PerkinElmer Clarus 600/560 D MS Hardware Manual
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PerkinElmer Clarus 600/560 D MS Hardware Manual

PerkinElmer Clarus 600/560 D MS Hardware Manual

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Clarus 600/560 D MS
Hardware Guide

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  • Page 1 Clarus 600/560 D MS Hardware Guide...
  • Page 2 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.

  • Page 3: Table Of Contents

    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................
  • Page 4 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 ............
  • Page 5 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 ........
  • Page 6 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..............

  • Page 7: Warnings And Safety Information

    Warnings and Safety Information...

  • Page 9: Conventions Used In This Manual

    Bold 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.
  • Page 10 Clarus 600/560 D MS Hardware Guide 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.
  • Page 11 Warnings and Safety Information Warning (Warnung) Bedeutet, daß es bei Nichtbeachten der genannten Anweisung zu einer Verletzung des Benutzers kommen kann Warning (Advarsel) Betyder, at brugeren kan blive kvæstet, hvis anvisningen ikke overholdes. Warning (Peligro) Utilizamos el término WARNING (PELIGRO) para informarle sobre situaciones que pueden provocar daños personales a usted o a otras personas.

  • Page 12: Customer Service

    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...

  • Page 13: Electromagnetic Compatibility (Emc)

    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.

  • Page 14: Electrical Symbols Used On Clarusms

    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.

  • Page 15: Label Location And Content

    Warnings and Safety Information Label Location and Content Clarus 600 Clarus 600 Mass Spectrom eter Mass Spectrometer Figure 1 Front View of Clarus 600 MS Front View of Clarus 560 D...
  • Page 16 Clarus 600/560 D MS Hardware Guide Mass Spectrometer Vents Interface Ethernet Connection Mass Spectrometer ETHERNET Processor Reset FCC Compliance Switch 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...
  • Page 17 EN 55011-Class A, Group 1 POWER IN REMOVE VENT LINE BLANKING CAP AT INSTALLATION. 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...

  • Page 18: Clarus Ms Safety Practices

    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.

  • Page 19: Moving The Clarus Ms

    Never operate the mass spectrometer with any covers or parts removed. WARNING Do not make adjustments, replacements or repairs to the mass spectrometer except as described in this manual. Only a PerkinElmer Service Representative or similarly trained and authorized person should be permitted to service the mass spectrometer.
  • Page 20 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.

  • Page 21: Decontamination And Cleaning

    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...

  • Page 22: Compressed Gases

    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.

  • Page 23: Heated Zones

    Warnings and Safety Information 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. WARNING Adequate ventilation must be provided, particularly if a liquid nitrogen or carbon dioxide subambient accessory is in constant use.

  • Page 24: Using Hydrogen, Methane Or Isobutane

    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.
  • Page 25 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.

  • Page 26: Definitions In Warnings For Hazardous Chemicals

    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]. Operator: Person operating equipment for its intended purpose. [per EN/IEC 61010-1].

  • Page 27: Temperature, Humidity And Environment

    Warnings and Safety Information Temperature, Humidity and Environment Operating Conditions The Clarus MS is designed for indoor use only in a laboratory CAUTION 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.

  • Page 28: Storage Conditions

    Clarus 600/560 D MS Hardware Guide Storage Conditions The mass spectrometer may be stored under the following conditions: • Ambient temperature is -20 °C to +60 °C (-4 to 140 °F). • Ambient relative humidity is 20 to 80 %, non-condensing.

  • Page 29: General Laboratory Safety

    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.).

  • Page 30: Weee Instructions For Perkinelmer Products

    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...

  • Page 31: Pre-Installation Requirements

    Warnings and Safety Information Pre-Installation Requirements Laboratory Space Requirements Size Weight Clarus 600 MS 32 cm (13 in.) wide x 50 cm Depending on the pump option (20 in.) high x 77 cm (30 in.) deep selected, the weight will range from 46.8 kg (102 lb) to 49.9 kg (110 lb).

  • Page 32: Environmental Requirements

    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 Install the GC/MS in an indoor laboratory environment that is Environment clean and free of drafts and direct sunlight.

  • Page 33: Power Requirements

    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.
  • Page 34 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.

  • Page 35: Safety Requirements

    Warnings and Safety Information Safety Requirements Gas Delivery Copper tubing that is free of grease, oil and organic material must Lines 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.
  • Page 36 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.

