: This equipment requires no specified inspection or preventive maintenance to ensure
the continuous functioning of its safety features.
The Mass Spectrometer should be used in accordance with the instructions provided
in the user’s manuals and tutorial supplied with the instrument. If used otherwise,
the protection provided by the instrument may be impaired.
Do not attempt to make adjustments, replacements or repairs to this
instrument except as described in the accompanying user documentation.
WARNING
Explosive Atmosphere. This instrument is not designed for operation in an
explosive atmosphere.
WARNING
Generic Warnings
Before installing or operating the MS, read the following topics concerning hazards
and potential hazards. Ensure that anyone involved with installation and/or operation
of the MS is knowledgeable in both general safety practices for the laboratory and
safety practices for this instrument. Get advice from your safety engineer, industrial
hygienist, environmental engineer, or safety manager before you install or use this
instrument.
This equipment requires no specified inspection or preventive maintenance to ensure
the continuous functioning of its safety features.
18
Warnings and Safety Information
Moving the Clarus MS
Depending on the Clarus 600 MS GC pump option selected, the
instrument weight will range from 46.8 kg (102 lb) to 49.9 kg (110 lb).
The Clarus 560 D MS is 48 kg (105 lb) in weight.
WARNING
WARNING
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.
Connect the mass spectrometer to an AC line power outlet that has a
protective ground connection. To ensure satisfactory and safe
operation of the mass spectrometer, it is essential that the protective
ground conductor (the green/yellow lead) of the line power cord is
connected to a true electrical ground. Any interruption of the protective
ground conductor, inside or outside the mass spectrometer, or
disconnection of the protective ground terminal may impair the
protection provided by the mass spectrometer.
Never operate the mass spectrometer with any covers or parts removed.
WARNING
WARNING
Do not make adjustments, replacements or repairs to the mass
spectrometer except as described in this manual. Only a PerkinElmer
Service Representative or similarly trained and authorized person
should be permitted to service the mass spectrometer.
Ensure that the power cord is correctly wired and that the ground leads of all
electrical units (for example, recorders, integrators) are connected together via the
19
Clarus 600/560 D MS Hardware Guide
circuit ground to earth. Use only three-prong outlets with common earth ground
connections.
•
Servicing of electrical components within the mass spectrometer should be
performed only by a PerkinElmer Service Representative or similarly trained
and authorized person.
•
Servicing of the incoming AC power line components in your laboratory
should be performed only by a licensed electrician.
Electrical shock hazard. To prevent electrical shock, disconnect the
power cord from the AC outlet before servicing.
WARNING
Disconnect AC power cord from outlet before removing any cover or
parts. Do not operate the instrument with any covers or parts removed.
WARNING
Under no circumstances should circuit boards be removed or inserted unless the
instrument is disconnected from line power.
20
Warnings and Safety Information
Decontamination and Cleaning
Before using any cleaning or decontamination methods except those specified by
PerkinElmer, users should check with PerkinElmer that the proposed method will
not damage the equipment.
Decontamination
Customers wishing to return instrumentation and/or associated materials to
PerkinElmer for repair, maintenance, warranty or trade-in purposes are
advised that all returned goods must be certified as clean and free from
contamination.
The customer’s responsible body is required to follow the "Equipment
Decontamination Procedure" and complete the “Certificate of Decontamination”.
These documents are available on the PerkinElmer public website:
http://las.perkinelmer.com/OneSource/decontamination.htm
If you do not have access to the internet and are located in the U.S., call toll free at
1-800-762-4000 or (+1) 203-925-4602, 8:30 a.m. – 7 p.m. EST and speak to
Customer Support.
In Canada, call toll free 800-561-4646 and speak to Customer Support.
If you are located outside of the United States or Canada, please call your local
PerkinElmer sales office for more information.
Cleaning the Instrument
Exterior surfaces may be cleaned with a soft cloth, dampened with a mild detergent
and water solution. Do not use abrasive cleaners or solvents.
21
Clarus 600/560 D MS Hardware Guide
Compressed Gases
Compressed Gases. High pressure gas cylinders can be dangerous if
mishandled or misused. Always handle gas cylinders with caution and
observe your local regulations for the safe handling of gas cylinders.
WARNING
Avoid banging the valves, and ensure that the correct valves and gauges are
installed. It is recommended that gas cylinders be stored and placed outside the
laboratory and connected to the instrument through specially cleaned copper tubing.
Take care not to kink or stress the gas tubing. For safety, cylinders must be firmly
clamped in an upright position.
Explosive hazard. When using hydrogen, methane or isobutane, special
care must be taken to avoid buildup of explosive gas mixtures either in the
GC oven or the mass spectrometer vacuum manifold.
WARNING
Ensure that all hydrogen line couplings are leak-free and do not allow hydrogen to
vent within the oven.
Ventilation
WARNING
22
Hazardous vapors. When analyzing hazardous compounds, such as
pesticides, or running in the chemical ionization (CI) mode, it is
necessary to vent the mass spectrometer effluent from the forepump
exhaust into a fume hood or charcoal trap.
Warnings and Safety Information
WARNING
Toxic Gases-Fume Ventilation System. Without adequate ventilation
potentially toxic vapors can build up in the laboratory. Your laboratory
must have reliable fume ventilation system before you use this
instrument.
Adequate ventilation must be provided, particularly if a liquid nitrogen or carbon
dioxide subambient accessory is in constant use. The area underneath the bench
(around the forepump) should be well ventilated. An oil separation filter and
charcoal trap should be installed at the outlet of the forepump exhaust to prevent
contamination if fume hood venting is unavailable.
To ensure adequate cooling of the instrument electronics, do not obstruct the gap at
the base of the Clarus MS/Clarus GC, and if practical, leave a minimum 6 inch
clearance between each instrument in the system (for example, the ATD or HS
40XL). This does not include the Clarus MS/Clarus 600 GC as they are connected
together.
Heated Zones
Risk of burns. Never touch a heated mass spectrometer transfer line or
a GC injector cap with unprotected (bare) fingers.
WARNING
Heated zones should be treated with caution, for example, the transfer line, injector
caps, and detectors. In addition, the detector cover may get hot, especially if flame
ionization detectors are operated at high temperatures. As a general rule, allow
heated zones to cool before attempting to work in the GC oven, on the transfer line,
on an injector, around the detector areas or inside the mass spectrometer manifold.
Cooling of the transfer line may require a wait of ½ to 1 hour.
23
Clarus 600/560 D MS Hardware Guide
Using Hydrogen, Methane or Isobutane
Explosive Hazard. If the hydrogen is turned on without a column
attached to the injector and/or detector fittings inside the oven, the gas
could diffuse into the oven creating the possibility of an explosion.
If the mass spectrometer is not under vacuum, hydrogen, methane, or
isobutane can fill the vacuum chamber thereby creating an explosive
hazard.
WARNING
To avoid possible injury, do not turn on the hydrogen unless a column
is attached, all joints have been leak-tested, and the mass spectrometer
is under vacuum with the forepump exhaust properly vented to a fume
hood.
Using Ammonia Gas
WARNING
Hazardous gas vapors. When using ammonia gas while running in the
chemical ionization (CI) mode, it is necessary to vent the mass
spectrometer effluent from the forepump exhaust into a fume hood or
outside the building.
Hazardous Chemicals
WARNING
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 mass spectrometer
may be hazardous. Do not store, handle, or work with any chemicals or hazardous
24
Warnings and Safety Information
materials unless you have received appropriate safety training and have read and
understood all related Material Safety Data Sheets (MSDS). MSDSs give
information on physical characteristics, precautions, first aid, spill clean up and
disposal procedures. Familiarize yourself with the information and precautions
contained in these documents before attempting to store, use or dispose of the
reagents. Comply with all federal, state, and local laws related to chemical storage,
handling and disposal.
You must work under a suitable hood when handling and mixing certain chemicals.
The room in which you work must have proper ventilation and a waste collection
system. Always wear appropriate safety attire (full-length laboratory coat, protective
glasses, gloves etc.) as indicated on Material Safety Data Sheets.
When using toxic samples, the mechanical pump oil is toxic waste.
WARNING
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.
25
Clarus 600/560 D MS Hardware Guide
Definitions in Warnings for Hazardous Chemicals
Responsible body: Individual or group responsible for the use and maintenance of
equipment, and for ensuring that operators are adequately
trained. [per EN/IEC 61010-1].
26
Operator:
Person operating equipment for its intended purpose. [per
EN/IEC 61010-1].
OSHA:
Occupational Safety and Health Administration (United States).
ACGIH:
American Conference of Governmental Industrial Hygienists.
COSHH:
Control of Substances Hazardous to Health (United Kingdom).
Warnings and Safety Information
Temperature, Humidity and Environment
Operating Conditions
CAUTION
The Clarus MS is designed for indoor use only in a laboratory
environment that is clean and is free of drafts, direct sunlight and
vibration.
Do not operate the mass spectrometer in a Cold Room or a refrigerated
area. Clarus MS operates under the following conditions:
Ambient temperature is 10 °C to 35 °C (50 °F and 95 °F) with a
variability of less than ± 4 °C (± 7 °F).
CAUTION
The Clarus MS will operate safely between 5°C and 40 °C
(41 °F and 104 °F).
If operating at ambient temperatures between 30°C and 35 °C, you will
need the water-cooling option for the turbopump.
Ambient relative humidity is 20 % to 80 % non-condensing.
Operating altitude is in the range of 0 to 2000 m.
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 MS will operate safely in environments that contain
non-conductive foreign matter up to Pollution Degree 2 in
EN/IEC 61010-1.
27
Clarus 600/560 D MS Hardware Guide
Storage Conditions
The mass spectrometer may be stored under the following conditions:
28
•
Ambient temperature is -20 °C to +60 °C (-4 to 140 °F).
•
Ambient relative humidity is 20 to 80 %, non-condensing.
•
Altitude is in the range 0 to 12000 m.
•
The instrument is stored in an upright position.
Warnings and Safety Information
General Laboratory Safety
Your laboratory should have all equipment ordinarily required for the safety of
individuals working with chemicals (fire extinguishers, first-aid equipment, safety
shower and eye-wash fountain, spill cleanup equipment, etc.).
29
Clarus 600/560 D MS Hardware Guide
WEEE Instructions for PerkinElmer Products
or
A label with a crossed-out wheeled bin symbol and a rectangular bar indicates that
the product is covered by the Waste Electrical and Electronic Equipment (WEEE)
Directive and is not to be disposed of as unsorted municipal waste. Any products
marked with this symbol must be collected separately, according to the regulatory
guidelines in your area.
The objectives of this program are to preserve, protect and improve the quality of
the environment, protect human health, and utilize natural resources prudently and
rationally. Specific treatment of WEEE is indispensable in order to avoid the
dispersion of pollutants into the recycled material or waste stream. Such treatment is
the most effective means of protecting the customer’s environment.
Requirements for waste collection, reuse, recycling, and recovery programs vary by
regulatory authority at your location. Contact your local responsible body (e.g., your
laboratory manager) or authorized representative for information regarding
applicable disposal regulations. Contact PerkinElmer at the web site listed below for
information specific to PerkinElmer products.
Web address:
http://las.perkinelmer.com/OneSource/Environmental-directives.htm
For Customer Care telephone numbers select “Contact us” on the web page.
Products from other manufacturers may also form a part of your PerkinElmer
system. These other producers are directly responsible for the collection and
processing of their own waste products under the terms of the WEEE Directive.
Please contact these producers directly before discarding any of their products.
Consult the PerkinElmer web site (above) for producer names and web
addresses.
30
Warnings and Safety Information
Pre-Installation Requirements
Laboratory Space Requirements
Size
Weight
Clarus 600 MS
32 cm (13 in.) wide x 50 cm
(20 in.) high x 77 cm (30 in.) deep
Clarus 560 D MS
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 600 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.
Bench Space
The laboratory bench should be sturdy enough to support the full weight of the GC/MS
as well as additional equipment (for example, computer and/or printer). Expect the
total weight of the GC/MS and accessory equipment to weigh at least 159 kg (350 lb).
Allow a minimum clearance of 15 cm (6 in.) on each side, 22.9 cm (9 in.) at the rear,
and 137.2 cm (54 in.) at the top of the GC/MS. If this is not possible, install the
GC/MS on a bench that has wheels. The bench requires an area underneath for the
forepump.
Do not position the Clarus 600 MS so that it is difficult to operate the
AC power on/off switch on the lower left side of the instrument in case of a
malfunction of the instrument. For the Clarus 650 D the AC power on/off switch on
the back of the instrument.
Peripherals, Printers
etc.
Allow at least 94 cm (36 in.) on either side of the instrument to accommodate
additional equipment (for example, the computer).
Depending on the pump option
selected, the weight will range from
46.8 kg (102 lb) to 49.9 kg (110 lb).
31
Warnings and Safety Information
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 600 C, 600 T, and 600 S
systems unless the turbomolecular pump is water cooled, and
between 10 °C and 35 °C (50 °F and 95 °F) for Clarus 600 D, or
for Clarus 600 C, 600 T, and 600 S systems with water cooling.
32
Clarus 600 GC-MS User’s Guide
Power Requirements
Clarus MS
All electrical supplies must be smooth, clean, and free of line transients
greater than 40 V peak to peak, and must meet and remain within the
following tolerances:
120 VAC ±10 % @ 50/60 Hz ±1 % 1000 VA maximum
230 VAC ±10 % @ 50/60 Hz ±1 % 1000 VA maximum
Add 100 VA for the computer and 108 VA for a printer.
Clarus GC
All electrical supplies must be smooth, clean, and free of line transients
greater than 40 V peak to peak, and must meet and remain within the
following tolerances:
For GC with slow heating rate as standard;
120 VAC ± 10% @ 50/60 Hz ± 1% @ 20 Amps, 2400 VA maximum
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 must not be connected to circuits with large
inductive or large and frequent loads (for example, large motors,
discharge lamps, photocopy systems, radio transmitters, etc.).
33
Clarus 600/560 D MS Hardware Guide
Power Outlets
Clarus MS: A minimum requirement of a power line separate from the
GC at 15 amps or greater.
Clarus GC: A minimum of one dedicated 120 VAC outlet at 20 A or
one 230 VAC outlet at 10 A (minimum) is required for the Standard
GC. When the optional oven heater is ordered, the outlets will be as
indicated above.
Additional equipment, such as computers and printers, should be
connected per their specifications.
34
Warnings and Safety Information
Safety Requirements
Gas Delivery
Lines
Copper tubing that is free of grease, oil and organic material must
always be used with the Clarus 600 MS on all gas lines, except
ammonia reagent gas. Ammonia reagent gas requires stainless steel.
Solvent-washed copper tubing must be used to avoid contamination
of the Gas Chromatograph. Suitable solvents are acetone or
dichloromethane (do not use if negative chemical ionization is
planned) followed by methanol. Clean helium or nitrogen should be
used to blow any residual solvent from the tubing. Cap all unused
tubing.
Care must be taken not to kink or overstress the gas delivery lines.
Strain relief consisting of two one inch coils of tubing should be
installed at every gas line connection.
Gas Cylinders
All gas cylinders should be firmly clamped to a suitable surface.
Gas cylinders should be located outside of the laboratory whenever
possible, and should always be stored and operated in a vertical
position.
Hydrogen
Ensure that all hydrogen lines and connections are leak-free. When
using a hydrogen tank, install an in-line hydrogen snubber (part
number 00090038) between the tank regulator and the delivery
tubing.
Ventilation
Always provide adequate ventilation. When analyzing hazardous
compounds such as pesticides, it may be necessary to arrange to
vent the mass spectrometer effluent from the forepump into a fume
hood. To prevent contamination if a fume hood is unavailable, an
oil separation filter should be installed at the outlet of the forepump
vented to a fume hood or an oil mist separator (Alcatel 68316) with
a charcoal trap (Koby KA1). An acceptable alternative is to attach a
½ inch Tygon tube and vent to a hood. Pump oil vapor is considered
toxic and must be vented properly.
35
Clarus 600/560 D MS Hardware Guide
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.
CAUTION
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.
Gases
GC/MS Carrier
Gases:
Minimum purity of 99.999% for helium or hydrogen. Carrier gas tubing
should be ultra-clean.
Helium
A number 1A (200 ft3) gas cylinder should be used for all carrier gases with a
high-purity, stainless-steel diaphragm, two-stage regulator. Filter through a
moisture filter and/or hydrocarbon trap and de-oxo filter designed for MS.
Gas delivery pressure to the GC should be 70 – 100 psi (483 – 689 kPa). Do
not exceed 100 psi (689 kPa) on the carrier gas inlet.
Reagent Gases:
Minimum purity of 99.999% for methane, minimum purity of 99.98% for
isobutane, minimum purity of 99.998% for ammonia. Carrier gas tubing
should be ultra-clean.
The gas delivery pressure required is 15 psi (103 kPa) to the bulkhead fitting
(1/8 in. Swagelok) on the mass spectrometer.
Ammonia
If ammonia is used for chemical ionization, all fittings and tubing must be
stainless steel to avoid corrosion. A single-stage regulator is required for
ammonia, rated for corrosive service. Also, the forepump must be vented to a
fume hood or outside the building.
Methane and
Isobutane
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 solvent-washed and nitrogen-dried. The
bulkhead connector at the rear of the instrument is a 1/8 in. Swagelok fitting.
The use of commercial gas purifiers for reagent gas is recommended.
