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Varian Saturn 2000 GC/MS Hardware Manual

Ion trap mass spectrometry
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Varian, Inc.
2700 Mitchell Drive
Walnut Creek, CA 94598-1675/usa
Saturn 2000 GC/MS
Hardware Manual
03-914978-00:Rev. 1
©Varian, Inc. 2002-2003
Printed in U.S.A.

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Summary of Contents for Varian Saturn 2000 GC/MS

  • Page 1 Varian, Inc. 2700 Mitchell Drive Walnut Creek, CA 94598-1675/usa Saturn 2000 GC/MS Hardware Manual 03-914978-00:Rev. 1 ©Varian, Inc. 2002-2003 Printed in U.S.A.

  • Page 2: Varian, Inc

    Any modification or any other reproduction, distribution, or use of this document or portions hereof is strictly prohibited without the express written permission of Varian, Inc. COPYRIGHT 2001 - 2003. All rights reserved.

  • Page 3: Varian, Inc

    TUV File Number(s): Mass Spectrometer Model: Saturn 2000 Series Type of Equipment: Authorized Representative in the EU Print Name: G. A. Wassink Company Name: Varian B.V. Herculesweg 8 Address: P.O. Box 8033 Signed: 4330 EA Middelburg Position: Quality Manager The Netherlands...
  • Page 4 9000 series registration constitutes an objective third-party report to determine the level of a supplier's commitment to quality. In 1992, Varian, Inc., Analytical Instruments became registered to the most comprehensive of the ISO 9000 series standards — ISO 9001. ISO 9001 registration means that every stage of our quality system, including product development, manufacturing, final test, shipping, and parts and supplies has been rigorously examined against the most exacting set of internationally recognized standards.
  • Page 5 Registrierung bildet einen objektiven Bericht von dritter Seite, um den Grad der Qualitätsanstrengung eines Lieferanten zu bestimmen. 1992 wurden die Varian, Inc., Analytical Instruments nach den umfassendsten Standards der ISO 9000 Serie registriert — ISO 9001. Die ISO 9001 Registrierung bedeutet, daß jedes Stadium unseres Qualitätssystems, einschließlich Produktentwicklung, Herstellung, Endkontrolle, Versand, sowie Teile...
  • Page 6 évaluation objective d'un tiers afin de déterminer le niveau d'engagement d'un fournisseur dans le domaine de la qualité. En 1992, Varian, Analytical Instruments a reçu l'homologation ISO 9001, normes des plus complètes de la série IS0 9000. En d'autres termes, chaque étape du processus de qualité, notamment le développement produit, la fabrication, le test final, l'expédition et les fournitures de pièces a étés oumis à...
  • Page 7 ISO 9000 costituisce un'attestazione imparziale di terzi del grado d'impegno di una determinata azienda nei confronti della qualità. Nel 1992 la Varian, Inc., Analytical Instruments ha ottenuto l'omologazione allo standard più completo della serie ISO 9000, l'ISO 9001. L'omologazione ISO 9001 significa che ogni singola fase del nostro sistema di qualità...
  • Page 8 Varian, Inc., Analytical Instruments fue registrada en 1992 con la norma más exhaustiva de la serie ISO 9000: la ISO 9001. La certificación por la norma ISO 9001 significa que todas las etapas de nuestro sistema de calidad, como el desarrollo del producto, la fabricación, las pruebas finales, la expedición, así...
  • Page 9 Customer to return the defective workmanship for the periods specified and in accessory or instrument to Varian or to send it to a accordance with the terms on the face of Varian's designated service facility.
  • Page 10 Garan- garantie wird die Reparatur der Instrumentstörungen tien der Verkäuflichkeit und Eignung für einen be- sein, die sich nach Varian's Ansicht auf Defekte in den sonderen Zweck, Gebrauch oder Anwendung und Originalteilen oder bei der Herstellung zurückführen läßt...
  • Page 11 Varian diffusera des mises à jour des de Varian au client d'origine. Cependant, lorsque le logiciels, le cas échéant, et si de l'avis de Varian, elles client a acquitté les frais d'installation ou que celle-ci est constituent la mesure corrective la plus appropriée en la inclue dans le prix d'achat, la période de garantie...
  • Page 12 In assenza d'un contratto di licenza e salvo diverso magnetico, fotomoltiplicatori, filamenti, guarnizioni per accordo scritto tra la Varian e il Cliente, vale il periodo di vuoto, e tutte le parti esposte all'azione dei campioni o garanzia indicato nell'offerta della Varian. La Varian delle fasi mobili.
  • Page 13 Esta garantía no tendrá efecto en los casos de accidente, Varian, u otro tipo de hardware en el que Varian certifique abuso, alteración, utilización incorrecta, negligencia, que funcionan según lo descrito en Manual de rotura, mantenimiento o uso inadecuados, modificaciones instrucciones, y que esté...
  • Page 14 NOTES CAUTIONS WARNINGS accordance with this instruction manual and any additional information which may be provided by Varian. Address any questions regarding the safe and proper use of your equipment to your local Varian office. NOTE Information to aid you in obtaining...
  • Page 15 It is the responsibility of the Customer to inform Varian Customer Support Representatives if the instrument has been used for the analysis of hazardous biological, radioactive, or toxic samples, prior to any instrument service being performed or when an instrument is being returned to the Service Center for repair.