  • Page 37: Computer And System Software Requirements

    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.

  • Page 38: Software

    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...

  • Page 39: Pre-Installation Checklist

    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...
  • Page 40 Clarus 600/560 D MS Hardware Guide...

  • Page 41: Introduction

    Introduction...

  • Page 43: Preface

    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.

  • Page 44: Summary Of This Guide

    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.

  • Page 45: About Part Numbers Listed In This Manual

    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.
  • Page 46 Clarus 600 MS User’s Guide...

  • Page 47: About The Clarus 600/560 D System

    About the Clarus 600/560 D System...

  • Page 49: About The Clarus 600/560 D System

    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.
  • Page 50 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.

  • Page 51: Clarus 600/560 D Gc

    About the Clarus 600/560 D System Clarus 600/560 D GC The Clarus 600/560 D Gas Chromatograph is a dual-channel, temperature- programmable gas chromatograph (GC). It is available in many configurations, such as with or without, an autosampler, programmable pneumatic control (PPC), and a variety of injector/detector combinations to provide you with total GC flexibility.
  • Page 52 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).

  • Page 53: Gc Interface (Transfer Line)

    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.

  • Page 54: Reference Gas Inlet

    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.
  • Page 55 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)
  • Page 56 Clarus 600 MS Hardware Guide RF Generator Reference Gas Vial Head Amplifier Wide Range Access Door Gauge 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...

  • Page 57: Ion Optics Path

    About the Clarus 600/560 D System Ion Optics Path The ion source consists of a removable EI or CI inner source and Ion Source 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.
  • Page 58 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.

  • Page 59: Vacuum System

    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 air- cooled oil diffusion pump (Clarus 600 D) is mounted under the ion optics chamber: Rotary Pump...
  • Page 60 Clarus 600 MS Hardware Guide Voltage Selection Switch Under Cover Handle TurboMass Connection Port Oil Filler Plug Exhaust Port On/Off Switch Gas Ballast Switch Mode Selection Drain Plug Switch 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.

  • Page 61: Vacuum Pump Options

    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.

  • Page 62: Diffusion Pump Operating States

    Clarus 600 MS Hardware Guide Diffusion Pump Operating States System Description System Diagram 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...

  • Page 63: Diffusion Pump Operating States Continued

    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 High vacuum pump is on.

  • Page 64: Turbomolecular Pump

    Clarus 600 MS Hardware Guide Turbomolecular Pump Pumping Down a Turbomolecular Pump Vacuum System Select from the menu on the Tune Pump/Vacuum System On Options page. The menu name will change from Pump/Vacuum System On Vent/Vacuum System Off , and the system will begin its pump-down sequence.
  • Page 65 About the Clarus 600/560 D System The software will not prohibit the use of the system prior to reaching CAUTION the desired vacuum. The software will monitor the vacuum gauge pressure to determine when the system has reached the proper operating vacuum ( Torr).
  • Page 66 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: •...

  • Page 67: Vacuum Gauge

    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.

  • Page 68: Turbomass Software

    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.

  • Page 69: Tune Page

    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.

  • Page 70: Analytical Column

    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.

  • Page 71: Pre-Operational Checklist

    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 Are the gases connected to the GC? Is the proper column connected? Is the proper liner installed in the injector? Are your samples prepared?
  • Page 72 Clarus 600 MS Hardware Guide...

  • Page 73: Maintenance

    Maintenance...

  • Page 75: Overview

    Overview 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. WARNING Disconnect AC power cord from outlet before removing any cover or parts.
  • Page 76 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.

  • Page 77: Typical Overall Maintenance Schedule

    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.

  • Page 78: Monthly

    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. •...

  • Page 79: Leak Checking

    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.
  • Page 80 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.
  • Page 81 Maintenance 6. Click next to the red indicator box. Press for Operate The indicator box color changes to green and the name of the button changes to Press for Standby 7. Select from the menu. Pump Options This starts the forepump and the turbomolecular pump or diffusion pump depending on which pump you have installed.

  • Page 82: Tuning Clarus 600/560 D Ms

    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.
  • Page 83 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.
  • Page 84 Clarus 600 MS Hardware Guide 5. Select from the menu to remove the check mark ( ), Reference Gas On or click to set it in the 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 field.