36
Warnings and Safety Information
Computer and System Software Requirements
To ensure that your system performs at the expected high level, your computer must
be configured to the minimum capabilities indicated below.
These requirements may be updated as the requirements for TurboMass software
and/or Microsoft Windows XP SP2 are changed. Consult the latest Product
Description List for current requirements.
NOTE: This guide does not cover the installation and configuration of your computer. If
you have purchased a complete system from PerkinElmer, the computer will be
configured by your Service Engineer during product installation.
PC Requirements
The TurboMass software is installed at PerkinElmer prior to shipment and tested
using the following minimum PC system specifications. If you need to reinstall the
software, verify that the PC meets the following minimum requirements:
•
Dell OptiPlex 745, GX620, GC270, or GX 280
•
Intel® Pentium processor
•
512 MB of Random Access Memory (RAM)
•
High Color (16 bit) at 1024 x 768 SVGA
•
Hard disk with 2.0 GB free space
•
8x speed CD-ROM drive
•
1 RS-232 port
•
2 RJ-45 10/100Base-T ports
•
A keyboard and PS/2®-style mouse
Operating System
Windows XP SP2
37
Clarus 600/560 D MS Hardware Guide
Software
TurboMass Software.
Instrument Firmware Versions
Internal dotLINK
Printers
•
HP LaserJet 4200 Printer Series (HP 4200, 4210, and 4250)
•
HP DeskJet 5650 Color InkJet Printer
NOTE: Using any printers other than the ones recommended above may not correctly
display the Communiqué reports.
.
38
Warnings and Safety Information
Pre-Installation Checklist
MODEL:
__________________________ DATE: _____________________
CUSTOMER:
__________________________________
SPO#:
__________________________________
Requirements
OK
Needs Prior To Installation
Customer Responsibility
Lab Space Requirements
Power Requirements
Gas Requirements
Environmental Requirements
Safety Requirements
Preparation of Samples
(Customer Responsibility)
Computer Configuration
Customer Experience
39
Clarus 600/560 D MS Hardware Guide
40
Introduction
2
Introduction
Preface
The Clarus MS is a benchtop mass spectrometer designed with the user in mind. The
small profile of combination Gas Chromatograph and Mass Spectrometer (GC/MS)
allows it to fit on a standard six foot long laboratory bench. Sophisticated software
controls the GC/MS from a Windows XP SP2 computer.
System Overview
The system consists of:
•
Clarus GC.
•
Clarus MS.
•
Computer.
•
TurboMass Software.
•
Foreline Pump.
43
Introduction
Summary of this Guide
Thoroughly read and understand the Safety and Regulatory Information chapter
before using the mass spectrometer.
Chapter 1:
Warnings and Safety Information
Contains all of the safety information and topics to comply
with EN/IEC 61010.
Chapter 2:
Introduction
Provides an instrument overview and the references to related
documentation.
Chapter 3:
About the Clarus 600/560 D System
Describes each of the components in the system and includes a
list of items to check before using the instrument.
Chapter 4:
Maintenance
Contains preventive and routine maintenance procedures that
typical users can perform.
Chapter 5:
Troubleshooting
Provides helpful troubleshooting tips and a table to help you
identify and solve typical problems.
Related Documentation
The Clarus 600/560 D family of manuals includes the following:
•
Clarus 600/560 D MS Tutorial (part number 09936769): The tutorial provides
a step-by-step guide to performing a number of tasks using the instruments and
software.
44
Warnings and Safety Information
•
Software User’s Guide (part number 09936767): A comprehensive manual
describing the functionality of each part of the TurboMass software. It
describes the keys and fields on each screen.
•
Clarus 600/560 D MS Hardware Manual (part number 09936768): Contains
the required safety and regulatory information required for EN/IEC 61010. It
contains an overview of mass spectrometry and of each component in this
system; a pre-operational checklist, typical user maintenance and a
troubleshooting guide.
•
Service Manual (not included): Contains information for trained service
engineers to completely service the Clarus.
About Part Numbers Listed in this Manual
The part numbers listed in this manual are available from PerkinElmer’s catalog
service.
Supplies, Accessories and Replacement Parts
Supplies, accessories, and replacement parts can be ordered directly from
PerkinElmer's catalog service. PerkinElmer offers a full selection of high-quality
chromatography data handling products and gas chromatography supplies and
columns through e-essentials.
To place an order for supplies and many replacement parts, request a free
e-essentials catalog, or ask for information:
Telephone:
•
U.S. only: Call toll free 1-800-762-4000, 8:30 a.m. to 7 p.m. EST. Your order
will be shipped promptly, usually within 24 hours.
•
Worldwide: Call your local PerkinElmer sales or service office or call
PerkinElmer, Shelton, CT USA
Internet: http://www.perkinelmer.com
45
Clarus 600 MS User’s Guide
46
About the
Clarus 600/560 D System
3
About the Clarus 500 System
About the Clarus 600/560 D System
The Clarus 600/560 D mass spectrometer is a compact benchtop instrument that
produces positive identification and quantitation of compounds separated by the
Clarus 600/560 D GC. Even if the compounds coelute, the mass spectrometer can
still positively identify and quantitate each compound. Clarus 600 MS is designed to
run analyses that best identify your sample by using the electron impact (EI) or
chemical ionization (CI) mode. The Clarus 560 D MS runs analyses that identify
your sample by using the electron impact (EI) mode.
The Clarus 600/560 D system is controlled by a PC using TurboMass Software. The
application runs in a Microsoft Windows XP SP2 operating environment. The
software user interface contains color graphics and provides full user interaction
with either the keyboard or the mouse. TurboMass completely controls the GC/MS
system from tuning and data acquisition (scanning or selected ion recording mode),
through quantifying your results. Complete operating instructions of all TurboMass
controls are in the TurboMass Software Guide (part number 0993-6767), supplied
with the system.
A high-performance, research-grade analytical quadrupole mass analyzer with a
quadrupole prefilter assembly transmits only those ions having your selected 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 converted to photons and detected by the
photomultiplier detector system. The low noise photomultiplier typically operates
with a gain of 105.
49
Clarus 600 MS Hardware Guide
Figure 3 Clarus MS with Clarus GC
The system consists of two major components: Clarus MS and the Clarus GC. Brief
descriptions of each major component follow.
50
About the Clarus 600/560 D System
Clarus 600/560 D GC
The Clarus 600/560 D Gas Chromatograph is a dual-channel, temperatureprogrammable gas chromatograph (GC). It is available in many configurations, such
as with or without, an autosampler, programmable pneumatic control (PPC), and a
variety of injector/detector combinations to provide you with total GC flexibility.
The Clarus 600/560 D GC is microprocessor controlled, where you enter the
operating parameters and view the prompting text and monitor instrument functions
on a large full-color touch screen display.
Figure 4 Clarus 600/560 D GC
The Programmed Pneumatic Control (PPC) Version of the Clarus 600/560 D GC
is used where the carrier gas and detector gases are monitored and controlled by the
microprocessor, thereby producing a fully automated system that is capable of
managing all pneumatic functions within the gas chromatograph.
51
Clarus 600 MS Hardware Guide
The Clarus 600/560 D GC can store up to five GC methods. Methods can be
generated, copied, deleted, edited, set up, and printed. These methods are normally
developed and stored on the TurboMass data system. The automatic liquid
autosampler can run up to 15 injections per vial from as many as 82 vials and one
priority vial using one or two autosampler programs (if not under TurboMass
control). In the latter case, a different GC method can be used by each program if
desired.
PPC provides real-time digital readouts to simplify setting carrier gas pressures and
flows.
Figure 5 Clarus 600 Mass Spectrometer
52
About the Clarus 600/560 D System
GC Interface (Transfer Line)
The detector end of a capillary GC column in the Clarus 600/560 D GC oven is
inserted through a temperature-controlled transfer line and optimally positioned so
that the column end is flush with the inner wall of the EI or CI ion source. The
transfer line is temperature controlled by Clarus MS and has a 350 °C upper limit. If
the Clarus 600 GC detects improper operation (for example, no carrier gas) and goes
into an alarm condition, it will turn off the temperature to the transfer line.
CAUTION
Do not use metal capillary columns in the transfer line. They may
electrically short-out the source.
Figure 6 The transfer line
53
Clarus 600 MS Hardware Guide
Reference Gas Inlet
The reference gas inlet system consists of a glass bulb filled with heptacosa (FC43)
connected to tubing which directs it to the ion source. You can switch the reference
gas solenoid valve on and off and also purge the reference gas lines from the Tune
screen.
Figure 7 and 8 shows the components or assemblies that comprise the Clarus
600/560 D MS with the manual vent switch (Clarus 600 D and Clarus 560 D) or the
CI adjustment valve (Clarus 600 C) configuration (see the following two pages).
54
About the Clarus 600/560 D System
RF Generator
Reference Gas Vial
Head Amplifier
Wide
Range
Gauge
Access Door
Forepump Line
Inner Source
Transfer Line
On/Off Switch
Diffusion Pump
Manual Vent Valve
For Diffusion Pump
Phosphor Plate
Conversion
Dynode
Photomultiplier
Tube
Grounding Plate
Lens 2
Exit Aperture
Lens 1
Analytical Quads
Pre-Quads
Outer
Source
Inner
Source
Figure 7 Components of the Clarus 600/560 D MS and a detail of the ion optics
path (manual vent valve for diffusion pump configuration)
55
Clarus 600 MS Hardware Guide
RF Generator
Reference Gas Vial
Head Amplifier
Wide
Range
Gauge
Access Door
Forepump Line
Inner Source
Transfer Line
On/Off Switch
Turbo Pump
CI Needle Valve
For Large Turbo Pump
Phosphor Plate
Conversion
Dynode
Photomultiplier
Tube
Grounding Plate
Lens 2
Exit Aperture
Lens 1
Analytical Quads
Pre-Quads
Outer
Source
Inner
Source
Figure 8 Components of the Clarus 600 MS and a detail of the ion optics path
(CI needle valve for large turbo pump configuration)
56
About the Clarus 600/560 D System
Ion Optics Path
Ion Source
The ion source consists of a removable EI or CI inner source and
a fixed outer source for the Clarus 600. The Clarus 560 D uses an
EI source only. In the EI source, molecules exit the column where
they are bombarded by electrons from the filament and ionized
into positive and negative ions as well as neutral species. The
positive electron trap attracts the negative ions and electrons to
the repeller that directs the positive ions out of the inner source
through focusing lens to the mass analyzer. Those remaining
molecules and neutral fragments are pumped away by the
vacuum. Heaters in the outer source raise the source temperature
high enough to prevent sample molecules from condensing in the
source and minimize any contamination.
Mass Analyzer
The mass analyzer element of this high performance quadrupole
mass spectrometer is a finely machined assembly that has been
precisely aligned using specialized equipment. Under no
circumstances should the main analyzer rod set assembly ever be
dismantled.
The mass spectrometer is fitted with a quadrupole prefilter
assembly that is designed to protect the main analyzer by
intercepting the majority of any contamination. As a
consequence, the main analyzer should never require cleaning.
On occasion, it may be necessary to remove the prefilter rods for
cleaning. The need to clean these rods is usually indicated by
poor peak shape or loss of resolution, although other more likely
causes, such as source contamination, should be eliminated first.
It is necessary to remove the inner and outer ion source assembly
before the prefilter assembly can be removed.
Detector
The detector consists of a conversion dynode, phosphor plate, and
photo-multiplier tube. The detector works by accelerating
positive or negative sample ions onto a dynode surface that emits
electrons. The electrons are then accelerated to strike a phosphor,
which produces photons of light that are amplified by the
photomultiplier and collected as the signal.
57
Clarus 600 MS Hardware Guide
Photomultiplier
The photomultiplier consists of a photosensitive surface and
electron multiplier sealed in a glass tube. The light strikes the
front window, electrons are emitted and accelerated onto the first
dynode of the electron multiplier and avalanche down the chain
of dynodes. The multiplier is sealed in its own permanent vacuum
chamber (glass tube) and cannot be contaminated. However,
contamination on the front window will raise the noise level and
lower the sensitivity.
Electronics
The Clarus 600/560 D MS electronics consist of a port in the PC,
an embedded processor & digital I/O board, analog board
(GC/MS), backplane board, PMT electrometer board, and high
voltage and low voltage power supply boards. The embedded
processor controls all aspects of instrument and data acquisition.
Ions exiting from the quadrupole are accelerated into a cupshaped dynode where they strike the inner surface. Electrons are
emitted into an electric field, which extracts them from the
conversion dynode and passes them onto the phosphor. The
phosphor is held at a higher positive potential than the dynode.
Light is emitted when the electrons strike the phosphor. The
resulting optical signal is detected by the photomultiplier (PMT).
58
About the Clarus 600/560 D System
Vacuum System
The source, ion optics, analyzer, and detector are fitted inside a cast aluminum
chamber. Vacuum is applied to the chamber using a rotary pump and a
turbomolecular pump. The vacuum is monitored through a wide range gauge. The
rotary pump sits on the floor and a turbomolecular high vacuum pump or an aircooled oil diffusion pump (Clarus 600 D) is mounted under the ion optics chamber:
Rotary Pump
The Clarus 600 MS has a 3 m3/hr computer controlled mechanical pump. The
turbomolecular or diffusion pump is backed by this direct drive rotary pump. The
rotary vane pump rests on the lab floor and may be positioned beneath the
instrument. Care should be taken to avoid mechanically coupling vibrations from
this pump to the mass spectrometer. Operation and maintenance details about these
pumps can be found in the manuals provided with the pump.
The rotary vane pump (also called the forepump) provides the first level of vacuum
to approximately 2 x 10-3 Torr. The pump has a switchable dual voltage.
59
Clarus 600 MS Hardware Guide
Voltage Selection
Switch Under Cover
Handle
TurboMass
Connection Port
Oil Filler Plug
Exhaust Port
Max
On/Off
Switch
Min
Gas Ballast
Switch
Mode Selection
Switch
Drain Plug
Oil Level
Indicator
Figure 9 The rotary (fore) pump
Connect the rotary pump exhaust to a line vented to the atmosphere outside the
laboratory or use an appropriate exhaust line filter.
CAUTION
The AC line cord for the rotary vane pump must be plugged into the
designated receptacle on the back of the Clarus 600 MS. The pump is
controlled by the TurboMass software.
Connecting the vacuum hose to the exhaust connection of the rotary
pump will severely contaminate the Clarus 600 MS.
60
About the Clarus 600/560 D System
Vacuum Pump Options
The Clarus 600 MS offers three different vacuum pump capacities. The
tubomolecular and diffusion pump options are designed to fit your applications,
performance and budgetary needs. The Clarus 560 D only utilizes a diffusion pump.
Turbomolecular Pump
Clarus 600 MS has two turbomolecular pump options in three configurations.
Turbomolecular pumps are high-speed turbines which transport the sample and
carrier gas molecules away from the mass spectrometer.
Clarus 600S - The 75 L/sec turbomolecular pump supports Electron Ionization
operation (EI) and has optional water cooling.
Clarus 600 T – All of the functions and options of the 600 S with a 255 L/sec
turbomolecular pump for higher column flow rates, pump-down time under three
minutes, and lower detection limits
Clarus 600 C - All of the functions and options of the 600 T with positive and
negative Chemical Ionization (CI) operation.
Diffusion Pump
Clarus 600 D and the 560 D MS has an air-cooled oil diffusion pump. This pump is
only available for Electrical Ionization (EI) operation.
Pump fluid is heated in the base of the pump to produce a vapor which passes
through the interior of the jet assembly and emerges from the jets as high-velocity
vapor streams. These streams entrain eluting compounds and carrier gas, condense
on the cooled pump body wall, and drain into the base of the pump for recirculation.
The entrained compounds are transferred to the forepump.
The diffusion pump system has a manual vent switch. This manual vacuum venting
is controlled by a push button toggle switch and a pump temperature sensing
switch. When you push the button in, the vent is opened. When the button is up
(not pushed in), the vent is closed. See the following illustration.
The mass spectrometer's vacuum system is controlled from the Tune page. Be sure that
this is done in accordance with the information provided in your Mass Spectrometry
Hardware Guide. The following procedures describe a Turbomolecular Pump system
and a Diffusion Pump system.
61
Clarus 600 MS Hardware Guide
Diffusion Pump Operating States
System Description
Vacuum System Off.
Backing pump turned on.
High vacuum pump is on.
Proper operating conditions reached.
Fault with high vacuum pump.
When vacuum system off has been initiated
62
System Diagram
About the Clarus 600/560 D System
Diffusion Pump Operating States Continued
System Description
System Diagram
When system has cooled and diffusion pump is
turned off.
When backing pump is turned off.
When vacuum leak is detected.
When vacuum gauge failure is detected.
When vacuum gauge failure is detected on start
up.
High vacuum pump is on.
When system has cooled and diffusion pump is
turned off.
Display count down
timer.
Display count down
timer.
63
Clarus 600 MS Hardware Guide
Turbomolecular Pump
Pumping Down a Turbomolecular Pump Vacuum System
¾ Select Pump/Vacuum System On from the Options menu on the Tune
page.
The menu name will change from Pump/Vacuum System On to
Vent/Vacuum System Off, and the system will begin its pump-down
sequence. Once OPERATE is enabled, it remains enabled unless the
Vent/Vacuum System Off command is given.
Venting the Vacuum System (Turbomolecular Pump)
1. Cool the source and inlet to below 100 °C.
2. Select Vent/Vacuum System Off from the Options menu on the Tune
page, and confirm that you want to vent the system.