  • Page 16 Flash Chromatography GC Safety Practices The operator should be familiar with the physico- Exhaust System chemical properties of the components of the mobile No special exhaust ducting is necessary for GC phase. detectors installed in a well-ventilated room except Keep solvents from direct contact with the polyurethane when the detectors are used to test hazardous supply tubing as certain solvents will cause weakening chemicals.
  • Page 17 Varian Analytical Instruments Sales Offices For Sales or Service assistance and to order Parts and Supplies, contact your local Varian office. Argentina France...
  • Page 18 WARNUNG, wie unten beschrieben. Es ist wichtig, daß Sie Ihr Gerät in Übereinstimmung mit dieser Arbeitsanleitung und allen möglichen zusätzlichen Informationen von Varian betreiben. Alle Fragen bezüglich Sicherheit und Handhabung Ihres Gerätes richten Sie an Ihr Varian Büro. ACHTUNG WARNUNG...
  • Page 19 Es muß mit geeigneten Gasen und/oder Lösungsmitteln und innerhalb der im Handbuch spezifizierten maximalen Werte für Druck, Flüsse und Temperaturen betrieben werden. Der Kunde ist vor der Durchführung irgendeines Geräteservices verpflichtet den Varian WARNUNG Kundendienstvertreter zu informieren, wenn das Instrument für Analysen gefährlicher biologischer, radioaktiver oder toxischer Proben benutzt worden ist.
  • Page 20 Öffnen Sie niemals eine unter Druck stehende GC Sicherheitspraktiken Lösungsmittelleitung oder ein Ventil. Halten Sie Abgassystem zuerst die Pumpe an und lassen Sie den Druck auf Für GC Detektoren, die in einem gut durchlüfteten Null abfallen. Raum installiert sind, ist keine spezielle Abgasführung Benutzen Sie splittersichere Reservoirs, die für erforderlich, außer wenn die Detektoren zum Testen einen Druck von 3,4 bis 4,1 bar ausgelegt sind.
  • Page 21 Verfügbarkeit von Ersatzteilen Serviceverfügbarkeit Varian bietet seinen Kunden auch Es ist Varian’s Grundsatz, Ersatzteile für alle Instrumente und die wichtig- nach dem Auslaufen der Garantie sten Zubehöre für einen Zeitraum von fünf (5) Jahren nach dem Fertigung- eine Vielfalt von Serviceleistungen sauslauf dieser Geräteserie verfügbar zu haben.
  • Page 22 AVERTISSEMENTS. matériel conformément aux instructions du présent manuel et à toute autre information émanant de Varian. S’adresser au bureau régional Varian pour toute question relative à la sécurité ou à l’utilisation correcte du matériel. NOTE Information destinée à tirer le Attire l’attention sur une situation...
  • Page 23 Le client est tenu d’informer le service Varian d’assistance à la clientèle que son matériel ATTENTION a été utilisé pour l’analyse d’échantillons biologiques dangereux, radioactifs ou toxiques avant que n’en soit effectué...
  • Page 24 Ne jamais déconnecter un conduit de solvant ou Mesures de sécurité en CPG une vanne sous pression. Arrêter préalablement la Système d’échappement pompe et laisser la pression descendre à zéro. Les détecteurs CPG installés dans une pièce bien Utiliser des réservoirs incassables à 50-60 psi. ventilée ne nécessitent pas de conduits spéciaux d’échappement excepté...
  • Page 25 Points de vente des instruments analytiques Varian Contactez votre point de vente régional Varian pour toute question commerciale ou de service d’assistance à la clientèle ou pour passer commande de pièces et de fournitures.
  • Page 26 . E’ importante che lo strumento venga utilizzato rispettando le istruzioni fornite in questo CAUTELA ATTENZIONE manuale o che verranno fornite successivamente dalla Varian. Per ogni eventuale chiarimento sull’uso o sulla sicurezza, si prega di contattare la Varian di Leinì (TO). ATTENZIONE...
  • Page 27 E’ responsabilità del Cliente informare il Servizio Tecnico Varian, prima di qualsiasi ATTENZIONE intervento di riparazione, se lo strumento è stato utilizzato per l’analisi di campioni biologicamente pericolosi, radioattivi o tossici.
  • Page 28 Procedure di Sicurezza in GC Non smontare mai una linea del solvente od una Scarico dei Gas valvola quando il sistema è sotto pressione. Per i rivelatori GC non è richiesto alcun sistema Fermare prima la pompa ed aspettare che la particolare di scarico dei gas, se lo strumento è...
  • Page 29 Disponibilità delle Parti di Ricambio Servizi Tecnico E’ politica della Varian il fornire le parti di ricambio per lo strumento ed La Varian, alla scadenza del periodo i suoi accessori per un periodo di cinque (5) anni a partire dalla data di di garanzia, è...
  • Page 30 PRECAUCION ATENCION instrumento de acuerdo con este Manual de Operación y cualquier otra información que le proporcione Varian. Remita a la Oficina Local de Varian cualquier cuestión que tenga respecto al correcto uso de su equipo. ¡PRECAUCION! ATENCI N Ó...
  • Page 31 Debe ser operado usando gases y/ó disolventes apropiados y con unos niveles máximos de presión, flujos y temperaturas, según se describe en este manual. El Usuario tiene la obligación de informar al Servicio Técnico de Varian cuando el ATENCI N Ó...
  • Page 32 Nunca abra una línea ó una válvula bajo presión. GC Prácticas de Seguridad Apague la bomba antes y deje que la presión baje a Sistema de Extracción cero. No se necesita un sistema de extracción para los Utilice depósitos irrompibles que sean capaces de detectores GC instalados en un laboratorio bien operar a 50-60 psi.
  • Page 33 Disponibilidad de Recambios Disponibilidad de Servicio Es Política de Varian disponer de Recambios para cualquier instrumento y la mayoría de los accesorios por un periodo de cinco (5) años después del Varian ofrece una gran variedad de último instrumento fabricado. Los recambios durante esos cinco años sistemas de Servicio para mantener estarán disponibles, pero siempre bajo el sistema “Según disponibilidad”.