  • Page 85: Preparing Clarus 600/560 D Ms For Hardware Maintenance

    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.
  • Page 86 Clarus 600 MS Hardware Guide Cool the Transfer Line, GC Column Oven, and the Source 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.
  • Page 87 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 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...

  • Page 88: Changing A Column

    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.
  • Page 89 Maintenance 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. Injector 1/16-inch Column Nut Remove Column Transfer Line Septum 1/16-inch Column Nut...
  • Page 90 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 Handle Thumbscrews Figure 11 Removing the source...

  • Page 91: Connecting The New Column To The Split/Splitless Injector

    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).
  • Page 92 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...
  • Page 93 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) 4.44 to 5.1 cm (1¾...

  • Page 94: Connecting A New Column To Clarus 600 Ms

    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.
  • Page 95 Maintenance Use glove. Slide the septum, column nut, and ferrule to this position. 1 cm Column Cut end of column off here Wipe the column with a Kimwipe dampened with MeOH. Figure 18 Preparing to install the column in the transfer line 4.
  • Page 96 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...
  • Page 97 Maintenance Septum 1/16-inch Column Nut 1/4-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. To prevent breaking the end off the column, you need to pull the column CAUTION back to reinstall the source in the mass spectrometer.
  • Page 98 Clarus 600 MS Hardware Guide Septum Column 1/16-inch Column Nut metric 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.
  • Page 99 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...

  • Page 100: Refilling The Reference Gas Vial

    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.
  • Page 101 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.
  • Page 102 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.
  • Page 103 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.

  • Page 104: Inner Source Maintenance

    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. Never clean the filament.

  • Page 105: Removing The Inner Source

    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.

  • Page 106: Ei Inner Source Maintenance

    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.
  • Page 107 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.
  • Page 108 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.
  • Page 109 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.
  • Page 110 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 lint- free tissue and/or clean compressed Nitrogen gas to prevent solvents from drying on these parts and leaving a residue.
  • Page 111 Maintenance Ion Trap Repeller (P/N E640-1220) (P/N E640-1219) 2 mm Spacer 2 mm Spacer (P/N E640-1222) (P/N E640-1222) 12 mm Spacer 12 mm Spacer (P/N E640-1221) (P/N E640-1221) Figure 31 Inserting the ion trap and repeller into the inner source 2.
  • Page 112 Clarus 600 MS Hardware Guide 5. Replace the filament assembly. (P/N E532-1018) Washer (P/N E533-1013) (P/N E532-1018) Trap Contact Washer (P/N E640-1217) (P/N E533-1013) Repeller Contact 6 mm Ceramic Spacer (P/N E640-1216) (P/N E640-1224) Locator (P/N E640-1218) and Clarus 560 D 6 mm Ceramic Spacer (P/N E640-1224) Post removed to show...

  • Page 113: Ci Inner Source Maintenance

    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.
  • Page 114 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.
  • Page 115 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...
  • Page 116 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.
  • Page 117 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.
  • Page 118 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...

  • Page 119: Reinstalling The Source

    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.
  • Page 120 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 from the Pump/Vacuum System On Options...

  • Page 121: Replacing A Filament

    Maintenance Replacing a Filament Make sure you are wearing powder-free PVC gloves (Part No. N621- CAUTION 2495), and that you wipe each part with a methanol dampened Kimwipe. Items and Tools Required • Filament assembly (Part No. E6400209). • Tweezers. •...
  • Page 122 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.
  • Page 123 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.
  • Page 124 Clarus 600 MS Hardware Guide Insert Contacts New Filament Assembly (P/N E647-0012) Contacts (2) (P/N E640-1215) 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.
  • Page 125 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 New Filament Assembly Screw Washer Contacts Tab positioned between contacts.

  • Page 126: Replacing The Head Amplifier

    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.
  • Page 127 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 Lock Washer Figure 45 Replacing the head amplifier...

  • Page 128: Mass Analyzer Maintenance

    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.

  • Page 129: Cleaning Materials

    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.
  • Page 130 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...
  • Page 131 Maintenance 6. Close the mass spectrometer access door. Access Door Inner Source Black Handle Thumbscrews 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.
  • Page 132 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 be removed from the instrument. It is removed in this illustration only to clearly show how to access the PMT Access Panel.
  • Page 133 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...
  • Page 134 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.
  • Page 135 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.
  • Page 136 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.
  • Page 137 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. Hexagon Fan Plug Head Bolt (4)
  • Page 138 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.