Diffusion Pump
Pumping Down a Diffusion Pump Vacuum System
¾ Select Pump/Vacuum System On from the Options menu on the Tune
page.
The menu name will change from Pump/Vacuum System On to Vent/Vacuum
System Off, the roughing pump turns on and waits for the system to achieve a
minimum vacuum level of 3.7 x 10-1 Torr. Once that vacuum level has been
achieved, a relay turns on the diffusion pump heater and a countdown timer
starts. A typical vacuum level will stay constant until the count down timer
reaches 10 minutes, the vacuum drops quickly to 1 x 10-4 Torr, and continue to
4 x 10-5 Torr before the countdown timer ends.
When the timer reaches 5 minutes, the software will enable OPERATE. If you
attempt to use the system prior to achieving a safe operating vacuum
(5 x 10-5 Torr), a warning message will appear.
64
About the Clarus 600/560 D System
CAUTION
The software will not prohibit the use of the system prior to reaching
the desired vacuum. The software will monitor the vacuum gauge
pressure to determine when the system has reached the proper
operating vacuum (5 x 10-5 Torr).
Once OPERATE is enabled, it remains enabled unless the Vent/Vacuum
System Off command is given.
Venting the Diffusion Pump Vacuum System
1. Cool the transfer line and source to under 100 °C.
2. Select Vent/Vacuum System Off from the Options menu on the Tune
page, and confirm that you want to vent the system.
The system will start its automatic venting sequence. The software monitors
the temperature of the source and the inlet. When the temperatures of both
of the source and the inlet are less than 100 °C, the software turns off the
diffusion pump heater and starts a 20 minute countdown timer.
During the cooling down period, the countdown timer will display the time
remaining in minutes and seconds. When the count down timer reaches 0,
the backing pump turns off.
Once the backing pump has been turned off, the software will display a
message indicating that the system is now cool enough to vent. The message
also reminds you to turn off the carrier gas.
3. Vent the mass spectrometer by pressing the push-button behind the front
door of the mass spectrometer. It will lock in the pressed-in position and
turn red indicating the vent valve is open.
CAUTION
If you try to vent a hot diffusion system, oxidation of the pump oil may
occur and cause oil to enter the analyzer tub which will damage the
mass spectrometer.
65
Clarus 600 MS Hardware Guide
Access Door
Source
Manual Vent Valve
for the Diffusion Pump
The depressed push button vent switch lights when venting is allowed. Before
pressing Pump/Vacuum System On, make sure the vent switch is closed (the
button is out and the light is off)
Never vent when:
• The diffusion pump is hot
• During the 20 minute cool-down period
Always check that the front panel vent button is out and the lamp is off when
starting to pump the system down.
66
About the Clarus 600/560 D System
NOTE: The vent valve will operate if the vent switch is pushed in (on) before the diffusion
pump becomes hot. This includes the first few minutes of Pump/Vacuum System
On. Venting during this period may cause a vacuum fault to occur and risk back
streaming the diffusion oil into the analyzer. It is a good reminder to leave the
instrument front door open whenever the push button switch is pushed in (on).
NOTE: When the diffusion pump is hot, the vent switch is deactivated and will not light
when pushed in (on). Since the vent switch may be left in the depressed position at
any time, you should be careful to avoid closing the instrument door and forgetting
that the push button switch is pushed in. (When the diffusion pump cools, the
pushed in push button switch will light and automatically vent the system).
Vacuum Gauge
The single wide range vacuum gauge monitors the system pressure from atmosphere
down to 10-9 Torr using a combined Pirani/Inverted Magnetron ionization sensor.
Normal operating pressure with 1 mL/min helium for the 255 L/sec turbomolecular
pump is between 9x10-6 Torr and 2x10-5 Torr after pump-down and ion source bakeout. The 75 L/sec turbomolecular and the diffusion pumps will operate at somewhat
higher pressures, typically below 4x10-5 Torr.
67
Clarus 600 MS Hardware Guide
TurboMass Software
TurboMass software is the user interface of the Clarus system. The following
screens show some examples of how you can control Clarus. Interaction is via the
mouse and keyboard using menu-driven commands. Printing, file management and
other routine procedures are performed using the appropriate Microsoft Windows
modules.
Top Level Screen
This screen contains the GC/MS status, sample list, sequence queue, and provides
you with access to all other functions.
68
Clarus 600 GC-MS User’s Guide
Tune Page
The Tune Page allows you to tune the mass spectrometer, control the gases, set the
GC interface temperature, and monitor the instrument vacuum pressure.
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Clarus 600 MS Hardware Guide
Analytical Column
The analytical column inside the Clarus GC oven provides the sample separation.
Make sure you select the proper column for your analysis. PerkinElmer offers a
wide range of columns in the Gas Chromatography Column Catalog. The
TurboMass Tutorial provides additional column selection tips.
There are several things to consider when choosing an analytical capillary column:
1. Know the types of samples you will be analyzing. Are they volatile, semi-volatile,
pesticides, solvents, etc?
2. Select a stationary phase based on polarity of the sample. A very general rule in
column selection is that like dissolves like. Column polarity has the greatest effect
on how the column separates the compounds of interest as the sample interacts with
the stationary phase. There are different degrees of polarity from non-polar to very
polar. When compounds are separated primarily on their boiling points the phase is
considered to be non-polar. Polar phases typically separate compounds based on the
chemical interactions between the sample components and the stationary phase.
3. The inside diameter of the capillary column has an effect on the column’s resolving
power and its capacity or concentration range. In general, the larger the inside
diameter of the column, the larger the sample capacity. However, the larger the
inside diameter, the higher the flow necessary to achieve good performance.
4. The next parameter is the phase or film thickness. Film thickness will primarily
affect the retentive character and the capacity of the column. Increasing the film
thickness will cause an increase in the retention of the compounds being analyzed.
Thick film columns are primarily used for extremely volatile compounds. The
thicker phases will retain components longer, allowing them to interact longer with
the stationary phase, thereby increasing the separation of closely eluting compounds.
5. The last variable to consider is column length. The effect of column length on a
separation becomes less important as column length increases. Resolution is a
function of the square root of the column length. An example of this relationship is
that, if you want to double the separation between two peaks without changing the
stationary phase, inside diameter, film thickness, or GC conditions, it would take a
four-fold increase in the column length. A 30 meter column is the most common
length and is usually sufficient for analyzing most samples. Typically, users doing
environmental EPA type analysis will use a 30 meter column for semi-volatile
compounds and 60 to 105 meter columns for volatile compounds.
70
About the Clarus 600/560 D System
Pre-Operational Checklist
This checklist provides you with a list of items to check to make sure everything are
in working order before you begin to use Clarus.
Item
OK
Are the gases connected to the GC?
Is the proper column connected?
Is the proper liner installed in the injector?
Are your samples prepared?
Is there a GC method?
Is the GC split vent open?
Is the proper mass spectrometer vacuum achieved?
Is the system leak-free?
Is there a mass spectrometer method?
Are the autosampler wash vials filled with solvent?
Are you using the proper column flow or pressure?
Did you check the air/water spectrum on the TurboMass Tune screen?
Is the injector hot and set to the proper temperature?
Is the transfer line hot and set to the proper temperature?
Is the source hot and set to the proper temperature?
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Clarus 600 MS Hardware Guide
72
Maintenance
4
Overview
WARNING
High electrical voltage is present inside the mass spectrometer. To
prevent the risk of electrical shock or injury from high voltage, unplug
the AC line cord from the AC outlet and wait at least one minute before
opening or removing an instrument panel.
Disconnect AC power cord from outlet before removing any cover or
parts. Do not operate the instrument with any covers or parts removed.
WARNING
Do not attempt to make adjustments, replacements or repairs to this
instrument except as described in the accompanying user
documentation.
WARNING
NOTE: This equipment requires no specified inspection or preventive maintenance to ensure
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.
Clarus 600 MS Hardware Guide
•
Use tweezers and pliers whenever possible.
•
If nylon or cotton gloves are used, prevent leaving fibers in sensitive areas.
NEVER use rubber gloves.
•
Before reassembling and replacing dismantled components, inspect O-rings
and other vacuum seals for damage. If you in doubt, replace the O-rings and
vacuum seals with new ones.
If a fault occurs soon after repairing or disturbing a particular part of the system,
ensure that this part has been correctly refitted and/or adjusted and that any adjacent
components have not been inadvertently disturbed.
WARNING
76
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.
Maintenance
Typical Overall Maintenance Schedule
Performing maintenance tasks on a routine basis can reduce the overall costs of
operation. If a fault occurs, you can correct it with minimum difficulty.
Advanced maintenance should be performed by a skilled person capable of
removing complicated mechanical assemblies. For example, an untrained individual
should not attempt to remove the manifold but may be able to perform basic
maintenance such as draining and filling the forepump.
Exterior surfaces may be cleaned with a soft cloth dampened with a mild detergent
and water solution. Do not use abrasive cleaners or solvents.
Factory trained service personnel can assist in any advanced training needs. All
tasks should be logged into a logbook to keep a record of any problems or trends.
Daily
•
Make sure all system components are in working order.
•
Check and ensure that there are gas supplies to the GC and to the mass
spectrometer.
•
Check the air/water spectrum. Perform leak checking if necessary.
•
Enter information into a logbook.
Weekly
•
Check the tune and mass calibration. Tune if necessary.
•
Check the forepump oil level and color. Replace if necessary.
•
If equipped with a water chiller, check the water level and temperature.
•
If using CI, at the end of the day gas ballast the forepump lightly for 20
minutes.
77
Clarus 600 MS Hardware Guide
Monthly
•
Clean the fan filters on the rear of Clarus MS.
•
Check the reference gas vial. Refill if necessary.
Every Six Months
•
Replace the forepump oil.
•
Check the inner source. Clean if necessary.
•
Check the analyzer prequadrupole. Clean if necessary.
Yearly
78
•
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.
Maintenance
Leak Checking
Checking for leaks is actually checking the integrity of the vacuum system. You
observe masses 4 (helium), 18 (water), 28 (nitrogen), and 32 (oxygen).
To leak-check the system, follow this procedure:
1. Ensure that all connections are made to the mass spectrometer.
2. Set the GC split flow to 50 mL/min by pressing the PSSI injector icon on the
Clarus GC touch screen. On the next screen, press the split flow setpoint and use
the up and down arrow or keypad
buttons to set the split flow to
50mL. For example, if the capillary injector is in position 1 and you selected split
flow in the PPC configuration software, the following screen is displayed.
The total flow (split vent + septum purge + column) is displayed in the lower left
of the screen. The split vent flow setpoint is displayed in the setpoint box in the
lower right.
3. Start the TurboMass software by clicking on the Windows Start button at the bottom
left of the screen and selects TurboMass under the
Programs/TurboMass/TurboMass path, or double-click on the TurboMass icon if it
is on your Windows desktop.
79
Clarus 600 MS Hardware Guide
The initial TurboMass window is displayed.
4. Display the Tune dialog by clicking
.
The Tune dialog is displayed.
5. Make sure the Tune parameters are similar to the values displayed.
NOTE: The inlet and source temperatures should be less than 100°C only when venting the
system.
80
Maintenance
6. Click Press for Operate next to the red indicator box.
The indicator box color changes to green and the name of the button changes to
Press for Standby.
7. Select Pump from the Options menu.
This starts the forepump and the turbomolecular pump or diffusion pump
depending on which pump you have installed. Watch the vacuum gauge readout
and allow time for the gauge to achieve 4 x 10-5 Torr.
8. Observe the displayed masses.
Mass 4 (helium) should be much larger than mass 18 (water), which should be
larger than mass 28 (nitrogen), which should be about 4 times larger than mass 32
(oxygen).
9. If the nitrogen and oxygen are larger it indicates an air leak, which could damage
the filament. Immediately click Press for Standby to turn off the filament.
10. If a leak exists, locate and fix it.
Typical areas to check for leaks are around fittings and areas under vacuum.
81
Clarus 600 MS Hardware Guide
Tuning Clarus 600/560 D MS
After determining that no leaks exist and before acquiring data, you may need to
check the mass spectrometer tuning conditions and, if necessary, modify one or
more of the tuning parameters. Clarus MS can be tuned either manually or
automatically from the Tune window.
The left side of the page holds the tuning parameters for a selected region of the
mass spectrometer. You can change the region by selecting an item from the
Window menu, or by pressing one of the buttons on the bottom-left of the Tune
page.
The panel in the top right of the Tune page displays the tune peak information and
instrument pressure information.
The tune peak display is located on the right side of the screen and allows you to
view up to four masses. The corresponding check boxes located above the peaks
allow you to control each peak display. Any one of the tune peaks can be zoomed so
that it occupies the entire tune peak area. When a tune peak has been zoomed, the
82
Maintenance
controls for the mass and span for that peak are displayed at the top of the display
window. This enables you to display the pressure information while having control
over the peak display.
To display the Tune page:
1. While displaying TurboMass sample list screen click
.
The Tune page is displayed.
2. Turn on the filament and high voltages by clicking Press for Operate at the
bottom right of the window.
The indicator box turns green to indicate that it is on.
3. Select UltraTune/Custom (AutoTune) from the Options menu, then click
Start.
You will hear a click when the reference gas solenoid valve opens and
AutoTune begins. Upon completion, the message AutoTune completed
successfully is displayed.
4. Click OK.
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Clarus 600 MS Hardware Guide
5. Select Reference Gas On from the Gas menu to remove the check mark (9),
or click
to set it in the up position.
6. Save this new Tune of the instrument by selecting Save As from the File menu
and entering a name for this tune in the File name field.
A way to keep track of the tunes is to use dates for the file names.
7. Click Save.
Your mass spectrometer is now Tuned.
To ensure proper operation, check the mass calibration.
84
Maintenance
Preparing Clarus 600/560 D MS for
Hardware Maintenance
To prepare Clarus MS for hardware maintenance, there are several steps that are
common and precursory to all maintenance procedures. They are as follows:
Turn off the Operate Mode
1. Display the Tune window.
2. If the Press for Standby button is green (indicating an operating instrument),
switch it off by clicking on it.
85
Clarus 600 MS Hardware Guide
Cool the Transfer Line, GC Column Oven, and the Source
WARNING
The transfer line, GC oven, and source are HOT. Touching them can
cause serious burns. To prevent personal injury, wait until the oven and
transfer line reach the lower setpoint temperature before touching
them. Only grab and hold the source by its handle.
1. On the left side of the Tune page enter 20 in the Inlet Line Temperature to
cool the GC Interface (transfer line).
CAUTION
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 Tune page, set the source temperature by entering 20 in the Source
Temp field.
4. Allow the transfer line, column oven, and source to cool before touching them.
Remember, the transfer line was heated and it may take at least
10 to 20 minutes to cool.
WARNING
CAUTION
86
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 be used. To properly
connect a source of dry nitrogen to the instrument order the
manifold venting kit (Part No. N647-0045).
Maintenance
Vent the System
1. Once both the Inlet Line and Source temperatures have dropped below 100 °C,
select Vent/Vacuum System Off from the Options menu.
The Vent Pump dialog appears. All pumps are turned off.
2. Click OK.
3. Observe the Vacuum Pressure Gauges status on the Tune window.
The gauge goes to ZERO after the turbopump reaches 50 % speed and the vent
valve is opened.
NOTE: Mass Spectrometer venting may take several minutes depending on the helium flow
and/or vent gas flow into the manifold.
4. The system is now vented to atmosphere (or optional dry gas).
Turn off the GC Carrier Gas
CAUTION
Turn off helium carrier gas flow to the MS if you do not have a purge
flow of high purity nitrogen.
Do not allow the vented mass spectrometer to fill with helium for more
than 5 hours.
Failure to do so can damage the photomultiplier detector and require
a service call not covered by warrantee or contract.
Set all temperatures to ambient. Once the GC column oven, source, and transfer line
are cool you may then turn off the GC carrier gas.
87
Clarus 600 MS Hardware Guide
Changing a Column
CAUTION
To ensure that the mass spectrometer remains contamination free, wear
powder-free, lint-free gloves while performing this procedure.
Tools and Items Required
•
New column.
•
Column wafer scribe (Part No. N930-1376).
•
Two high-temperature septa.
•
Two ¼-inch open-end wrenches
•
Lint-free, powder-free PVC gloves (Part No. N621-2495).
•
1/16-inch graphite/Vespel ferrules (0.8 mm i.d., Part No. 0992-0107, 0.25 mm
i.d., Part No. 0992-0104 or 0.325 mm i.d., Part No. 0992-0105).
Removing a Column
1. Prepare the mass spectrometer for hardware maintenance (see Preparing
Clarus 600/560 D MS for
Hardware Maintenance on page 85).
2. Using a ¼-inch open-end wrench, loosen the 1/16-inch column nut attached to
the injector fitting and slide the column tubing completely from the injector
and column nut.
88
Maintenance
Injector
1/16-inch Column Nut
Remove Column
3. Using a ¼-inch open-end wrench, loosen the 1/16-inch column nut on the
transfer line. Slide the column tubing completely from the transfer line and
column nut. Remove the column from the GC oven.
Remove Column
Transfer Line
Septum
1/16-inch Column Nut
Figure 10 Removing a column
4. Open the Clarus 600 MS access door, loosen and remove the two black
thumbscrews, hold the source by the handle, and pull it out.
CAUTION
To prevent contamination, only hold the source by its handle. Never
touch the part of the source that comes in contact with ions with your
bare fingers.