  • Page 34: Table Of Contents

    Contents Functional Description ......................7 Introduction ................................7 Technical Specifications ............................9 Saturn 2000 GC/MS System Performance Specifications .................. 9 Physical Specifications ............................9 The Gas Chromatograph ............................9 The Mass Spectrometer............................10 Mechanical Assemblies ............................10 Controls and Indicators............................10 Cooling Fans ..............................
  • Page 35 Use Polypropylene Caps to Preserve Liquids in Reservoirs................43 Setting Flows of Vapor from Liquid CI Reagents ....................44 Returning to Gaseous CI Reagent Operation ....................44 Installing and Using the Multiple CI Module......................45 Pre-Installation Checklist ........................... 46 Installing the Multiple CI Assembly........................46 Cable Connections to the GC External Events Board..................
  • Page 36 Remove the Analyzer Assembly ..........................102 Replace the Electron Multiplier ..........................104 Replace the Filament(s)............................105 Remove the Ion Trap Oven............................ 106 Cleaning the Trap Components ..........................106 Disassemble the Trap Components ........................ 106 Clean the Trap Components ........................... 107 Clean SilChrom Ion Trap Electrodes.......................
  • Page 37 Check the Ion Content of the Trap ........................134 Check the Axial Modulation Setting......................... 135 What To Do If There is a High Baseline at High Masses ..................135 What To Do If the Trap Function Calibration Fails After the Calibration Ions Have Been Correctly Identified..136 Check the Electron Multiplier Voltage ......................
  • Page 38 GC Spares ............................... 164 Tools, Test Samples, etc..........................164 Additional Saturn Spares..........................165 CI Parts/Spares ............................... 165 Multiple CI Module Parts Lists......................... 165 MCI Module Accessory Kit ..........................166 Open Split Interface............................166 Calling Varian Service............................167 03-914978-00:1 Contents...
  • Page 39 Contents 2000 MS Hardware Maintenance...