  • Page 139: Replacing An Outer Source Thermocouple

    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). •...
  • Page 140 Clarus 600 MS Hardware Guide Remove the screw securing thermocouple (1) (P/N E640-0213) Loosen and Remove Nut Feed Connector Remove all wires from contact pins (10) Pull all wires down through feed connector Thread all new wires up through feed connector and connect wires on contact pins Tighten Secure the...

  • Page 141: Removing The Outer Source From The Ion Optics

    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): Position the ion optics assembly as shown. Outer Source Assembly of Ion Optics Assembly Detach wires and tubes from outer source assembly as required.

  • Page 142: Replacing Outer Source Heaters

    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.
  • Page 143 Maintenance Screw (1 of 3) (P/N E531-4016) Clamp Plate (P/N E640-1322) Contact Support Plate (P/N E640-1229) Pillar (P/N E640-1320) Heater Locking Screws Source Heaters (P/N E640-0265) Figure 56 Replacing heaters in the outer source...

  • Page 144: Replacing The Quadrupole Heater

    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.
  • Page 145 Maintenance Outer Source Assembly of Ion Optics Assembly Cartridge Heater Setscrew To outer source Quadrupole cartridge heater (other side) Cartridge Heater (P/N E640-0266) Purple wire To outer source cartridge heater (this side) Quadrupole Cartridge Heater Connections Figure 57 Removing the quadrupole heater...

  • Page 146: Cleaning The Outer Source Lens

    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. •...
  • Page 147 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.
  • Page 148 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 Clean these areas.

  • Page 149: Reassembling The Ion Optics Assembly

    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) Clamp Plate (P/N E531-4016) (P/N E640-1322) Wavy Washer (1 of 8) (P/N E533-5005) Typical Contact Attachment...
  • Page 150 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. Place the assembled outer source on the ion optics assembly and secure it in place with the two screws.
  • Page 151 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 Contact Support Plate Quadrapole Cartridge Heater cartridge heater (other side) (See Detail) Thermocouple Wires Ground (green/yellow wire) Purple wire To outer source...

  • Page 152: Reassembling The Clarus 600/560 D Ms

    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.
  • Page 153 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 Lock Washer Figure 62 Reinstalling the PMT 8. Reinstall the PMT head amplifier cover and secure it in place with the two captured screws.

  • Page 154: Vacuum System Maintenance

    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.
  • Page 155 Maintenance Voltage Selection Switch Under Cover Handle TurboMass Connection Port Oil Filler Plug Exhaust Port On/Off Switch Gas Ballast Switch Mode Selection Drain Plug Switch 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.

  • Page 156: Adding Oil To The Forepump Reservoir

    Clarus 600 MS Hardware Guide Adding Oil to the Forepump Reservoir Vent the mass spectrometer before opening the plug to add oil. CAUTION 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 mark on the top of the sight glass.
  • Page 157 Maintenance Filler Plug Max Oil Level Min Oil Level Drain Plug 2 Liter Drain Container Figure 64 Draining forepump oil...
  • Page 158 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.

  • Page 159: Inline Gas Purifiers

    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.

  • Page 160: Changing From Ei To Ci Mode

    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 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.
  • Page 161 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.

  • Page 162: Changing To Ci

    Clarus 600 MS Hardware Guide ROTARY PUMP Rotary Pump Warning Power POWER IN Power In WATER WATER 4 10 CI GAS VENT Warning 15 psi 5 psi 50 psi (103 kPa) (35 kPa) (345 kPa) 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.

  • Page 163: Leak Checking

    Maintenance 4. Select from the menu. Pump Options 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 Leak Checking Before running in the CI mode, confirm that the column is properly installed and the...
  • Page 164 Clarus 600 MS Hardware Guide To leak-check the system: 1. Display the Tune page. 2. Select from the Ion Mode menu.

  • Page 165: Setting-Up Ci

    Maintenance 3. Click and observe the air/water masses. Press for Operate 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.
  • Page 166 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: Parameter: CI+ Values and Comments: Electron energy 30 eV Emission Should be below 200 µA, although 200 to 300 µA is acceptable.
  • Page 167 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 (CH ) and 29 (C should be of approximately equal intensity.
  • Page 168 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.
  • Page 169 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.
  • Page 170 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.
  • Page 171 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.
  • Page 172 Clarus 600 MS Hardware Guide Adjust the Reagent Gas for CI- 1. Open the CI gas inlet by selecting CI Gas from the Gas menu. Wait at least 10 seconds before clicking Press for Operate Parameter: CI− value and comments: Electron Energy 30 to 70 eV (This parameter should be optimized.)
  • Page 173 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.
  • Page 174 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 to begin calibration. You are now ready to run CI analysis.