89
Clarus 600 MS Hardware Guide
5. Place the source on a clean surface. Preferably place the handle end on a flat
surface so that the source stands in an upright position.
Access
Door
Inner Source
Black
Thumbscrews
Handle
Figure 11 Removing the source
90
Maintenance
Connecting the New Column to the Split/Splitless
Injector
This procedure describes how to connect a column to a capillary injector. For
procedures to connect a column to a PSS or POC injector refer to “Installing a
Capillary Column” in Chapter 6 of the Clarus GC User’s Manual (Part Number
0993-6780).
CAUTION
This injector has a fragile 1/16-inch fitting. To preserve the integrity of
the fitting:
• Carefully tighten the nut on the fitting.
• Do not cross-thread or overtighten the nut on the fitting.
• Allow the injector to cool before connecting a nut.
1. Unwind 20 cm (8 inches) from one end of the column.
20 cm
Column
Figure 12 Unwinding 20 cm from the injector end
91
Clarus 600 MS Hardware Guide
2. Insert a septum, 1/16-inch column nut (part number 09903392), and 1/16-inch
graphite ferrule (0.8-mm i.d. Part Number 0992-0141, or 0.5-mm i.d. Part
Number 0990-3700) over one end of the column as shown in Figure 13 .
1/16-inch
Graphite/Vespel
Ferrule
Column
1/16-inch Column Nut
Septum
Column
Figure 13 Inserting the nut and ferrule on the column
NOTE: Verify that the tapered end of the ferrule is facing towards the nut as shown above.
3. Cut about 1 cm (3/8 inch) from the column end using a wafer scribe
(part number N930-1376, pkg. of 10 scribes). Break off the tubing at the score
mark so that the break is clean and square. Examine the cut with a magnifying
glass and compare it to the examples shown in Figure 14.
Good Cut
Bad Cuts
Figure 14 Good cut and bad cuts
92
Maintenance
4. Locate the capillary injector fitting inside the oven.
1/8-inch Capillary
Injector Fitting
Figure 15 Location of the capillary injector in the oven
5. Position the septum on the column as shown in the following table:
Injector Type
Column Insertion Dept
(measured from the back of the nut to the end of the column)
CAP
4.44 to 5.1 cm (1¾ to 2 inches)
PSS
3.8 to 4.44 cm (1½ to 1¾ inches)
POC
Flush with the septum end of the injector
6. Insert the column into the capillary injector fitting.
7. Hand-tighten the column nut ¼ turn past fingertight.
8. Using two ¼-inch wrenches tighten the column nut only until the column
cannot be pulled out of the fitting.
CAUTION
Do not overtighten column nuts. Overtightening can cause damage to
the ferrule and/or column.
93
Clarus 600 MS Hardware Guide
Connecting a New Column to Clarus 600 MS
1. Uncoil 50 cm (20 inches) from the new column. Place the column on the
column hanger in the oven.
50 cm
Column
Figure 16 Uncoiling 50 cm from the transfer line end
2. Slide the septum, 1/16-inch column nut and 1/16-inch graphite/Vespel ferrule
over the end of the column.
Column
1/16-inch
Graphite/Vespel
Ferrule
1/16-inch Column Nut
Column
Septum
Figure 17 Inserting a septum, column nut and ferrule on a column
3. Slide the septum, column nut, and ferrule along the column to the position
shown below. Score and break 1.0 cm off the end of the column. Wipe the
column with a methanol dampened lab tissue (for example, a Kimwipe).
94
Maintenance
Use glove.
the septum, column nut,
1. Slide
and ferrule to this position.
1 cm
Column
end of column
2. Cut
off here
the column
3. Wipe
with a Kimwipe
dampened with MeOH.
Figure 18 Preparing to install the column in the transfer line
4. Carefully insert the end of the column through the transfer line and into the
mass spectrometer source until it is positioned midway between the hole and
the wall on the right side of the source. See Figure 19.
5. Hold the column in this position as you slide the column nut and ferrule to the
transfer line and tighten the nut fingertight. Slide the septum until it is flush
against the rear of the column nut. See Figure 20.
This marks the position of the column end in the source.
NOTE: Finger tight means just tight enough to hold the column in place so that you are still
able to move the column slightly if necessary to reposition it.
95
Clarus 600 MS Hardware Guide
Clarus 600
Mass Spectrometer
Clarus 600
Gas Chromatograph
Insert Column into Transfer Line
Transfer Line
2 mm or midway
between the hole
and the wall
Hole
Column End
Wall
Figure 19 Positioning the column end in the source assembly
96
Maintenance
Septum
1/4-inch Column Nut
1/16-inch Column Nut
Figure 20 Marking the column position in the source
6. Pull the column back until the distance between the back of the nut and septum
is about 10 cm.
CAUTION
To prevent breaking the end off the column, you need to pull the column
back to reinstall the source in the mass spectrometer.
97
Clarus 600 MS Hardware Guide
Septum
1/16-inch Column Nut
10
metric
20
30
Column
40
50
60
70
8
Slide the column back until the
septum is 10 mm from nut.
Figure 21 Pulling the column back to reinstall the source
7. Position the inner source so it aligns with the guide pin, gently insert the source
into the mass spectrometer, and secure it in place with the two black
thumbscrews. Tighten the black thumbscrews until they are fingertight.
Do not overtighten.
Access
Door
Ma ssClarus 60
Spec 0
tro me
Inner Source
Black
Thumbscrews
Handle
Figure 22 Reinstalling the source
98
ter
Maintenance
8. Carefully slide the column into the transfer line until the septum is flush to the
back of the column nut. To make a leak-free seal, use a ¼-inch wrench to
tighten the column nut ¼ turn past fingertight.
Injector
1/16-inch Column Nut
Slide Column
Flats for the 5/32-inch
(4 mm) on the transfer line
Septum flush to the back
of the column nut.
1/16-inch Column Nut
Figure 23 Repositioning the column in the source
Checking for Leaks
1. Start the carrier gas flow and leak-check the fittings for leaks.
CAUTION
To ensure maximum sensitivity, if this is a new column condition the
column to its maximum accepted operating temperature, even if the
column manufacturer claims that it is preconditioned.
2. Start the vacuum by selecting Pump from the Options menu on the Tune
window. Monitor the vacuum and search for leaks if necessary.
Refer to the vacuum leak-checking procedure described in Leak Checking on
page 79.
3. Once you have verified that no leaks exist, set the transfer line temperature to
its original value and close the GC oven door to heat the column.
99
Clarus 600 MS Hardware Guide
Refilling the Reference Gas Vial
It is time to refill the reference gas vial when you lose reference gas peaks intensity
and you do not see a liquid in the reference gas vial, or any time the mass
spectrometer is vented, and the liquid in the vial level appears low.
NOTE: You should check liquid level in the reference gas vial any time you need to remove
the mass spectrometer cover and vent the instrument. Using a tool such as a dental
mirror will help you observe the liquid level in the Reference Gas Vial.
Items Required
•
Lint-free, powder-free PVC or polypropylene gloves (Part No. N621-2495).
•
Pasteur Pipette or 50 µL syringe.
•
Heptacosa (FC43) (Part No. N621-2407).
To refill the reference gas vial, follow this procedure:
Make sure to vent the instrument and turn the power off.
WARNING
1. Ensure that the solenoid have been switched off.
100
Maintenance
2. With the power off, unplug the source connector for more room to work. Use a
5/32 inch Allen wrench to remove the two allen nuts from the handle. See
following photo.
Source Connector
Allen Nuts
3. With the handle off remove the reference gas vial assembly and bracket out.
See the following figure.
101
Clarus 600 MS Hardware Guide
Figure 24 Removing the reference gas vial from the mass spectrometer
The toxicity of the FC-43 calibrant is uncertain. Take appropriate
precautions to avoid getting the calibrant on your skin or in your eyes.
WARNING
4. Loosen the knurled fitting behind the gas vial by ½ turn, and pull out the vial.
A black O-ring may remain in the fitting.
5. Using a pipette or syringe, add 25 to 50 µL but no more than 50 µL of
Heptacosa (FC43). See the following figure. Fill the bulb.
Never add more than 50 µL.
102
Maintenance
Gas Tight
Syringe
Reference
Gas Vial
Figure 25 Filling the reference gas vial
6. Re-insert the reference gas vial into the mass spectrometer. Make sure the O-ring
is still present and the tapered end of the ferrule faces the mass spectrometer.
7. Tighten the knurled nut with your fingers until fingertight.
8. Return the bracket to the proper position and use a 5/32 inch Allen wrench to
retighten the two Allen nuts to the bracket.
9. Replace the top cover and pump the system down to the proper vacuum.
10. From the Gas Menu select the Reference Gas Option from the drop down menu.
Leave the Reference Gas Valve open for 60 minutes with Operate off to pump to
pump out the gas from the bulb before tuning the mass spectrometer.
NOTE: On the Tune Page the Gas drop down the Pump Out Reference Gas choice no
longer works. If you try to have both the Reference Gas On and the Pump Out
Reference Gas options selected you will get an error message. To avoid an error
message make sure to only check Reference Gas On.
103
Clarus 600 MS Hardware Guide
Inner Source Maintenance
Inner source maintenance consists of cleaning those components that contact ions.
For example,
•
EI source: the ionization chamber, repeller, trap, ion exit plate, and ion entry
area.
•
CI source: the ionization chamber, ion entry area, and ion exit plate.
CAUTION
Never clean the filament. If the filament is open, replace it by following
the procedure in this chapter.
Items and Tools Required
104
•
Ultrasonic bath.
•
Aluminum foil or lint-free disposable cloth squares.
•
Aluminum oxide powder.
•
Wooden stick cotton swabs.
•
2 mm open-end wrench (for EI source).
•
Tweezers.
•
Powder-free, lint-free gloves (Part No. N621-2495).
•
Small flat-blade screwdriver.
•
Reagent Grade acetone.
•
Reagent Grade methanol.
•
De-ionized Water
•
Clean 100 mL glass beaker.
•
6000 Grade Micro Mesh (Part No. N930-3420).
•
8000 Grade Micro Mesh (Part No. N930-3421).
•
600 grit aluminum oxide in DI Water with a few drops of methanol to make a
paste
Maintenance
Removing the Inner Source
To remove the inner source, follow this procedure:
CAUTION
Before performing source maintenance, always prepare the mass
spectrometer by following the instructions in Preparing Clarus 600/560
D MS for
Hardware Maintenance on page 85.
1. Prepare the mass spectrometer for maintenance as described in Preparing
Clarus 600/560 D MS for
Hardware Maintenance on page 85.
2. Open the GC oven door and locate the Clarus MS transfer line.
3. Using a 9/16-inch wrench, loosen the ¼-inch nut on the transfer line.
4. Pull the inner transfer line tube back 25 mm (1 inch).
Transfer Line
Remove
Column
1/4-inch Nut
Figure 26 Pulling back the transfer line
105
Clarus 600 MS Hardware Guide
5. Loosen the two thumbscrews on the inner source, grab it by its handle, pull it
out of the mass spectrometer and set it on a clean surface.
6. Close the mass spectrometer access door.
7. Put on a pair of powder-free, lint-free gloves (Part No. N621-2495).
Access
Door
Inner Source
Black
Thumbscrews
Handle
Figure 27 Removing the inner source
EI Inner Source Maintenance
To gain access to the parts on the EI inner source that need cleaning, follow this
procedure.
NOTE: For this procedure use the Inner Source Rebuild Kit Part No. E640-0043.
CAUTION
106
To ensure that the mass spectrometer remains contamination free, wear
lint-free, powder-free gloves (Part No. N621-2495) while performing
this procedure.
Maintenance
Disassembling
1. Prepare a clean, uncluttered work area and place a square of aluminum foil
with the shiny side up. Obtain some clean, small containers (for example, small
beakers) to store the screws and small parts as you remove them.
2. Using a small flat-blade screwdriver, loosen the screw that secures the old
filament assembly to the source. Use tweezers to remove the screw and washer.
Pull out the filament assembly.
Defective
Filament
Assembly
Screw
(P/N E531-4043)
Washer
(P/N E533-1031)
Figure 28 Removing the filament assembly
107
Clarus 600 MS Hardware Guide
3. Using a small flat-blade screwdriver, loosen and remove the four screws on the
ion chamber cover plate and remove the cover plate.
4. Using a 2 mm open-end wrench, loosen and remove the nut and washer that
secure the repeller. Then remove the repeller.
5. Using a 2 mm open-end wrench, loosen and remove the nut and washer that
secure the ion trap. Then remove the ion trap.
Trap
(P/N E640-1220)
Clean this
area.
Screw (4)
2 mmSpacer
(P/N E640-1222)
12 mm Spacer
(P/N E640-1221)
Clean underside
of Ion Exit Plate.
(P/N E640-1213)
Clean this
area.
Repeller
(P/N E640-1219)
Clean these
areas.
2 mm Spacer
(P/N E640-1222)
12 mm Spacer
(P/N E640-1221)
6 mm Ceramic Spacer
(P/N E640-1224)
Trap Contact
(P/N E640-1217)
6 mm Ceramic Spacer
(P/N E640-1224)
Washer
Nut
Viton O-Ring
(P/N E571-1061)
Insulator
(P/N E640-1218)
Repeller Contact
(P/N E640-1216)
Washer
Nut
Figure 29 Removing the ion chamber cover plate and repeller
108
Maintenance
Cleaning
NOTE: You can do the following cleaning method of aluminum oxide paste or use the 6000
or 8000 grade micro mesh to polish the flat surfaces of the parts. For either
cleaning method, the final step you must sonicate the parts in an ultrasonic bath of
methanol for at least five minutes. Dry off the parts using lint-free tissue and/or
clean compressed Nitrogen gas to prevent solvents from drying on these parts and
leaving a residue
1. Mix together aluminum oxide and de-ionized water and a few drops of
methanol to make a watery paste.
2. Dip a wooden-stick cotton swab in the solution and clean the darkened areas on
the source. Work quickly to prevent the mixture from drying on the surface.
Place the cleaned components in de-ionized water prior to rinsing to prevent
drying.
Rinsing
1. Add 50 mL of acetone to a 100 mL beaker, insert the source assembly, repeller,
ion trap, ion chamber plate, and sonicate in an ultrasonic bath for ten minutes.
CAUTION
Do not allow the acetone and methanol to touch the O-ring on the
source.
2. Carefully drain the acetone.
3. Add 50 mL of methanol to another 100 mL beaker, insert the source assembly,
repeller, ion trap, ion chamber plate, and sonicate in an ultrasonic bath for at
least ten minutes.
4. Carefully drain the methanol.
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Clarus 600 MS Hardware Guide
Source Assembly
50 mL sonocation solution
in 100 mL Beaker
Figure 30 Rinsing the aluminum oxide from the source
5. Dry off the repeller, ion trap, source assembly and ion chamber plate using lintfree tissue and/or clean compressed Nitrogen gas to prevent solvents from
drying on these parts and leaving a residue.
6. Take the parts amd wrap them in a clean, lint-free cloth and bake them in the
GC oven at about 80 ºC for about fifteen minutes.
Reassembling
1. Insert the ion trap and repeller through the spacer and insulator. Then insert it
into the source.
110
Maintenance
Ion Trap
(P/N E640-1220)
Repeller
(P/N E640-1219)
2 mm Spacer
(P/N E640-1222)
2 mm Spacer
(P/N E640-1222)
12 mm Spacer
(P/N E640-1221)
12 mm Spacer
(P/N E640-1221)
Figure 31 Inserting the ion trap and repeller into the inner source
2. Invert the source and insert a crumpled laboratory wipe into the repeller and
ion trap.
3. Using tweezers, install the remaining ceramic pieces, spacers and nut first on
the ion trap and then on the repeller.
4. Tighten each nut with a 2 mm open-end wrench.
111
Clarus 600 MS Hardware Guide
5. Replace the filament assembly.
Nut
(P/N E532-1018)
Washer
(P/N E533-1013)
Nut
(P/N E532-1018)
Trap Contact
(P/N E640-1217)
Washer
(P/N E533-1013)
6 mm Ceramic Spacer
(P/N E640-1224)
Repeller Contact
(P/N E640-1216)
Locator
(P/N E640-1218)
and Clarus 560 D
6 mm Ceramic Spacer
(P/N E640-1224)
Post removed to show
parts assembly path
Laboratory Wipe crumpled and inserted
into the ion chamber and trap areas.
Figure 32 Installing the ceramics, contacts, washers and nuts on the repeller
and ion trap
112
Maintenance
Ensure filament coil
aligns with hole.
Rhenium
Filament Assembly
(P/N N6470012)
Screw
Washer
Contacts
Figure 33 Replacing the filament assembly
CI Inner Source Maintenance
The supplied CI inner source assembly can be used for both negative CI and positive
CI. The maintenance procedures for the CI source are very similar to those of the EI;
however, the CI does not have a repeller or ion trap. It does have a smaller exit
aperture to ensure that the sample ions properly react with the CI gas.
CAUTION
To ensure that the mass spectrometer remains contamination free, wear
lint-free, powder-free gloves (Part No. N621-2495) while performing
this procedure.
To gain access to the parts on the CI inner source that need cleaning, follow this
procedure.
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Clarus 600 MS Hardware Guide
Disassembling
1. Prepare a clean, uncluttered work area and place a square of aluminum foil
with the shiny side up. Obtain some small containers (for example, small
beakers) to store the screws and small parts as you remove them.