  • Page 40: Functional Description

    Functional Description Introduction The Saturn 2000 GC/MS has four principal components: • Gas chromatograph (GC) • Mass spectrometer (MS) • Data system (DS) • AutoSampler (optional) The following figure is a functional block diagram of the Saturn GC/MS. A short, line-of-sight transfer line connects the GC and mass spectrometer.
  • Page 41 A Foreline Pump B Transfer Line C GC Oven D Capillary Column E Turbomolecular Pump F Ion Trap Assembly Principal Components of Saturn GC/MS (Top View) 2000 MS Hardware Maintenance Functional Description...

  • Page 42: Technical Specifications

    Pollution Degree: 2 The Gas Chromatograph The Saturn GC/MS employs the high performance Varian Model 3800 or 3900 Gas Chromatograph. The gas chromatograph comes with a 1079 or 1177 Universal Capillary Injector which provides five modes of injection - isothermal split and splitless, temperature-ramped splitless, on-column and large volume.

  • Page 43: The Mass Spectrometer

    The Mass Spectrometer The Saturn GC/MS employs an ultra trace ion trap mass spectrometer. The mass spectrometer consists of the mechanical and electronic assemblies. The following sections describe these assemblies. The instrument is separated into the electronics and analyzer compartments. The electronics compartment includes the •...

  • Page 44: Cooling Fans

    Cooling Fans CI Cal Gas Adjust CI Shutoff Valve Cal Gas Adjust Saturn 2000 GC/MS Mass Spectrometer Cooling Fans To prevent overheating, do not block air intakes. Turbomolecular Pump System Two fans mounted on the rear of the spectrometer cool the unit. The analyzer compartment fan draws air from the back, blowing it directly on the bearing end of the turbomolecular pump in the analyzer compartment.
  • Page 45 The electronics section fan draws air from the back, and blows it across the SAP/WAVE and power boards in the electronics compartment. Hot air from the GC oven does not affect the MS as long as the system is at least six inches from a wall.

  • Page 46: Turbomolecular Pump Vacuum System

    Zone 3 is the diffusion pump compartment. The lower fan on the rear panel pulls air in through carefully positioned vents in the left side panel. Airflow is ducted around the diffusion pump’s cooling fins, and expelled through the rear of the instrument.
  • Page 47 The vacuum manifold sits atop the RF coil housing. The turbomolecular pump makes an airtight seal with the manifold, to which it is mounted horizontally with a Viton O-ring. The ion trap assembly suspends from the analyzer flange, and extends into the body of the manifold. The manifold makes an airtight seal with the analyzer flange, also via a Viton...

  • Page 48: Diffusion Pump Vacuum System

    If the speed of the pump is 92% or more of the maximum operating speed, the signal from the controller prompts the power control board to send a TURBOMOLECULAR SPEED OK signal to the SAP/Wave board. The SAP/Wave board uses the signal for enable or disable the filament, electron multiplier voltage, RF generator, CI reagent gas valve, and calibration gas valve by means of an electronic interlock.
  • Page 49 Diffusion Pump Vacuum Manifold The vacuum manifold is a stainless steel tube that maintains the ion trap assembly in a vacuum. Carrier gas is fed into the ion trap via the transfer line, and calibration gas and Chemical Ionization gases are fed into the ion trap via the pneumatics assembly.
  • Page 50 The ion trap assembly requires a vacuum of approximately 1 x 10 Torr (1.3 x Pa) for the generation and detection of ions. The Varian AX65 air-cooled diffusion pump with a pumping speed of 30 l/s for air and 65 l/s for helium provides this.