  • Page 175: Troubleshooting

    Troubleshooting...
  • Page 176 Clarus 600 MS Hardware Guide...

  • Page 177: Overview

    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.

  • Page 178: Spare Components

    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.
  • Page 179 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.

  • Page 180: Troubleshooting Chart

    AC outlet. instrument). No AC power to the outlet. Check the outlet. Fuse blown. Call a PerkinElmer service engineer. Mass Spectrometer is on Forepump is not plugged into Plug the forepump line but the forepump is not...
  • Page 181 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. Is the backing pressure Check for a leak in the backing high? pipeline and poor backing pump performance.
  • Page 182 Clarus 600 MS Hardware Guide Problem Probable Cause Solution Turbo pump will not Pump malfunction. Call a PerkinElmer service accelerate engineer. Pump controller Call a PerkinElmer service malfunction. engineer. GC is not properly Set the proper GC configured. configuration for your site.
  • Page 183 No spectra, not even noise at Loose electrometer cable. Reset the cable. a high PMT voltage. Defective electrometer Call a PerkinElmer service board. engineer. No filament current. Defective filament. Replace the filament. Wavering baseline (by...
  • Page 184 Clarus 600 MS Hardware Guide Problem Probable Cause Solution Poor or inadequate Leaking injector septum. Replace the septum. sensitivity. Leak from injector Tighten/replace ferrules. ferrules. Foreign material in the Clean the injector. injector. Peak splitting. Prevent double injections. Dry the outside of the injector needle.
  • Page 185 Problem Probable Cause Solution Solvent tailing. Inadequate splitter flow. Increase the splitter flow. Column not properly Reinstall the column in the installed in the injector. injector. Loss of high end compounds. Temperature setting too Increase the injector, column low on the injector, oven or transfer line column oven or transfer temperature to allow the less...
  • Page 186 Clarus 600 MS Hardware Guide Problem Probable Cause Solution Poor sensitivity (correct Column is improperly Reinstall the column and amount of sample is reaching positioned in the ion check the cut at the end the mass spectrometer). source. that fits in the source. Improper tuning, or a Check the tuning.
  • Page 187 Blow the particulates off the rods with helium or dry nitrogen. Defective or damaged Call a PerkinElmer service analyzer. engineer. No reference peak. Reference gas off. Turn on the reference gas. Empty reference vial.
  • Page 188 Large air leak. See procedure for leak- status OK. checking. Detector voltage too low. Increase PMT value. Electronics failure. Call a PerkinElmer service engineer. Poor sensitivity. Beam Column improperly Check and reinstall the instability/peaks breaking up. installed. column if necessary.
  • Page 189 Source filament is bent. Check and replace filament if necessary. RF generator malfunction. Call a PerkinElmer service engineer. Analyzer drive electronics Call a PerkinElmer service malfunction. engineer. Total Ion Chromatogram Dirty source.
  • Page 190 Clarus 600 MS Hardware Guide Problem Probable Cause Solution Excessive noise. Dirty source. Clean the source. GC and MS on separate power Connect GC and MS together supplies. with the ground strap. PMT voltage too high. Run AutoTune. Data acquisition thresholds set too Raise the thresholds.

  • Page 191: Chromatography Related

    Chromatography Related Problem Probable Cause Solution Inconsistent retention Injector septum leak. Replace the septum. time. Carrier gas manifold leak. Locate and fix the leak. Rising Total Ion Column bleed. Disconnect the column from Chromatogram baseline. the mass spectrometer and condition the column. Vacuum leak.
  • Page 192 Clarus 600 MS Hardware Guide Problem Probable Cause Solution Dirty injector liner. Clean or replace. Column has active sites. Equilibrate or replace. Chromatographic peaks Injector too cool. Raise injector temperature. too wide. Sample overloading the Use a split injection or a smaller column.
  • Page 193 Problem Probable Cause Solution Slowly falling baseline Split valve left closed during Open the split valve. (from a high initial value). acquisition. Inadequate purge flow rate. Increase flow rate. Poor off for too long. Reduce purge time. Low sensitivity. Dirty source. Clean the source.
  • Page 194 Poor calibration. Recalibrate. Air leak. Locate and fix. Active sites in column/liner. Replace column/liner. Intermittent source heater Call a PerkinElmer service failure. engineer. Poor S/N on test standards. See low sensitivity causes above. Incorrect GC/MS method Use the correct method.