2. Using a small flat-blade screwdriver, loosen the screw that secures the old
filament assembly to the source. Use tweezers to remove the screw and washer.
Pull out the filament assembly.
Defective
Filament
Assembly
Screw
(P/N E531-4043)
Washer
(P/N E533-1031)
Figure 34 Removing the filament assembly
3. Using a small flat-blade screwdriver, loosen and remove the four screws on the
ion chamber cover plate and ion aperture plate, then remove the plates.
114
Maintenance
Screw (1 of 4)
Underside of the Ion Exit
Plate (P/N E640-1213) shown.
Clean the underside
of the CI Ion Exit Plate
(P/N E640-1214).
Clean these
areas.
Figure 35 Removing the ion chamber and aperture plates and cleaning the
areas shown
Cleaning
NOTE: You can do the following cleaning method of aluminum oxide paste or use the 6000
or 8000 grade micro mesh to polish the flat surfaces of the parts. For either
cleaning method, the final step you must sonicate the parts in an ultrasonic bath of
methanol for at least five minutes. Dry off the parts using lint-free tissue and/or
clean compressed Nitrogen gas to prevent solvents from drying on these parts and
leaving a residue
115
Clarus 600 MS Hardware Guide
1. Mix together aluminum oxide and de-ionized water and a few drops of
methanol to make a watery paste.
2. Dip a wooden-stick cotton swab in the solution and scrub the darkened areas on
the source. Work quickly to prevent the mixture from drying on the surface.
Rinsing and Reassembling
1. Add 50 mL of acetone to a 100 mL beaker, insert the source assembly, ion
aperture plate, ion chamber plate, and sonicate in an ultrasonic bath for ten
minutes.
CAUTION
Do not allow the acetone and methanol to touch the O-ring on the
source.
2. Carefully drain the acetone.
3. Add 50 mL of methanol to another 100 mL beaker, insert the source assembly,
ion aperture plate, ion chamber plate, and sonicate in an ultrasonic bath for at
least ten minutes.
4. Carefully drain the methanol.
Source Assembly
50 mL sonocation solution
in 100 mL Beaker
Figure 36 Rinsing the aluminum oxide from the source
116
Maintenance
5. Dry off source assembly and plates using lint-free tissue and/or clean
compressed Nitrogen gas to prevent solvents from drying on these parts and
leaving a residue.
6. Take the parts amd wrap them in a clean, lint-free cloth and bake them in the
GC oven at about 80 ºC for about fifteen minutes.
7. Reassemble the ion aperture plate and ion chamber plate on the source.
8. Replace the filament assembly.
Screw (1 of 4)
Underside of the Ion Exit
Plate (P/N E640-1213) shown.
Clean the underside
of the CI Ion Exit Plate
(P/N E640-1214).
Clean these
areas.
Figure 37 Reassembling the CI inner source
117
Clarus 600 MS Hardware Guide
Ensure filament coil
aligns with hole.
Rhenium
Filament Assembly
(P/N N6470012)
Screw
Washer
Contacts
Figure 38 Replacing the filament assembly
118
Maintenance
Reinstalling the Source
1. Position the source so it aligns with the guide pin, gently insert the source into
the mass spectrometer, and secure it in place with the two black thumbscrews.
Tighten the black thumbscrews until they are fingertight. Do not overtighten
the thumbscrews.
Access
Door
Inner Source
Black
Thumbscrews
Handle
Figure 39 Reinstalling the source in the mass spectrometer
2. Insert the inner transfer line tube back in the outer transfer line.
3. Tighten the ¼ inch transfer line nut fingertight.
To make a leak-free seal use a 9/16 inch wrench to tighten the ¼ inch nut an
additional 1/8 turn. Tighten it enough to make a leak-free seal but do not
overtighten the nut.
119
Clarus 600 MS Hardware Guide
Transfer Line
Replace
Column
1/4-inch Transfer
Line Nut
Figure 40 Reconnecting the transfer line
Checking for Leaks
1. Start the carrier gas flowing and leak-check the fittings for leaks.
2. Start the vacuum by selecting Pump/Vacuum System On from the Options
menu on the Tune window. Monitor the vacuum and search for leaks if
necessary. Refer to the leak checking procedure described in Leak Checking on
page 79.
3. Once you have verified that no leaks exist, set the transfer line temperature to
its original value, and close the GC oven door to heat the column.
120
Maintenance
Replacing a Filament
CAUTION
Make sure you are wearing powder-free PVC gloves (Part No. N6212495), and that you wipe each part with a methanol dampened
Kimwipe.
Items and Tools Required
•
Filament assembly (Part No. E6400209).
•
Tweezers.
•
0.8 mm hex wrench.
•
Methanol.
•
Powder-free, lint-free gloves (Part No. N621-2495).
•
Small flat-blade screwdriver.
•
Aluminum foil or lint-free disposable cloth squares.
To replace a filament, follow this procedure.
1. Prepare a clean, uncluttered work area and place a square of aluminum foil with
the shiny side up.
2. Remove the EI source by following the procedure Removing the Inner Source as
described on page 105.
CAUTION
To ensure that the mass spectrometer remains contamination free,
make sure you are wearing powder-free, lint-free gloves (Part No.
N621-2495), and that all tools have been cleaned with a methanoldampened laboratory wipe.
3. Using a small flat-blade screwdriver, loosen the screw that secures the defective
filament assembly to the source. Use tweezers to remove the screw and washer.
4. Pull out the defective filament assembly.
121
Clarus 600 MS Hardware Guide
Defective
Filament
Assembly
Screw
(P/N E531-4043)
Washer
(P/N E533-1031)
Figure 41 Removing the defective filament assembly
5. Using a 0.8 mm hex wrench, loosen the two screws that secure the contacts to
the filament assembly leads. Remove the two contacts.
122
Maintenance
0.8 mm
Hex Wrench
Contacts
Defective Filiment
Assembly
Figure 42 Removing contacts from the defective filament assembly
6. Position the new filament assembly with the filament side up.
7. Insert the contacts on the new filament assembly leads so that they are flush with
the white ceramic and positioned with the hex screw side facing up.
8. Secure the contacts to the filament assembly by tightening the hex screws with a
0.8 mm hex wrench. Tighten firmly but do not overtighten.
123
Clarus 600 MS Hardware Guide
1. Insert Contacts
New Filament Assembly
(P/N E647-0012)
Contacts (2)
(P/N E640-1215)
2. Secure Contacts
0.8 mm
Hex Wrench
Figure 43 Installing contacts on the new filament assembly
9. Position the new filament assembly so that it faces the source and the white
ceramic rests on the tab.
10. Ensure that the filament coil is aligned with the entrance hole on the inner source
assembly.
124
Maintenance
11. Using a small flat-blade screwdriver, secure the filament assembly in place with
the screw and washer that you previously removed.
Ensure that the filament coil
aligns with the entrance hole.
Filament Coil
Tab
New Filament
Assembly
Screw
Washer
Contacts
Tab positioned between contacts.
Figure 44 Installing a new filament assembly on the source
12. Install the source assembly back into the mass spectrometer by following the
procedure described in Reinstalling the Source on page 119.
125
Clarus 600 MS Hardware Guide
Replacing the Head Amplifier
To replace the Photomultiplier head amplifier (Part Number E649-9032), follow this
procedure and refer to Figure 45:
The mass spectrometer contains high voltage. To prevent the risk of
shock, unplug the line cord from the AC outlet and wait at least one
minute before opening or removing any instrument cover or panel.
WARNING
1. Vent the vacuum from the mass spectrometer.
2. Turn off the mass spectrometer.
3. Unplug the AC line cords from the AC outlets.
4. Remove the four screws securing the rear panel and remove the rear panel.
5. Remove the two screws on the left side of the top panel and remove the top
panel.
6. Remove the head amplifier board cover.
7. Remove the cable connector to the board.
8. Pull off head amplifier board, removing the screw with the ground wire on it.
9. Install a new board, making sure that you do not over-tighten the screw with
the ground wire.
NOTE: Pins on the photomultiplier are key for proper alignment.
10. Replace the photomultiplier head amplifier board cover, cable connector,
replace the panels, turn on the mass spectrometer, and pump-down the system
to the proper vacuum.
126
Maintenance
11. Go to the Head Amplifier electronic adjustment procedure.
Detail of Photomultiplier
Tube Pin Connections
Note keying position of
short pin when plugging
the Photomultiplier Tube
into the Head Amplifier
Board
Head Amplifier Board
(P/N E640-9032)
Cover
Ground Cable
Nut
Lock
Washer
Figure 45 Replacing the head amplifier
127
Clarus 600 MS Hardware Guide
Mass Analyzer Maintenance
The analyzer element of any high performance quadrupole mass spectrometer is, of
necessity, a finely machined assembly that has been precisely aligned using
specialized equipment. Under no circumstances should you ever disassemble the
main mass analyzer assembly.
The mass spectrometer is fitted with prequads that act as a prefilter assembly
designed to protect the analytical quads by intercepting the majority of any
contamination. As a consequence, the analytical quads should never, under normal
working conditions, require cleaning. Occasionally, it may be necessary to remove
the prefilter rods for cleaning. The need to clean these rods is usually indicated by
poor peak shape or loss of resolution, although other more likely causes, such as
source contamination, should be eliminated first.
Items and Tools Required
•
•
•
•
•
•
•
•
•
•
•
•
•
•
128
4 mm hex wrench.
5 mm hex wrench.
Lint-free, powder-free PVC gloves (Part No. N621-2495).
Wooden stick cotton swabs.
Deionized Water
6000 Grade Micro Mesh (Part No. N930-3420).
8000 Grade Micro Mesh (Part No. N930-3421).
600 grit aluminum oxide in DI Water with a few drops of methanol to make a
paste
Small flat-blade screwdriver.
Long flat-blade screwdriver.
Aluminum foil.
Acetone.
Methanol.
Tweezers.
Maintenance
Cleaning Materials
When cleaning internal components it is important to maintain the quality of the
surface finish. Deep scratches or pits can cause loss of performance. Where no
specific cleaning procedure is provided, you should use fine abrasives to remove dirt
from metal components. Recommended abrasives are:
•
6000 Grade Micro Mesh (Part No. N930-3420).
•
8000 Grade Micro Mesh (Part No. N930-3421).
•
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 the Ion Optics Assembly
To remove the EI inner source, follow this procedure:
CAUTION
Before performing source maintenance, always prepare the mass
spectrometer by following the instructions in Preparing Clarus 600/560
D MS for
Hardware Maintenance on page 85.
1. Prepare the mass spectrometer for maintenance as described in Preparing
Clarus 600/560 D MS for
Hardware Maintenance on page 85.
2. Open the GC oven door and locate the mass spectrometer transfer line.
3. Using a 9/16-inch wrench, loosen the ¼-inch nut on the transfer line.
129
Clarus 600 MS Hardware Guide
Risk of burns. Never touch a heated mass spectrometer transfer line or
a GC injector cap with unprotected (bare) fingers.
WARNING
4. Pull the inner transfer line tube back 25 mm (1 inch).
Transfer Line
Remove
Column
1/4-inch Nut
Figure 46 Pulling back the transfer line
5. Loosen the two thumbscrews on the inner source, grab it by its handle, gently
pull it out of the mass spectrometer, and set it on a clean surface.
130
Maintenance
6. Close the mass spectrometer access door.
Access
Door
Inner Source
Black
Thumbscrews
Handle
Figure 47 Removing the inner source
Removing the Mass Spectrometer Cover Panels
The mass spectrometer contains high voltage. To prevent the risk of
shock, unplug the line cord from the AC outlet and wait at least one
minute before opening or removing any instrument cover or panel.
WARNING
1. Turn off the Clarus GC and Clarus MS.
2. Unplug the AC line cords from the AC outlets.
3. Remove the four screws securing the rear panel, remove the rear panel, and lay it
on the bench. If necessary, disconnect the fan wires.
4. When reconnecting the fan wires, make sure the fan blows the air into the mass
spectrometer.
131
Clarus 600 MS Hardware Guide
5. Remove the two screws on the left side of the top panel and remove the top panel.
NOTE:
The rear panel vent fan should NOT be removed
from the instrument. It is removed in this illustration
only to clearly show how to access the PMT Access
Panel. ONLY remove the PMT Access Panel.
Screws (4)
Figure 48 Removing the mass spectrometer panels
132
Maintenance
Removing the Photomultiplier Tube
1. Unplug the cable from the head amplifier board.
2. Using a long flat-blade screwdriver, loosen the two captured screws securing
the photomultiplier tube (PMT) amplifier cover, and remove the cover.
PMT Amp
Cover
Lock
Screw
NOTE:
The rear panel vent fan should NOT be removed
from the instrument. It is removed in this illustration
only to clearly show how to access the PMT Access
Panel. ONLY remove the PMT Access Panel.
Figure 49 Removing the PMT amplifier cover
3. Using a 4 mm hex wrench, remove the screw securing the PMT amplifier
board-grounding strap.
4. Carefully remove the amplifier board from the PMT by pulling it straight back.
133
Clarus 600 MS Hardware Guide
5. Using a 4 mm hex wrench, remove the screws securing the PMT flange to the
vacuum chamber.
6. Put on a pair of powder-free, lint-free gloves.
7. Carefully remove the PMT. Cover it with a laboratory wipe and place it in a
safe, dark place.
8. Insert a crumpled laboratory wipe into the PMT hole in the vacuum chamber to
prevent particulates from entering the vacuum chamber.
Head Amplifier Board
(P/N E640-9032)
Cover
Ground Cable
NOTE:
The rear panel vent fan should NOT be removed
from the instrument. It is removed in this illustration
only to clearly show how to access the PMT Access
Panel. ONLY remove the PMT Access Panel.
Nut
Lock
Washer
Figure 50 Removing the head amplifier board and the PMT
134
Maintenance
Removing the Ion Optics Assembly
Make sure to vent the instrument and turn the power off and
unplug the mass spectrometer from the AC power source.
WARNING
1. Disconnect the cables connected to the ion optics assembly and place them to
the side so they will not interfere with the removal of the ion optics assembly.
See the following figure.
2. Disconnect the Reference and CI gas lines from the top of the ion optics
assembly. See the following figure.
REAR VIEW
Ion Optics Assembly
Phosphor
Dynode
Source
Reference Gas
CI Gas
RF Generator
Cable
Location of Reference
Gas Vial Assembly
Handle
Fan Plug
Figure 51 Disconnecting cables and tubing from the ion optics assembly
135
Clarus 600 MS Hardware Guide
3. With the power off , unplug the source connector for more room to work. Use a
5/32 inch Allen wrench to remove the two allen nuts from the handle. See
following photo.
Source Connector
Allen Nuts
4. With the handle off remove the reference gas vial assembly and bracket out and
move it out to the side of the instrument. See the following photo.
136
Maintenance
5. Remove the four hex head bolts loosely holding the ion optics assembly to the
vacuum chamber. See the following figure.
6. Grabbing the ion optics assembly by the two handles, carefully lift the ion
optics assembly straight up and away. See the following figure.
Fan Plug
Hexagon
Head Bolt (4)
Handle
Handle
Guide Pins
Figure 52 Lifting the ion optics assembly from the vacuum manifold
137
Clarus 600 MS Hardware Guide
7. Place the ion optics assembly on a clean work surface, with the RF box down
and the mass analyzer facing up (see Figure 3).
8. Cover the open vacuum chamber with aluminum foil to prevent particulates
from contaminating the chamber.
Outer Source
Assembly
of Ion Optics
Assembly
Prequads
Analytical Quads
Figure 53 Positioning the ion optics for maintenance
Cleaning the Prequads
When operating under normal circumstances, you may not have to remove the
prequads from the ion optics assembly. To clean the prequads, follow this
procedure.
1. Using a very fine abrasive paper (8000 grade) gently clean the ion burns off of
the prefilters.
138
Maintenance
2. Wipe the prequads with a methanol dampened laboratory wipe.
3. Blow dry with helium or dry nitrogen.
Replacing an Outer Source Thermocouple
Items and Tools Required
•
Thermocouple (Part No. E640-0213).
•
Lint-free, powder-free PVC gloves (Part No. N621-2495).
•
Small flat-blade screwdriver.
•
Small adjustable wrench.
To replace the thermocouple, follow this procedure and refer to the following figure:
CAUTION
To ensure that the mass spectrometer remains contamination free, wear
lint-free, powder-free gloves while performing this procedure.
1. Using a small flat-blade screwdriver, remove the screw and the thermocouple.
2. Loosen and remove the nut.
3. Remove all wires from the contact pins.
4. Pull all the wires down through the feed connector
5. Thread the new wires up through the feed connector and connect all the wires
on the contact pins. Tighten the nuts.
6. Secure the new thermocouple with the screw.
139
Clarus 600 MS Hardware Guide
1.
Remove the
screw securing
thermocouple (1)
(P/N E640-0213)
2.
Loosen and
Remove Nut
Feed
Connector
3.
Remove all wires
from contact pins
(10)
4.
Pull all wires down
through feed connector
5.
Thread all new wires
up through feed connector and
connect wires on contact pins
6.
7.
Secure the
replacement
thermocouple
with the screw.
Figure 54 Replacing the thermocouple
140
Tighten
Nut
Maintenance
Removing the Outer Source from the Ion Optics
To remove the outer source from the ion optics, follow this procedure (use Outer
Source Rebuild Kit, Part No.E640-0042):
1. Position the ion optics assembly as shown.
Outer Source Assembly
of Ion Optics
Assembly
2. Detach wires and tubes from outer source assembly as required.
Remove tubes
Remove screw
Disconnect wires
3. Remove
the two screws securing
outer source to the ion optics.
the outer source assembly
4. Place
on a clean work surface.