  • Page 51: The Pneumatics Manifold

    The diffusion pump may be restarted at any time during the shutdown procedure providing no fault condition exists. The controller will restore power to the diffusion pump if it receives a restart command during the first fifteen minutes of the shut down procedure. The diffusion pump will reach operational temperature, and the controller will issue a “DIFFUSION PUMP NORMAL”...

  • Page 52: The Transfer Line

    The Transfer Line A stainless-steel-tube transfer line directly couples the GC to the mass spectrometer. The transfer line keeps the GC column warm as the column enters the mass spectrometer. The transfer line is 12 cm (5 in.) long, and has a diameter of 4.1 cm (1.6 in.).

  • Page 53: Ion Trap Assembly

    Heating Cable O-ring Boot Transfer Line Tip Heating Cable Slot Ferrule Nose Clip Transfer Line/Alignment Bayonet Mount Tool Nose Analyzer Assembly Tongue Nose Hole Analyzer Assembly Lock-Down Tabs Transfer Line Exploded View Ion Trap Assembly The ion trap assembly consists of •...
  • Page 54 Screw, 6/32, 4 places Wave Washer Clamping Plate Gate Conductor Exit End Cap Trap Oven, “T” is located this side. Quartz or Silica Coated Spacer, 2 places Filament Assembly RF Ring Electrode Filament Clip Filament End Cap Screw Electron Gate Ion Trap Assembly Trap Oven The trap oven is a heated anodized aluminum block that maintains a uniform...
  • Page 55 Filament Assembly Shown with Ion Trap Each filament is a rhenium wire. When sufficiently heated by electric current, the filament produces electrons by thermionic emission. The filament emission current refers to the flow of emitted electrons from the filament. The magnitude of the filament emission current is set in the Instrument Control Page.
  • Page 56 Ion Trap Electrodes The ion trap assembly contains three stainless steel electrodes: • Filament endcap electrode • Exit endcap electrode • RF ring electrode The filament endcap, exit endcap, and RF-ring electrodes have hyperbolic inner surfaces. Together, these electrodes form a cavity in which ionization, fragmentation, storage, and mass analysis take place.

  • Page 57: Ion Gauge

    Exit End Cap Multiplier Contacts Electron Multiplier Track Multiplier High Voltage Pin Multiplier Signal Pin Transfer Line Alignment EM Grid Transfer Line Entrance Hole Electron Multiplier Mount Position of the Electron Multiplier Relative to the Ion Trap The negative voltage applied to the cathode attracts the positive ions ejected from the ion trap cavity.

  • Page 58: Foreline Pump

    In general, the ion gauge exhibits good repeatability. However, the ion gauge response depends on gas composition. A certain pressure of air and water will give a different reading than that of Helium. The Ion Gauge is meant to be a rough indicator of vacuum conditions.
  • Page 59 The RF generator attaches to the rear of the RF coil assembly. Below are diagrams of the electronic assemblies used in the Turbomolecular and Diffusion Pump Saturn 2000 GC/MS. The Saturn 2000 GC/MS Turbomolecular Pump Electronic Assemblies Functional Description 2000 MS Hardware Maintenance...

  • Page 60: The Power Input Subsystem And Turbomolecular Pump Controller

    The Saturn 2000 GC/MS Diffusion Pump Electronic Assemblies The Power Input Subsystem and Turbomolecular Pump Controller The power input subsystem contains the following circuits and switches: • Main power switch • SERVICE switch • Line voltage switches Main Power Circuit Line power of 115 Vac ±15%, 60 Hz ±3 Hz (or 230 ±15 Vac, 50 Hz ±3 Hz) first...

  • Page 61: Power Board

    electronics service switch allows the vacuum to the maintained in the event that the electronics need to be serviced. The line voltage switches are located on the power board and the turbomolecular controller. These switches are set at the factory. The turbo controller regulates the speed of the turbo pump.

  • Page 62: The Rf Generator Assembly

    • The electron energy control circuits, which controls the dc bias on both the ion trap and ion gauge filaments. • The diagnostic multiplexer circuit, which routes the voltage output of various components, and circuits on the power control board to the SAP/Wave board.