  • Page 195: Spectral Related

    Spectral Related Problem Probable Cause Solution Noisy spectra. 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.
  • Page 196 Clarus 600 MS Hardware Guide Problem 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. Section of a mass range Corruption of data file. Reacquire data. missing from a spectrum.

  • Page 197: Communications Related

    RS 232 communications Check and restart the mass cable loose connections. spectrometer. Power failure/transient surge to GC or autosampler. GC electronic malfunction. Call a PerkinElmer service engineer. Communication cable GC electronics Call a PerkinElmer service intermittent contact. malfunction. engineer. Crashes when starting an Software corrupted.

  • Page 198: Forepump Related

    Probable Cause Solution Pump does not start. Forepump switched off. Switch on the pump. Blown fuse. Call a PerkinElmer service engineer. Electrical supply voltage Determine the correct voltages, does not match that of the and correct. Check the voltage pump motor.
  • Page 199 Drain and refill with new oil. Vacuum fitting dirty or Check and replace if damaged. necessary. Noisy Pump. Motor fan cover damaged. Call a PerkinElmer service engineer. Worn motor bearings. Call a PerkinElmer service engineer. Oil contaminated with solid Determine cause and replace particles.
  • Page 200 Clarus 600 MS Hardware Guide Problem Probable Cause Solution External oil leak. Outer shaft seal worn or Call a PerkinElmer service damaged. engineer. Oil box gaskets deteriorated. Call a PerkinElmer service engineer. Oil leak from gas ballast Call a PerkinElmer service control.

  • Page 201: Message Dialogs

    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.
  • Page 202 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 The system has not reached the Press Yes if you wish to pressure proper operating pressure.
  • Page 203 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 The backing pump could not reach the Press OK to close the...
  • Page 204 Gauge gauge. message. Failure Restart the system, if you still have this failure message contact your PerkinElmer service representatives. Pump Press OK to close the The vacuum system is off and the failure- message. system can now be vented. The carrier Safe to Vent gas should be turned off.
  • Page 205 If detected. Please look in the the problem continues Hardware Guide for additional contact your instruction. PerkinElmer service representatives. Vacuum Gauge The vacuum system is off and the Press OK to close the Failure-Safe to system can now be vented. The message.
  • Page 206 Clarus 600 MS Hardware Guide Message Title Icon Message Action Backing Pump is The system is not in an operating If the transfer line or the state. A diffusion pump failure, a source temperatures are vacuum leak or a vacuum gauge above 100C, please wait failure could have occurred.

  • Page 207: Replacement Parts

    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...
  • Page 208 Clarus 600 MS Hardware Guide...

  • Page 209: Index

    Index...
  • Page 211 Index Index EI Inner Source maintenance, 106 EI to CI mode changing, 160 Electricity, safety practices, 20 Environmental requirements, 32 Aluminum oxide, 109, 116 Filament Caution, 9, 86 replacing, 121 Changing a column, 88 Checklist pre-installation, 39 pre-operational, 71 Chemicals Gases, 36 definitions of warnings, 26 hazardous, 24...
  • Page 212 Clarus 600 MS Hardware Guide Power requirements, 33 Pre-installation checklist, 39 Maintenance, 75 Pre-operational checklist, 71 cable removal, 135 cleaning the prequads, 138 EI inner source, 106 inner source, 104 Reference Gas Inlet, 54 leak-checking, 79 Refilling the reference gas vial, 100 mass analyzer, 128 Removing a column, 88 outer source...
  • Page 213 Index Troubleshooting, 177 Vacuum Gauge, 67 chart, 180 Vacuum system, 59 overview, 177 options, 61 spare components, 178 rotary pump, 59 Tune page, 69 Vacuum System Tuning, 82 diffusion pump, 61, 64 TurboMass turbomolcular pump venting, 64 system requirements, 37 turbomolecular pump, 61 TurboMass Software, 68 Ventilation, safety practices, 23...

Table of Contents