Screw (1 of 2)
(one each side)
Figure 55 Removing the outer source from the ion optics assembly
141
Clarus 600 MS Hardware Guide
Replacing Outer Source Heaters
Items and Tools Required
•
Two Cartridge heaters (Part No. E640-0202).
•
Tweezers.
•
Lint-free, powder-free PVC gloves (Part No. N621-2495).
•
Small flat-blade screwdriver.
To replace the outer source heaters, follow this procedure:
1. Position the outer source base plate on a clean work area so that the clamp plate
faces up.
2. Using a flat blade screwdriver, loosen the three screws that connect to the three
pillars.
CAUTION
The four ceramic rods (Part Number E640-1319) are very fragile. Use
extreme care when removing the support plate and lens.
3. Carefully lift the clamp plate (Part Number E640-1322) straight up and put it
aside.
4. Carefully lift and remove the contact support plate from the four ceramic rods.
5. Remove the pillar.
6. Unplug the outer source heaters from the quadrupole heater.
7. Using a flat-blade screwdriver, loosen the outer source heater setscrews.
8. Slide the old heaters out of the outer source block and insert the new heaters
(Part Number E640-0202).
9. Tighten the setscrews 1/8 turn past fingertight.
Do not overtighten the setscrews.
10. Connect the heater wires together and plug the quadrupole heater wire into the
remaining connector.
11. Reassemble the outer source.
142
Maintenance
Screw (1 of 3)
(P/N E531-4016)
Clamp Plate
(P/N E640-1322)
Contact Support Plate
(P/N E640-1229)
Heater
Locking
Screws
Pillar
(P/N E640-1320)
Source Heaters
(P/N E640-0265)
Figure 56 Replacing heaters in the outer source
143
Clarus 600 MS Hardware Guide
Replacing the Quadrupole Heater
The quadrupole heater is connected in series with the two outer source heaters.
Items and Tools Required
•
Cartridge heater (Part No. E640-0202).
•
Small flat-blade screwdriver.
•
Lint-free, powder-free PVC gloves (Part No. N621-2495).
To replace the quadrupole heater, follow this procedure:
1. Unplug the quadrupole heater wire from the outer source heater wires.
2. Loosen the setscrew that secures the quadrupole heater to the standoff.
3. Slide the heater out, discard it, and slide the new heater into the standoff.
4. Secure the heater in place by tightening the setscrew 1/8 turn past fingertight.
Do not overtighten the setscrew.
5. Plug the quadrupole heater wire into the outer source heater wire connector.
144
Maintenance
Outer Source Assembly
of Ion Optics
Assembly
Cartridge Heater Setscrew
Quadrupole
Cartridge Heater
(P/N E640-0266)
To outer source
cartridge heater (other side)
Purple wire
To outer source
cartridge heater (this side)
Quadrupole Cartridge
Heater Connections
Figure 57 Removing the quadrupole heater
145
Clarus 600 MS Hardware Guide
Cleaning the Outer Source Lens
Items and Tools Required
•
600 grit aluminum oxide.
•
Tweezers.
•
Methanol.
•
Laboratory wipes.
•
Acetone.
•
Lint-free, powder-free PVC gloves (Part No. N621-2495).
•
Small flat-blade screwdriver.
•
Wooden stick cotton swabs.
To clean the outer source, follow this procedure:
1. Position the outer source on a clean work area so that the side with the support
plate is facing up.
2. Using a flat-blade screwdriver, loosen the three screws that connect to the three
pillars.
3. Carefully lift the support plate straight up and put it aside.
4. Carefully remove the Lens 2, then Lens 1 focus plates.
146
Maintenance
Cleaning
1. Mix together aluminum oxide and methanol to make a watery paste.
2. Dip a wooden-stick cotton swab in the solution and clean the darkened areas on
the source. Work quickly to prevent the mixture from drying on the surface.
3. Remove the residual aluminum oxide by sonication in a beaker of methanol for
ten minutes.
4. Blow dry with helium or dry nitrogen.
5. Reassemble the outer source.
147
Clarus 600 MS Hardware Guide
3 x 10 Screw (1)
(P/N E531-4017)
3 x 6 Screw (1 of 2)
(P/N E531-4016)
Support Plate
(P/N E640-1321)
2mm Ceramic Spacer
(1 of 4)
(P/N E640-1222)
Lens 2 Focus Plate
(P/N E640-1235)
5mm Ceramic Spacer
(1 of 4)
(P/N E640-1325)
Clean these areas.
Lens 1 Focus Plate
(P/N E640-1307)
Ceramic Rod
(1 of 4)
(P/N E640-1319)
Pillar (1 of 3)
(P/N E640-1320)
Figure 58 Removing the lenses from the outer source for cleaning
148
Maintenance
Reassembling the Ion Optics Assembly
The following drawing is an exploded view of the outer source showing all parts
with their part numbers.
3 x 6 Screw (1 of 3 top)
(P/N E531-4016)
Clamp Plate
(P/N E640-1322)
Wavy Washer
(1 of 8)
(P/N E533-5005)
Typical Contact Attachment
2mm Ceramic Spacer
(1 of 4)
(P/N E640-1222)
Ceramic Rod
(1 of 4)
(P/N E640-1319)
Stainless Steel Spring Contact
(P/N E640-1389)
Copper Spring Contact
(P/N E640-1230)
Screw (1 of 7)
(P/N E531-4044)
Stainless Steel Spring Contact
(1 of 3) (P/N E640-1390)
Copper Spring Contact
(1 of 3) (P/N E640-1231)
Pillar (1 of 3)
(P/N E640-1320)
12mm Metal Spacer
(1 of 4)
(P/N E640-1324)
Outer Ion Block
(without magnet)
(P/N E640-1233)
7.7mm Metal Spacer
(1 of 4)
(P/N E640-1323)
2mm Ceramic Spacer
(1 of 4)
(P/N E640-1222)
5mm Ceramic Spacer
(1 of 4)
(P/N E640-1325)
2mm Ceramic Spacer
(1 of 4)
(P/N E640-1222)
Contact Terminal
(1 of 3)
(P/N E640-1328)
Copper Spring
Contact
(P/N E640-1232)
Contact Support Plate
(P/N E640-1229)
Stainless Steel Spring
Contact
(P/N E640-1391)
Magnet
(P/N E640-1227)
Magnet Cap
(P/N E640-1226)
4mm Ceramic
Insulating Spacer
(P/N E640-1317)
Lens 1 Focus Plate
(P/N E640-1307)
2mm Ceramic
Insulating Spacer
(P/N E640-1222)
Lens 2 Focus Plate
(P/N E640-1235)
Washer
(P/N E533-1013)
Nut
(P/N E532-1018)
Support Plate
(P/N E640-1321)
3 x 6 Screw (1 of 2 bottom)
(P/N E531-4016)
3 x 10 Screw (1)
(P/N E531-4017)
Earth Plate
(P/N E640-1326)
Figure 59 Exploded view of the outer source
149
Clarus 600 MS Hardware Guide
1. Place the assembled outer source on the ion optics assembly and secure it in
place with the two screws.
2. Reattach the tubing to the outer source.
the assembled outer source on the ion optics
1. Place
assembly and secure it in place with the two screws.
Ion Optics
Outer Source
Screws (2)
(one each side)
2. Reattach the tubes to the outer source assembly.
Reattach tubes
Figure 60 Reinstalling the outer source
3. Using a flat-blade screwdriver, reconnect the thermocouple to the outer source.
150
Maintenance
4. Reconnect the wires to the outer source as shown in the following illustration.
Outer Source Assembly
of Ion Optics
Assembly
To outer source
cartridge heater (other side)
Quadrapole Cartridge Heater
Contact Support Plate
(See Detail)
Thermocouple Wires
Ground
(green/yellow wire)
Purple wire
To outer source
cartridge heater (this side)
Lens 2 Focus Plate
(green wire)
Wiring Connections
to the Contact
Support Plate
Orange wire
Lens 1 Focus Plate
(gray wire)
Trap (yellow wire)
(View from Front)
Contact Ring
Part No.
N6470055
Repeller
(white wire)
(black wire)
(red wire)
Filament
Figure 61 Reconnecting the wires to the outer source
151
Clarus 600 MS Hardware Guide
Reassembling the Clarus 600/560 D MS
To reassemble the mass spectrometer, follow this procedure:
1. Remove the aluminum foil covering the vacuum manifold.
2. Hold the ion optics assembly by its handles and align the guide pins with the
holes in the vacuum manifold.
3. Gently lower the ion optics assembly until it is seated on the vacuum manifold.
4. Replace the four screws and tighten fingertight.
5. Remove the laboratory wipe from the PMT hole and reinstall the PMT
assembly. Observe the orientation of the PMT tube as shown in the detail.
6. Insert the end of the head amplifier ground wire through one of the screws for
the PMT assembly. Insert this screw into the hole in the 2 o’clock position and
insert the other screw in the other hole. Tighten both screws fingertight. Using
a 4 mm hex wrench, tighten both screws ¼ turn past fingertight.
7. Plug the head amplifier board onto the pins on the PMT.
152
Maintenance
Detail of Photomultiplier
Tube Pin Connections
Note keying position of
short pin when plugging
the Photomultiplier Tube
into the Head Amplifier
Board
Head Amplifier Board
(P/N E640-9032)
Cover
Ground Cable
Nut
Lock
Washer
Figure 62 Reinstalling the PMT
8. Reinstall the PMT head amplifier cover and secure it in place with the two
captured screws.
9. Replug all the cables and reconnect the tubing.
10. Reinstall the top and rear panels.
11. Reinstall the source.
153
Clarus 600 MS Hardware Guide
Vacuum System Maintenance
Vacuum system maintenance consists of the following:
•
Checking the forepump to ensure the oil is at the proper level.
•
Adding oil to the forepump reservoir.
•
Replacing forepump oil.
•
Replacing foreline trap pellets.
Complete pump instructions are in the instruction manual supplied with the pump.
Maintanenace of the Turbomolecular and Diffusion
Pump
You should never service the turbomolecular and diffusion pumps. Call your
PerkinElmer Service Representative for the maintenance and any problems you may
have with these pumps.
Checking the Forepump Oil Level
1. Locate the oil level indicator window on the forepump.
154
Maintenance
Voltage Selection
Switch Under Cover
Handle
TurboMass
Connection Port
Oil Filler Plug
Exhaust Port
Max
On/Off
Switch
Min
Gas Ballast
Switch
Mode Selection
Switch
Drain Plug
Oil Level
Indicator
Figure 63 Location of the forepump oil viewing window
2. Determine if the oil level is between the Max Oil Level and Min Oil Level
marks next to the window.
•
If the oil level is closer to the Min Oil Level mark, add oil. Use Edwards 45 oil
(Part No. 0992-3492, 1 liter).
•
If it is near the scheduled six-month service, drain and refill the pump with
clean oil.
•
If the oil is contaminated (indicated by a darkened color), try gas ballasting and
if that does not help, drain and refill the pump with clean oil.
155
Clarus 600 MS Hardware Guide
Adding Oil to the Forepump Reservoir
CAUTION
Vent the mass spectrometer before opening the plug to add oil.
1. Unscrew and remove one of the filler plugs on the top of the pump.
2. Locate the bottle of pump oil supplied with the pump and add oil until it
reaches the MAX mark on the top of the sight glass. Do not overfill.
3. Replace the oil filler plug by tightening it until it is fingertight. Do not
overtighten the oil filler plug.
4. After restarting the pump and allowing it to run for a few minutes, recheck the
oil level. If the oil level is below the MAX mark, repeat the above procedure by
adding more oil until it reaches the MAX mark.
Decontaminating the Oil
The pump oil should be clear. If the oil is cloudy or discolored, it is contaminated
with residual sample vapors.
1. Observe the oil in the oil sight glass.
2. Turn the mode selector fully counterclockwise to select the High Throughput
mode and set the gas ballast control to the low flow (position I).
3. Run the pump until the oil appears clear.
Replacing the Oil
1. Warm the oil by running the pump for at least 10 minutes, and then switch off
the vacuum system.
2. Unplug the pump from the AC outlet and disconnect it from your vacuum
system.
3. Remove one of the oil filler plugs.
156
Maintenance
Filler Plug
Max Oil Level
Min Oil Level
Drain Plug
2 Liter
Drain Container
Figure 64 Draining forepump oil
157
Clarus 600 MS Hardware Guide
4. Place the pump on a table. Place a drain container under the drain plug. Raise
the end of the pump opposite the drain plug by putting a block under it.
If you were running toxic samples, the oil is contaminated as toxic
waste. Handle and dispose of waste oil appropriately.
WARNING
5. Remove the drain plug and allow the oil to drain into the container.
If the pump oil was contaminated, pour clean oil into the filler hole and allow it
to drain until the oil appears clear.
6. Replace the drain plug, remove the block and reconnect the vacuum system.
7. Add oil until it reaches the MAX mark on the top of the sight glass.
Do not overfill.
8. Replace the oil filler plug by tightening it until it is fingertight.
Do not overtighten the oil filler plug.
9. After restarting the pump and allowing it to run for a few minutes, recheck the
oil level. If the oil level is below the MAX mark, repeat the above procedure by
adding more oil until it reaches the MAX mark.
158
Maintenance
Inline Gas Purifiers
The inline gas purifier lets you change the trap without introducing contaminants
into your system. This eliminates the need to flush the system. The trap contains
oxygen, moisture and hydrogen adsorbents and is packed and purged under helium.
Color changes in the glass indicating trap will indicated when filter needs to be
replaced.
The click on connector fitting has a spring loaded needle valve, which seals when
the trap is removed and only opens when the new trap is connected and locked into
position. When the click on connectors are installed into the gas line here is no need
to loosen or tighten any fittings, the new trap will just click in.
Replacement Traps
Description
Part No.
Indicating Glass Triple Gas specific (He)
Oxygen/Moisture/Hydrocarbons
N09306107
Indicating Glass Triple Gas specific (He)
Oxygen/Moisture/Hydrocarbons with 1/8” Brass Connector (2)
N09306114
Indicating Glass Triple Gas specific (He)
Oxygen/Moisture/Hydrocarbons with 1/8” Steel Connector (2)
N09306116
Click On Connectors
Description
Part No.
1/8” Brass Connector (2)
N09306119
1/8” Steel Connector (2)
N09306120
Stain steel Connector (for connecting two click on traps)
N09306121
Refer to the installation instructions that accompany your new in line gas purifier
trap for detailed installation and operating instructions.
159
Clarus 600 MS Hardware Guide
Changing from EI to CI Mode
Changing modes consists of the following:
•
Connecting the CI gas.
•
Changing the source and instrument control mode.
•
Leak-checking.
•
Setting-up CI.
Connecting the CI Gas
WARNING
Hazardous gas vapors. When using ammonia gas when running in the
chemical ionization (CI) mode, it is necessary to vent the mass
spectrometer effluent from the forepump exhaust into a fume hood or
outside the building.
Explosive Hazard. If the hydrogen is turned on without a column
attached to the injector and/or detector fittings inside the oven, the gas
could diffuse into the oven creating the possibility of an explosion.
If the mass spectrometer is not under vacuum, hydrogen, can fill the
vacuum chamber thereby creating an explosive hazard.
WARNING
160
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.
Maintenance
Recommended Gases
Reagent gases used in chemical ionization (CI) are methane with a minimum purity
of 99.999%, isobutene with a minimum purity of 99.98% and ammonia with a
minimum purity of 99.998%. Carrier gas tubing should be ultra-clean.
Methane and isobutene require a gas delivery pressure of 15 psi (104 kPa) to the
bulkhead fitting on the back of the mass spectrometer. A two-stage stainless steel
diaphragm, high purity regulator is. A single-stage stainless steel diaphragm, high
purity, rated for corrosive service is required for ammonia. Clean tubing must be
used. It must be solvent-washed and nitrogen-dried. The bulkhead connector at the
rear of the instrument is a 1/8 inch Swagelok fitting.
To prepare Clarus 600 MS for CI:
NOTE: Make sure to purge the CI line before you attach it to the rear of the mass
spectrometer.
1.
Obtain the CI gas cylinder for your analysis.
2.
Connect the gas line to the CI Gas connector on the rear of the mass
spectrometer.
3.
Ensure that the mass spectrometer is at the proper vacuum level.
4.
Turn on the CI gas and set the delivery pressure to 15 psi (104 kPa).
5.
Leak-check all connections.
161
Clarus 600 MS Hardware Guide
ROTARY PUMP
Rotary
Pump
Power
Warning
POWER IN
NH 3
CH4
C 4H 10
CI GAS
N2
VENT
WATER
IN
15 psi
(103 kPa)
MAX
5 psi
(35 kPa)
MAX
50 psi
(345 kPa)
MAX
WATER
OUT
Warning
Labels
Vacuum
Line
Figure 65 CI Gas connection on the rear panel of the mass spectrometer
Changing to CI
To change from the EI to the CI mode:
1. Remove the EI inner source by following the procedure described in earlier in
this chapter, Removing the Inner Source.
2. Install the CI source by following the procedure described in on page 105.
Properly cover and protect the EI source and put it in a safe place.
3. Select CI+ from the Ion Mode menu.
The CI+ window appears.
162
Power In
Maintenance
4. Select Pump from the Options menu.
This starts the forepump and the turbomolecular pump.