  • Page 63: The Manifold Electronics Assembly

    The Ion Trap Assembly The Manifold Electronics Assembly Two boards reside in the enclosure directly atop the Analyzer flange. The following circuitry, which is critical to the functioning of the ion trap or that must be in close proximity to the trap, resides on these boards. •...
  • Page 64 • The Scan Acquisition Processor/Waveform Generator Board • The scan acquisition processor/waveform generator (SAP/Wave) board is a real-time control and acquisition microcomputer that makes use of an 80C186 microprocessor. The SAP/Wave board communicates with the data system via an IEEE-488 interface board installed in the data system computer bus.

  • Page 65: The Data System

    NOTE: Before you can use any of the waveform options, i.e., SECI, MS/MS, or SIS, the waveform key(s) must be inserted into sockets U5, U6 and/or U7. The key(s) should be installed by the factory, or by a Varian Customer Support Representative.

  • Page 66: Chemical Ionization Options

    Chemical Ionization Options Introduction Chemical ionization (CI) provides mass spectral data that complement electron ionization (EI) data for the analysis of complex compounds. In the standard CI mode of operation, a CI reagent gas is introduced into the ion trap analyzer from an external gas supply cylinder.

  • Page 67: Ci Reagent Gas Requirements

    NOTE: Gases other than methane, isobutane, or ammonia can be used successfully as CI reagent gases with the Saturn GC/MS. For assistance in selecting and using other reagent gases, please contact your Varian Customer Support Representative. The CI reagent gas should contain less than 1 ppm of water. Water in the CI reagent gas may interfere with CI operation.
  • Page 68 CI reagent gases may be hazardous. Use proper protection when installing the reagent gas. 1. Enter the System Control and select the Manual Control tab dialog. 2. Make sure that the electron multiplier, filament, and RF voltage are all off. The Multiplier, Filament, and RF text should be red or black - not green.
  • Page 69 7. On the back of the Saturn GC/MS instrument, loosen the two screws that hold the plug in the CI Shutoff Manifold 2 to 3 turns. Remove the plug by pulling straight out and twisting. A Power Switch B Shutoff Manifold C Plug D 6/32" Screws (2 each) E Vacuum Hose F Fans Connecting CI Gas Supply 8.

  • Page 70: Checking The Reagent Gas Plumbing For Leaks

    Checking the Reagent Gas Plumbing for Leaks To check for air leaks in the reagent gas line connections and the presence of water vapor in the gas line, follow the procedure using a Leak Detection Gas to Troubleshoot for Air Leaks in the Troubleshooting Section. Depending upon the results you obtain, you may need to modify the procedure as follows: If a large air leak exists, check the CI GAS fitting on the rear of the instrument and the fitting on the pressure regulator for tightness.

  • Page 71: Default Parameters For Gaseous Ci Reagents

    You are now ready to operate the system in the CI mode. If you are a new user, we recommend that you perform the introductory example of CI operation in tuning the Saturn for Chemical Ionization in the Tutorial Manual. Default Parameters for Gaseous CI Reagents Reagent Gas Methane...

  • Page 72: Ion Intensities For Standard Ci Reagents

    Ion Intensities for Standard CI Reagents The CI Adjust function gives recommendations of an acceptable level of CI reagent ions for each of the five standard CI reagents. The general principles used in implementing these tests are: Methane Adjust the reagent gas pressure so that the peak heights at m/z 17 (CH ) and 29 (C ) are about...

  • Page 73: The Liquid Ci Inlet Option

    • Note the Diffusion Pump Foreline Pressure reading under the Vacuum System field. The reading should be less than 100 mTorr. Higher readings may indicate problems (i.e., leaks) and the user should refer to the Troubleshooting section for additional information. Click on the Manual Control button, and then click the CI icon to the left of the ion trap symbol (it will turn green when On).
  • Page 74 d. Loosely attach the Liquid CI Inlet assembly to the back of the instrument via the L-bracket with the screw that was removed. e. Rotate the Liquid CI Inlet assembly out of the way to remove the remaining screw. Rotate the Liquid CI Inlet assembly back into position and loosely attach the liquid CI inlet assembly with the remaining long screw (12-222006- 25).
  • Page 75 e. Gently install the PEEK tube end into the pneumatics manifold, being careful not to let the retaining plate scratch the tube. Do not retighten the 4 screws on the pneumatics manifold yet. g. Insert the other end of the PEEK tube into the CI shut-off block and tighten the 2 screws from the rear of the instrument.

  • Page 76: Filling/Refilling The Liquid Ci Reservoir Bulb

    Filling/Refilling the Liquid CI Reservoir Bulb 1. Be sure the CI valves are closed. Disengage the 4 screws that retain the liquid CI reservoir cover. They may remain in the block. 2. Remove the reservoir cover. 3. Gently pull the bulb down to remove it from the block. The O-ring and O-ring retainer may stay attached to the bulb.

  • Page 77: Setting Flows Of Vapor From Liquid Ci Reagents

    Setting Flows of Vapor from Liquid CI Reagents 1. Connect a liquid reagent reservoir containing the chosen liquid to the liquid reagent inlet block. 2. Open the CI needle valve 6-7 turns counterclockwise. 3. Open the CI solenoids by clicking on the CI button on the Manual Control page and allow the vapor flow from the reservoir to equilibrate.

  • Page 78: Installing And Using The Multiple Ci Module

    1. Loosen the 2 screws that attach the liquid CI inlet L-bracket to the back of the instrument. Also, loosen the 2 screws that attach the L-bracket to the liquid CI inlet block. 2. Remove the liquid CI restrictor end that inserts into the back of the instrument; rotate the restrictor out of the way.

  • Page 79: Pre-Installation Checklist

    Schematic Diagram of the MCI Module Multiple CI Module (shown with and without cover) Pre-Installation Checklist 1. Preparing the Mass Spec a. The Saturn MS should be shut down, vented, and unplugged. 2. Tools Required a. #2 Philips screw driver b.
  • Page 80 3. Vent the mass spec. 4. Unplug the power cord from the back of the mass spec. 5. Unpack the Multiple CI kit and place the parts on a table. 6. Open the front door on the mass spec until it presses against the right side panel. 7.
  • Page 81 13. Use two #6 x 0.50 inch long screws to attach the multiple CI manifold to the register plate and side panel. 14. Stand the side panel next to the right side of the mass spec. 15. Guide the two tubes past the power board and through the opening in the chassis halfway up the middle bulkhead, behind the front panel.
  • Page 82 20. There are now three openings in the pneumatics block. 21. Connect the metal tube from the multiple CI assembly to the opening on the left. 22. Connect the previously removed U-shaped tube, to the two right openings in the pneumatics block.
  • Page 83 3800 GC If you are installing the MCI Module on a 3400 or 3600 GC, skip to the installation instructions following this section. 1. The Multiple CI solenoid cable plugs into the External Events on the 3800 2. Remove the GC left side, top cover, and the detector cover. 3.

  • Page 84: Cable Connections To The Gc External Events Board

    5. Unplug the power cord. 6. Remove the top covers. 7. Remove the high voltage cover. 8. Connect the Rectifier PWA to pins 3 - 8 on the External Events board in the GC. 9. Tighten all six of the connector screws to ensure good electrical contact. If there are other electrical devices connected to the GC External Events 2, 3, or 4, they will have to be disconnected while Multiple CI is connected.

  • Page 85: Adding Liquid Ci Reagents To The Mci Module

    Adding Liquid CI Reagents to the MCI Module The addition of liquid reagents to the MCI Module is accomplished in much the same manner as addition of liquid reagent to the single Liquid CI option (LCI). The LCI liquid filling process is shown in detail on the Saturn Maintenance Tutorial CD under the heading MS Maintenance …...