5. In the Vacuum Pressure Gauges area of the window, observe the Pirani gauge
time line and the Penning gauge time line. Wait about 5 minutes until the
vacuum gauge achieves about 2.5 x 10-5.
Leak Checking
Before running in the CI mode, confirm that the column is properly installed and the
system is leak-free. The best way to check this is by running CI without the reagent
gas.
163
Clarus 600 MS Hardware Guide
To leak-check the system:
1. Display the Tune page.
2. Select CI+ from the Ion Mode menu.
164
Maintenance
3. Click Press for Operate and observe the air/water masses.
The CI source running in the CI mode without reagent gas to produce an EI
emission similar to the EI mode but with reduced sensitivity. You will leak-check
your system this way.
If mass 28 is larger than mass 18, you have a leak. Determine the source of the leak
and correct it. For example, leak-check all fittings and connections.
Setting-Up CI
After verifying that no leaks exist, you can proceed to set up the CI mode for an
analysis.
165
Clarus 600 MS Hardware Guide
Setting the Parameter Values
1. Display the following CI window:
2. Set the values as shown above.
The following table describes the CI parameters to check:
166
Parameter:
CI+ Values and Comments:
Electron energy
30 eV
Emission
Should be below 200 µA, although 200 to 300 µA is acceptable.
(Above 200 mA may cause hydrocarbon “cracking” patterns with
methane and isobutane.) Emission measures the real emission current,
i.e. the source current from the source block, there is no trap "source
current" in CI.
Lens 1 and 2
The tuning of these lenses may be different from the optimum values set
for EI, since the source pressure is much higher in CI.
Multiplier
200V to 600V
Ion Energy
Approx. 1. Similar to EI.
Source temperature
150 ºC
Maintenance
Adjust the Reagent Gas for CI+
When running in the CI+ mode with reagent gas off, the resulting EI spectra have
about 10x lower sensitivity than with the EI source.
If using methane reagent gas, the reagent ions at m/z 17 (CH5+) and 29 (C2H5+)
should be of approximately equal intensity. Maximize the m/z 29 intensity. With
m/z 29 maximized, the ion at m/z 16 should be about 1% of the m/z 17 peak height.
(Higher indicates a leak at the transfer line/inner source connection.) Operate
slightly to the low-pressure side of the maximum to minimize gas load on the MS.
(The vacuum gauge pressure will be 1.5x10-4 to 5x10-4 Torr.)
If using ammonia reagent gas, reagent ions at m/z 18 (NH4+) and 35 [(NH3)2H+]
should be present and the ions at m/z 35 should be optimized.
If using isobutane reagent gas, the reagent ions at m/z 43 (C3H7+) and 57 (C4H9+)
should be tuned in the approximate ratio of 1:2.
The following example uses methane reagent gas.
NOTE: The CI gas adjustment knob controls a delicate needle valve. To avoid damaging the
needle valve, do not overtighten it. Always use the CI gas button on the screen to
turn off the CI gas.
167
Clarus 600 MS Hardware Guide
Access Door
Inner Source
Black Knurled Knobs
Figure 66 CI reagent gas needle valve adjustment knob
1. Carefully turn the delicate CI Gas adjustment knob fully clockwise until you
feel it stop.
2. Select CI Gas On from the Gas menu. A check mark appears next to the
option.
NOTE: Always turn on the CI gas before Operate to avoid a pressure surge hitting the
filament.
168
Maintenance
3. Click Press for Operate and monitor the Penning gauge as you adjust the CI
gas. Observe that mass 16 initially grows larger. As pressure increases in the
ion chamber of CI source, the mass 29 peak will begin to grow. Keep the
pressure below 5 e-4 Torr.
4. When using methane gas, carefully turn the CI adjustment knob
counterclockwise until m/z 16 is low or non-existent, and m/z 29 is maximized.
As you turn the knob, reduce the multiplier voltage to keep the peaks on scale.
A typical multiplier value is 235.
m/z 17 and 29 will typically be 80 – 100%.
5. Continue to turn the knob counterclockwise. Observe that the pressure
increases and mass 41 will start to grow. Stop when mass 29 is at 100%.
169
Clarus 600 MS Hardware Guide
6. Turn the knob to maximize the intensity of mass 29. Also verify that mass 16 is
small (< 1.0% of the height of the peak at mass 17).
If mass 16 does not appear as a small peak, STOP. You probably have a gas
leak at the transfer line/inner source connection. Locate and correct the leak.
7. After you have maximized the peak, slightly decrease the reagent gas by
turning the knob clockwise 1/8 turn.
170
Maintenance
8. Tuning may be optimized on the m/z 69, 219, 414, and 652 ions of the
heptacosa reference gas.
9. Click Press for Standby to turn off Operate, followed by the CI gas.
You are now ready to run your CI+ analysis.
171
Clarus 600 MS Hardware Guide
Adjust the Reagent Gas for CI1. Open the CI gas inlet by selecting CI Gas from the Gas menu. Wait at least 10
seconds before clicking Press for Operate.
Parameter:
Electron Energy
Emission
CI− value and comments:
30 to 70 eV
(This parameter should be optimized.)
200 to 300 μA is acceptable
(Emission measures the real emission current, i.e. the
source current from the source block, there is no separate
measurement of source current in CI.)
Lens 1 and 2
The tuning of these lenses may be different
from the optimum values set for EI, since the
source pressure is much higher in CI.
Multiplier
200V to 600V
Source temperature
150 °C is standard. Higher temperatures keep
the source cleaner, but may increase
fragmentation.
For example, down a little from EI to minimize
fragmentation. 120 °C is the practical lower limit.
Ion Energy
Approx. 1 or 2
2. Optimize the amount of reagent gas flowing into the source by using two
heptacosa ions, m/z 452 and 633, which usually produce relative intensities of
65 – 85% and 95% respectively.
Heptacosa can be used to calibrate the m/z range for negative ion CI analyses.
172
Maintenance
3. Maximize the peak intensities, then slightly decrease the reagent gas by turning
the knob clockwise 1/8 turn.
Optimize the tuning parameters for maximum intensity.
4. Save the Tune page parameters by selecting Save As…from the File menu.
5. Select Calibrate Instrument from the Tune page Calibration menu.
6. Select heptaneg.ref from the drop-down menu.
CAUTION
Make sure the “Use Air Refs” check box is not selected.
173
Clarus 600 MS Hardware Guide
7. Click the Start button to display the following dialog box.
8. Click Acquisition Parameters and enter the following values.
9. Click OK to begin calibration.
You are now ready to run CI analysis.
174
Troubleshooting
5
Clarus 600 MS Hardware Guide
176
Overview
The following sources of problems can occur in gas chromatography and mass
spectrometry:
•
The operator: When the operator is new to chromatography/mass
spectrometry and/or a new instrument, problems can be introduced during the
learning curve. Once the operator becomes familiar with both the technique
and the instrument, this problem source diminishes greatly.
•
The sample: Unlike clean standards, real world samples such as
environmental samples can introduce problems because they are difficult to
handle, have complicated matrices, contain unknown constituents, etc.
•
The column: The column is most often the major factor contributing to poor
analyses. The more a column is used, the greater the possibility of
contamination, loss of substrate, etc. Columns do not last forever and should be
changed when results become suspect.
•
The gas flow system: Gas leaks are a major concern in gas chromatography
and can lead to many problems.
•
The vacuum system: Vacuum leaks are a major concern in mass spectrometry
and can lead to many problems.
•
Ion Optics: Over time, the ion optics can become contaminated. This results in
reduced sensitivity and difficult or impossible tuning.
•
The electronics: The problem must be identified as either chromatographic or
hardware. Electronics used in the system can malfunction.
•
Data handling: Today, most chromatographers rely on sophisticated data
handling systems to integrate their results. Some problems can be related to the
incorrect data handling parameter settings or hardware problems with the
computer.
Clarus 600 MS Hardware Guide
Spare Components
The following list contains items you should have on hand to help solve problems.
•
New syringes: a syringe can break, become plugged or begin leaking. Always
have spare syringes available.
•
Duplicate columns: a column does not last forever; always have a duplicate
column on hand in the event that your separation begins to degrade. Also,
capillary columns can be damaged if oxygen is introduced at high
temperatures. A duplicate column will allow you to determine if the column is
the cause of the problem.
•
Septa: this is the one area of the gas chromatograph that requires routine
maintenance. Always have spare septa available.
•
Leak detector: the gas flow system can be a problem as fittings wear with age
and can begin to leak. You should have a thermal conductivity leak detector to
help find and fix leaks.
•
Injector liners: are made of glass or fused silica and can be easily broken when
removed. You should keep a supply of spare liners on hand. Please remember
that you cannot run satisfactory analyses without an injector liner.
Logical Troubleshooting Steps
There are some simple steps that you should take when trying to locate a problem.
Use the following guide to troubleshoot your system.
1. Note the symptoms - define the problem. Compare your runs with good
analysis, that is, with the results normally obtained.
2. Systematically eliminate possible causes.
The first rule here is, "What did you change last?" Many times a problem
arises when a change is made to the system, such as changing a gas tank,
column, septum or glass liner. If the problem occurred after such a change,
then the change is the most likely cause of the problem.
Change the simplest thing first. For example, if you suspect a gas leak, the
easiest change to make is the GC septum instead of replumbing the internal
pneumatics.
178
Change only one parameter at a time and check for its effect. If you change
three items at once and your problem goes away, you may not know which of
the three moves or combination of moves corrected the problem. This way, if
the problem happens again, you will know exactly what corrective action to
take.
179
Clarus 600 MS Hardware Guide
Troubleshooting Chart
Problem
Probable Cause
Solution
Mass Spectrometer will
not turn on (no indication
of power to the
instrument).
AC line cord not plugged into
an AC outlet.
Plug the Mass
Spectrometer AC line cord
into an AC outlet.
No AC power to the outlet.
Check the outlet.
Fuse blown.
Call a PerkinElmer service
engineer.
Forepump is not plugged into
the AC outlet on the rear of
the mass spectrometer.
Plug the forepump line
cord into the mass
spectrometer.
Forepump is not operating
correctly ( mass spectrometer
does not pump down).
Make sure the forepump is
switched on.
Blown fuse in Mass
Spectrometer.
Call a PerkinElmer service
engineer.
Mass Spectrometer is on
but the forepump is not
running.
180
Problem
The ultimate pressure is
poor.
Probable Cause
Solution
Is the cooling inadequate? Check the cooling-air flow and
correct if possible.
Check the cooling-air duct for
obstructions and correct as
necessary.
If the cooling air flow is fine
and there are no obstructions
contact your PerkinElmer
service representatives.
The pump is very noisy or
there is excessive vibration
or both.
181
Is the backing pressure
high?
Check for a leak in the backing
pipeline and poor backing
pump performance. Correct as
necessary.
Is the noise irregular and
getting progressively
worse?
If so, a bearing may be
defective. Contact your
PerkinElmer service
representative.
Is the pump making a
constant high pitched
noise?
If so, the rotor may be out of
balance. Contact your
PerkinElmer service
representative.
Clarus 600 MS Hardware Guide
Problem
Turbo pump will not
accelerate
Solution
Pump malfunction.
Call a PerkinElmer service
engineer.
Pump controller
malfunction.
Call a PerkinElmer service
engineer.
GC is not properly
configured.
Set the proper GC
configuration for your site.
Large leak.
Locate vacuum leak and
correct.
Foreline trap has
excessive moisture.
Replace filter.
Rotary pump set to gas
ballast.
Switch the gas ballasting off.
Rotary pump requires oil
change.
Change oil.
High mass spectra appears
as a large blotch, or loss of
high mass spectra.
Bad tune.
Run AutoTune.
Drastic change in mass peak
shape for no apparent
reason.
Bad tune.
Run AutoTune.
No spectra, or large blotch.
Bad tune.
Run AutoTune.
Vacuum light continues to
blink.
182
Probable Cause
Problem
Probable Cause
Solution
No spectra, or very little
spectra at the low mass end.
Bad tune.
Run AutoTune.
No spectra, not even noise at
a high PMT voltage.
Loose electrometer cable.
Reset the cable.
Defective electrometer
board.
Call a PerkinElmer service
engineer.
No filament current.
Defective filament.
Replace the filament.
Wavering baseline (by
several hundred counts).
Defective outer source
temperature sensor or a
defective electrometer.
Replace the temperature
sensor.
Call a PerkinElmer service
engineer.
183
Clarus 600 MS Hardware Guide
Problem
Poor or inadequate
sensitivity.
Probable Cause
Solution
Leaking injector septum.
Replace the septum.
Leak from injector
ferrules.
Tighten/replace ferrules.
Foreign material in the
injector.
Clean the injector.
Peak splitting.
Prevent double injections.
Dry the outside of the injector
needle.
Replace the injector septum.
Injector and column are
more active toward
acid/base compounds.
Install a silanized injector
liner, or silanize the current
injector liner.
Check or replace the injector
packing material, such as
quartz wool.
Cut off the first 30 cm of the
column and rerun the test mix.
If the results do not improve
replace the column.
184
Problem
Solvent tailing.
Probable Cause
Solution
Inadequate splitter flow.
Increase the splitter flow.
Column not properly
installed in the injector.
Reinstall the column in the
injector.
Loss of high end compounds.
Temperature setting too
low on the injector,
column oven or transfer
line.
Increase the injector, column
oven or transfer line
temperature to allow the less
volatile compounds of the
sample to reach the mass
spectrometer.
Peaks at masses 28 (nitrogen)
and 32 AMU (oxygen) are in a
ratio of < 4 to 1, and the peak at
mass 28 is larger than the peak
at mass 18.
Leaks in or around
vacuum or column
fittings.
Tighten the fittings and
connection points to the high
vacuum system.
Peaks at masses 14 and 16 are
larger than the peak at mass 28.
Leaks or improper tuning.
Set the injector split flow to
50:1.
Tighten the fittings and
connection points to the high
vacuum system.
Set the injector split flow to
50:1.
Run AutoTune.
185
Clarus 600 MS Hardware Guide
Problem
Poor sensitivity (correct
amount of sample is reaching
the mass spectrometer).
Probable Cause
Solution
Column is improperly
positioned in the ion
source.
Reinstall the column and
check the cut at the end
that fits in the source.
Improper tuning, or a
dirty or defective ion
source.
Check the tuning. Increase
the PMT voltage.
Shut down the system,
remove the inner source,
clean or replace lenses in
the outer source, and
install a new filament.
Loss of resolution (especially
at high mass).
Dirty prequadrupole rods.
Clean the prequadrupole
rods.
Mass assignment drifts.
Large temperature
fluctuations in the
laboratory.
Stabilize the lab
temperature, or isolate the
GC/MS system from large
temperature fluctuations.
Mass assignment incorrect.
186
Run mass calibration.
Skewed spectra.
Improper scan speed (too
slow for the narrow peaks
produced by capillary
columns).
Increase the scan speed.
Unusually high repeller
voltage.
Repeller dirty.
Clean repeller.
Problem
Unusually high emission
setting.
Tuning peaks show
precursors (forward slope
shoulders).
Probable Cause
Solution
Ion volume dirty.
Clean the inner source.
Prefilters dirty.
Clean the prefilters.
Poor tuning.
Retune.
Poor tuning.
Retune.
Dirty prefilter.
Clean prefilters.
Dirty source.
Clean source.
Particulates on analyzer
rods.
Clean the particulates of the rods
with a methanol-dampened lab
wipe.
Blow the particulates off the rods
with helium or dry nitrogen.
No reference peak.
187
Defective or damaged
analyzer.
Call a PerkinElmer service
engineer.
Reference gas off.
Turn on the reference gas.
Empty reference vial.
Visually check and refill.
Faulty solenoid.
Listen for click when
activating/deactivating the valve.
Clarus 600 MS Hardware Guide
Problem
Inconsistent peak widths.
Solution
Poor tubing.
Retune.
Ground loop from GC and
MS on different power
supplies.
Unify supplies.
Peaks shifted from their
nominal mass position.
Poor calibration.
Perform mass calibration.
Tuned peaks are too narrow.
Over-resolved tuning.
Retune.
Tuned peaks are too wide.
Under-resolved tuning.
Retune.
Big peaks observed at m/z
18, 28, 32.
Air leak developed.
Check column
connections.
Change carrier gas tank.
Fit oxygen scrubber.
Moisture from recent
source clean/column
change.
Bake out source
overnight.
Large air leak.
See procedure for leakchecking.
Detector voltage too low.
Increase PMT value.
Electronics failure.
Call a PerkinElmer
service engineer.
Column improperly
installed.
Check and reinstall the
column if necessary.
No ion beam but the filament
status OK.
Poor sensitivity. Beam
instability/peaks breaking up.
188
Probable Cause
Problem
Total Ion Chromatogram
too high.
No noise on mass
chromatogram.
189
Probable Cause
Solution
Piece of column broken off in
the ion chamber.
Remove the inner source,
check for and remove piece of
column.
Source filament is bent.
Check and replace filament if
necessary.
RF generator malfunction.
Call a PerkinElmer service
engineer.
Analyzer drive electronics
malfunction.
Call a PerkinElmer service
engineer.
Dirty source.
Clean the source.
Contamination from poor
handling technique.
Set source and transfer line to
250 ºC and maintain this
temperature overnight.
Stationary phase of column
de-polymerizing (bleeding).
Change column.
Air leak.
Find the leak and fix it.
Poor quality carrier gas.
Replace the carrier gas tank.
Carrier gas filter is ineffective
and needs replacing.
Replace the carrier gas filter.
Detector multiplier voltage too
low.
Increase the multiplier
voltage.
Clarus 600 MS Hardware Guide
Problem
Excessive noise.
Instrument won’t calibrate
(after retuning and
recalibrating).
190
Probable Cause
Solution
Dirty source.
Clean the source.
GC and MS on separate power
supplies.
Connect GC and MS together
with the ground strap.
PMT voltage too high.
Run AutoTune.
Data acquisition thresholds set too
low.
Raise the thresholds.
Poor AutoTune/Manual tune.
Retune.
Contaminated ion source.
Clean the ion source. Set the
source temperature to 250 ºC and
maintain this temperature
overnight.
Source too hot/cool.
Set the correct source
temperature.
Air leak.
Find the leak and fix it.
Wrong calibration reference file
selected.
Select the correct file.
Incorrect calibration calculation
parameters.
Set the calibration parameters to
the default values.
No calibration gas.
Refill the calibration gas vial.
Incorrect electron energy.
Reset to 70 eV.
Chromatography Related
Problem
Inconsistent retention
time.
Rising Total Ion
Chromatogram baseline.
Discreet high intensity
contaminant peaks.
Tailing peaks (sloping on
RHS).
191
Probable Cause
Solution
Injector septum leak.
Replace the septum.
Carrier gas manifold leak.
Locate and fix the leak.
Column bleed.
Disconnect the column from
the mass spectrometer and
condition the column.
Vacuum leak.
Locate and fix the leak.
Column bleed.
Disconnect the column from
the mass spectrometer and
condition the column.
Injector septum bleed.
Replace the septum and/or
glass liner.
Improperly installed column.
Check the column and
reinstall if necessary.
Injector too cool.
Raise the injector
temperature.
Interface temperature too cool.
Raise the interface
temperature.
Inadequate carrier gas flow.
Set proper flow.
Clarus 600 MS Hardware Guide
Problem
Chromatographic peaks
too wide.
Discrimination of relative
peak intensities.
Peaks are flat-topped.
High baseline.
192
Probable Cause
Solution
Dirty injector liner.
Clean or replace.
Column has active sites.
Equilibrate or replace.
Injector too cool.
Raise injector temperature.
Sample overloading the
column.
Use a split injection or a smaller
sample.
Incorrect GC oven program.
Enter a new oven program.
Poor resolution or improper
tuning.
Retune.
Unstable filament.
Replace filament.
Poor calibration.
Recalibrate.
Air leaks at detector.
Check He/Air ratio.
Signal strength exceeds
dynamic range of detector.
Reduce PMT voltage.
Sample is too strong.
Dilute or split.
Dirty sample.
Prepare and filter a new sample.
Air leak at injector.
Locate and fix the air leak.
Contaminated carrier gas.
Replace the gas tank.
Problem
Slowly falling baseline
(from a high initial value).
Low sensitivity.
193
Probable Cause
Solution
Split valve left closed during
acquisition.
Open the split valve.
Inadequate purge flow rate.
Increase flow rate.
Poor off for too long.
Reduce purge time.
Dirty source.
Clean the source.
Poor column performance.
Replace column.
Dirty injector.
Replace injector liner.
Source temperature not
optimized.
Set the proper source
temperature.
Detector voltage set too low.
Increase PMT voltage.
Tune not set correctly.
Run AutoTune.
Poor filament alignment.
Realign or replace filament.
Incorrect column position in
the source.
Reposition the column.
Clarus 600 MS Hardware Guide
Problem
Poor reproducibility.
Poor S/N on test standards.
194
Probable Cause
Solution
Dirty source.
Remove and clean the source.
Defective injector liner.
Replace injector liner.
Defective syringe.
Replace syringe.
Old or damaged filament.
Examine and replace
filament.
Poor tuning.
Retune.
Poor calibration.
Recalibrate.
Air leak.
Locate and fix.
Active sites in column/liner.
Replace column/liner.
Intermittent source heater
failure.
Call a PerkinElmer service
engineer.
See low sensitivity causes
above.
Incorrect GC/MS method
Use the correct method.
Accidental split injection.
Set the proper split.
Detector voltage set too low.
Increase PMT voltage.
Column flow rate too high.
Reset the column flow rate.
Spectral Related
Problem
Noisy spectra.
Solution
Dirty source.
Remove and clean the source.
Peak detection threshold set too low.
Raise the thresholds.
PMT voltage set too high.
Lower the PMT voltage.
Spectrum distortion.
Scanning too fast or slow.
Reset the scan rate.
Incorrect Isotope ratios.
Poor calibration.
Recalibrate.
Incorrect tune.
Retune.
Defective filament.
Replace filament.
Air leak.
Find and fix.
Bad calibration.
Recalibrate.
Poor tuning.
Retune.
Dirty source.
Clean source.
Sample too weak.
Use a higher sample
concentration.
Peak detection thresholds set too
high.
Lower the thresholds.
PMT voltage set too low.
Raise the PMT voltage.
Missing Isotopes in
spectrum.
195
Probable Cause
Clarus 600 MS Hardware Guide
Problem
Section of a mass range
missing from a
spectrum.
Molecular Ion too
weak.
196
Probable Cause
Solution
Contamination.
Locate the contamination and
eliminate it.
Co-eluting components.
Change your sample
preparation or
chromatography.
Incorrect column alignment.
Reinstall the column.
Corruption of data file.
Reacquire data.
Scanning too fast.
Reduce the rate.
Hard disk has too much
fragmentation.
Defrag the hard drive.
Hard disk full.
Remove unnecessary files.
Source temperature too high.
Reduce the source
temperature.
Communications Related
Problem
Will not boot MS.
Will not control GC.
Probable Cause
Solution
PC (computer) to MS cable
has a loose connection.
Check and reset the cable.
Transient in power supply
has halted communications.
Reboot the PC (computer).
RS 232 communications
cable loose connections.
Check and restart the mass
spectrometer.
Power failure/transient
surge to GC or
autosampler.
197
GC electronic malfunction.
Call a PerkinElmer service
engineer.
Communication cable
intermittent contact.
GC electronics
malfunction.
Call a PerkinElmer service
engineer.
Crashes when starting an
acquisition.
Software corrupted.
Reload software.
Rotary pump malfunction.
Call a PerkinElmer service
engineer.
Clarus 600 MS Hardware Guide
Forepump Related
Problem
Pump does not start.
Pump has failed to reach
vacuum.
198
Probable Cause
Solution
Forepump switched off.
Switch on the pump.
Blown fuse.
Call a PerkinElmer service
engineer.
Electrical supply voltage
does not match that of the
pump motor.
Determine the correct voltages,
and correct. Check the voltage
switch at the pump.
The outlet filter is
blocked.
Find and unblock.
Pressure measurement or
gauge head gives an
incorrect indication of
pressure.
A contaminated Pirani gauge
can indicate a pressure several
times higher that the actual.
Replace if necessary.
Pump contains the wrong
type of oil.
Drain and refill with the
correct oil - Edwards
Ultragrade 19 Oil. Consult
your Edwards Pump
instruction manual.
Mode selector and/or gas
ballast control are
incorrectly set.
Check and set to correct
position.
High oil level.
Drain to the high oil level
mark.
Low oil level.
Check and fill to correct level.
Problem
Noisy Pump.
199
Probable Cause
Solution
Contaminated oil.
Drain and refill with new oil.
Vacuum fitting dirty or
damaged.
Check and replace if
necessary.
Motor fan cover damaged.
Call a PerkinElmer service
engineer.
Worn motor bearings.
Call a PerkinElmer service
engineer.
Oil contaminated with solid
particles.
Determine cause and replace
oil.
Oil saturated from CI
analysis.
Drain and refill with clean oil.
Clarus 600 MS Hardware Guide
200
Problem
Probable Cause
Solution
External oil leak.
Outer shaft seal worn or
damaged.
Call a PerkinElmer service
engineer.
Oil box gaskets deteriorated.
Call a PerkinElmer service
engineer.
Oil leak from gas ballast
control.
Call a PerkinElmer service
engineer.
Oil leak from drain plug.
Tighten the drain plug or
replace.
Oil leak from sight glass.
Tighten sight glass screws or
call a PerkinElmer service
engineer.
Message Dialogs
When operating the instrument message dialog boxes will sometimes appear. The
following table is the Icon Key followed by tables that show the Message Title, icon,
dialog message and recommended action.
Icon Key
Icon
Meaning
Press this icon to close the
message.
Press this informational icon
to get more details on the
message.
201
Clarus 600 MS Hardware Guide
Message Title
Icon
Message
There is a problem with the
diffusion pump. Either the
diffusion pump fan has failed or
the pump has over heated.
Please look in the Hardware
Guide for additional instruction.
Diffusion pump
failure
Action
Press OK to close the
message.
Check the cooling-air flow
and correct if possible.
Check the cooling-air duct for
obstructions and correct as
necessary.
If the cooling air flow is fine
and there are no obstructions
contact your PerkinElmer
service representatives.
System not at
pressure
Caution
Safe to vent
202
The system has not reached the
proper operating pressure. The
filament could be damaged by
starting the system now. Do you
wish to continue?
Press Yes if you wish to
continue.
The vacuum system is off and
the system can now be vented.
The GC carrier gas should be
turned off.
Press OK to close the
message.
Press No if you wish to stop.
See the Maintenance chapter
in this Hardware Guide for
the procedure to replace a
filament.
Message
Title
Diffusion
Pump
failure
Icon
Message
There is a problem with the diffusion
pump. Either the diffusion pump fan
has failed or the pump has over heated.
Please look in the Hardware Guide for
additional instruction.
Action
Press OK to close the
message.
Check the cooling-air flow and
correct if possible.
Check the cooling-air duct for
obstructions and correct as
necessary.
If the cooling air flow is fine
and there are no obstructions
contact your PerkinElmer
service representatives.
Vacuum
Leak
Detected
203
The backing pump could not reach the
necessary vacuum level to start the
diffusion pump. There could be a
problem with a vacuum leak, the
backing pump or the vacuum gauge.
The backing pump will be turned off.
Make sure that the vent valve is closed
before restarting the backing pump.
Press OK to close the
message.
Check the system for any leaks
and correct. If the problem
continues contact your
PerkinElmer service
representatives.
Clarus 600 MS Hardware Guide
Message
Title
Vacuum
Gauge
Failure
Icon
Message
There is a problem with the vacuum
gauge.
Action
Press OK to close the
message.
Restart the system, if
you still have this failure
message contact your
PerkinElmer service
representatives.
Pump
failureSafe to Vent
The vacuum system is off and the
system can now be vented. The carrier
gas should be turned off.
There is a problem with the diffusion
pump. Either the diffusion pump fan
has failed or the pump has over heated.
Press OK to close the
message.
Check the cooling-air
flow and correct if
possible.
Check the cooling-air
duct for obstructions and
correct as necessary.
If the cooling air flow is
fine and there are no
obstructions contact
your PerkinElmer
service representatives.
204
Message Title
Vacuum LeakSafe to Vent
Icon
Message
The vacuum system is off and the
system can now be vented. The
carrier gas should be turned off
A Vacuum Leak has been
detected. Please look in the
Hardware Guide for additional
instruction.
Vacuum Gauge
Failure-Safe to
Vent
The vacuum system is off and the
system can now be vented. The
carrier gas should be turned off.
There is a problem with the
vacuum gauge. Please look in the
Hardware Guide for additional
instruction.
Action
Press OK to close the
message.
Check the system for
any leaks and correct. If
the problem continues
contact your
PerkinElmer service
representatives.
Press OK to close the
message.
To replace the vacuum
gauge contact your
PerkinElmer service
representatives.
Exit TurboMassVacuum System
pumping down
The vacuum system is in the
process of the pumping down the
spectrometer. Exiting TurboMass
at this time may prevent a
successful pump down.
Press OK to close the
message.
Exit TurboMassVacuum System
pumping down
The vacuum system is in the
process of shutting down. Exiting
TurboMass at this time may
prevent a successful completion of
this task.
Press OK to close the
message.
205
Clarus 600 MS Hardware Guide
Message Title
Backing Pump is
on
Icon
Message
The system is not in an operating
state. A diffusion pump failure, a
vacuum leak or a vacuum gauge
failure could have occurred.
If the transfer line or the source
temperatures are above 100C, please
wait until they have cooled before
pressing OK.
Action
If the transfer line or the
source temperatures are
above 100C, please wait
until they have cooled
before pressing OK.
Pressing the OK button
will turn off the backing
pump.
Pressing the OK button will turn off
the backing pump.
Problem with
Vacuum
The backing pump could not reach
the necessary vacuum level to start
the diffusion pump.
There could be a problem with a
vacuum leak, the backing pump or
the vacuum gauge.
The backing pump will be turned off.
Make sure that the vent valve is
closed before restarting the backing
pump.
206
Press OK to close the
message.
Replacement Parts
Contact PerkinElmer for Columns, Supplies, Accessories, and Replacement Parts.
Supplies, accessories and replacement parts can be ordered directly from
PerkinElmer's catalog service. PerkinElmer offers a full selection of high-quality
chromatography data handling products and gas chromatography supplies and
columns through the Gas Chromatography Supplies Catalog and the Gas
Chromatography Column Catalog.
To place an order for supplies and many replacement parts, request a free catalog, or
ask for information:
Telephone:
•
U.S. only: Call toll free 1-888-PE-CHROM, 8 a.m. to 8 p.m. EST. Your order
will be shipped promptly, usually within 24 hours.
•
Worldwide: Call your local PerkinElmer sales or service office or call
PerkinElmer, Shelton, CT USA 1-203-925-4600.
Internet: http://www.perkinelmer.com
e-mail: chrom@perkinelmer.com
207
Clarus 600 MS Hardware Guide
208
Index
Index
Index
A
Aluminum oxide, 109, 116
EI Inner Source maintenance, 106
EI to CI mode changing, 160
Electricity, safety practices, 20
Environmental requirements, 32
F
C
Caution, 9, 86
Changing a column, 88
Checklist
pre-installation, 39
pre-operational, 71
Chemicals
definitions of warnings, 26
hazardous, 24
CI
leak checking, 163
setting parameter values, 166
setting up, 165
CI Inner Source, 113
disassembling, 114
maintenance, 113
rinsing and reassembling, 116
Cleaning the Instrument, 21
Column, 70
leak checking, 99
selection, 70
Compressed gases, safety practices, 22
Computer requirements, 37
D
Diffusion Pump, 61
pumping down, 64
E
EI Inner Source, 106
cleaning, 109, 115
disassembling, 107
reassembling, 110
rinsing, 109
Filament
replacing, 121
G
Gases, 36
H
Hardware
maintenance, 85
Heated surfaces, warnings, 23
Heaters
quad, replacing, 144
source, replacing, 142
I
Inline Gas Purifiers, 159
Inner Source, 104
maintenance, 104
removing, 105
Introduction to TurboMass, 49
Ion optics assembly
removing, 129, 135
Ion source, 57
L
Labels
WEEE Instructions, 30
Leak checking, 79
CI, 163
211
Clarus 600 MS Hardware Guide
M
Maintenance, 75
cable removal, 135
cleaning the prequads, 138
EI inner source, 106
inner source, 104
leak-checking, 79
mass analyzer, 128
outer source
wire connections, 151
outer source, cleaning, 146
outer source, detail view, 149
overview, 75
PMT tube removal, 133
preparing for, 85
reassembling TurboMass, 152
removing the cover panels, 131
replacing an outer source themocouple, 139
replacing the quadrupole heater, 144
schedule, 77
source heaters, 142
tuning, 82
vacuum system, 154
oil, 154
venting the system, 87
Mass analyzer
maintenance, 128
O
Operating conditions, 27
Outer source
cleaning, 146
detail view, 149
Overview
Clarus 600/560D GC, 51
ion source, 57
maintenance, 75
reference gas inlet, 54
troubleshooting, 177
P
Photomultiplier Tube (PMT)
removing, 133
Pollution degree, 27
212
Power requirements, 33
Pre-installation checklist, 39
Pre-operational checklist, 71
R
Reference Gas Inlet, 54
Refilling the reference gas vial, 100
Removing a column, 88
Removing the photomultiplier tube, 133
S
Safety practices
ammonia gas, 24
compressed gases, 22
electricity, 20
environmental requirements, 32
general laboratory safety, 29
generic warnings, 18
heated zones, 23
hydrogen, methane, isobutane, 24
overview, 18
pollution degree, 27
requirements, 35
space, 31
storage, 28
ventilation, 23
Software, 68
top level screen, 68
Tune page, 69
Source, 119
reinstalling, 119
Space requirements, 31
Spare components, 178
Storage, 28
Supplies, accessories, replacement parts, 45
system requirements, 37
T
Transfer line
cooling, 86
Traps
click on connectors, 159
replacement, 159
Index
Troubleshooting, 177
chart, 180
overview, 177
spare components, 178
Tune page, 69
Tuning, 82
TurboMass
system requirements, 37
TurboMass Software, 68
Turbomolcular Pump
venting, 64
Turbomolecular Pump, 61
V
Vacuum Gauge, 67
Vacuum system, 59
options, 61
rotary pump, 59
Vacuum System
diffusion pump, 61, 64
turbomolcular pump venting, 64
turbomolecular pump, 61
Ventilation, safety practices, 23
Venting, 87
W
Warnings, 10, 18
hazardous chemicals, 26
Vacuum Controls, 61
213
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