  • Page 86: Adjusting Flows Of Ci Reagents

    Adjusting Flows of CI Reagents There are two ways to turn Channels of the MCI Module On and Off. The simplest way, which you may want to use when you are adjusting CI flows, is from the keyboard of the GC. The second way is to program a GC/MS Method in the Saturn GCMS Workstation software and download the method to the GC.
  • Page 87 Select the section GC Relays under 3400 or 3600 GC Control. You will see the following screen: If you wish to adjust flows of all three CI reagents in the MCI Module, you will want to save three Methods with Relays turned on for each specific reagent. If Channel A is connected to External Event 1 in the GC, click in the box for Relay 1.
  • Page 88 Now use the menu command File…Save As to save the method with a name such as ChannelA. Check the box for either Relay 2 (Channel B) or Relay 3 (Channel C) and save these methods as ChannelB and ChannelC. You may now open Channels A, B, or C by using the menu command File…Activate…...
  • Page 89 Highlight External Event A and release the mouse button. You will see the following display: Now, if Channels B and C are connected to Valves 2 and 3, enter the appropriate state by highlighting the first row under Valve 2 and Valve 3. Otherwise, enter External Events A through C under the appropriate Valve column.

  • Page 90: Setting Ci/Ms Parameters In The Ms Method Editor

    Setting CI/MS Parameters in the MS Method Editor To adjust CI reagent flows for a given CI gas and to use the appropriate parameters in a CI/MS acquisition, you will need to modify the GC/MS Method for each reagent Channel so that CI/MS parameters for each reagent are appropriate.

  • Page 91: Adjusting Reagent Flow For Each Ci Reagent

    The values of each parameter for acetonitrile CI are identified in the table Default Parameters for Liquid CI Reagents and already entered into the fields on the right side of the table. (If we were setting up for any of the standard gaseous or liquid reagents, their parameters can be entered automatically by clicking on the appropriate Reagent Gas selection.
  • Page 92 the Manual Control comes up with the Method tab displayed. Note that the method Name, Mode, and Scan Range are displayed. 5. Click on the Adjustments tab dialog and then choose Acetonitrile as the gas and click on Adjust. 6. The adjustment process will begin, as shown. 7.

  • Page 93: Building Gc/Ms Methods To Use Different Ci Reagents

    8. While observing the spectrum using Adjust CI Gas, turn the CI needle valve for the selected channel on the MCI Module clockwise to increase (or counterclockwise to decrease) the amount of reagent until the reagent ions abundances meet the requirements outlined for the chosen reagent in the table shown in Ion Intensities for Standard CI Reagents.
  • Page 94 Now choose the Method Directory item Column Oven and set an appropriate column oven program. The following program requires a 30-minute run: Choose the Method Directory item Sample Delivery and create a Sample Delivery method with all External Events Off: Click on the MS Method Editor item under 2000 Mass Spec Control and create a standard EI/MS section with a run time matching that of your EI_GC section.

  • Page 95: Methods For Single Ci Reagents

    Save the GC/MS Method. Methods for Single CI Reagents Open the standard GC/MS Method you have created and saved (e.g., EI_GC.mth) in the Saturn GC/MS Workstation. Before proceeding use the Method Editor menu command File… Save As to save the file with a name specific to the first CI reagent you want to use (e.g.

  • Page 96: Gc/Ms Samplelist For Alternating Ei/Ms And Ci/Ms Acquisitions

    If you are planning to use a different CI reagent in each Channel of the MCI Module, save a unique GC/MS Method specific to each Channel of the MCI, each with External Events programming of the correct Event. Under Saturn 2000 Mass Spec Control choose the Method Directory item MS Method Editor to prepare a CI/MS section of the Method.
  • Page 97 To prepare the Sample List for alternating EI/CI acquisitions, click on the Edit Automation Files button on the Star Toolbar or choose the option Start…Programs…Saturn GCMS Workstation…Automation File Editor. The Automation File Editor Dialog Box will open. Click on the option File…New…SampleList.
  • Page 98 Since EI and CI analyses are to be performed on three samples in succession, enter the appropriate names for the data files in each row of the SampleList. Use the scroll bar at the bottom of the dialog to display fields farther to the right in the SampleList.

  • Page 99: Multiple Ci Reagents In Consecutive Runs

    acquisition in the Command field and click OK. In this example the method is EI_GC.mth. Since the same EI_GC method will be used later in the list highlight the AutoLink button in the list and click on Fill Down. The EI_GC method is now selected for all entries in the SampleList. The final step in the process is to click on the AutoLink field for each acetonitrile CI sample and substitute the method ACN_CI.

  • Page 100: Multiple Ci Reagents In The Same Run

    Use the AutoLink field to activate the appropriate method for the EI or particular CI reagent required. Multiple CI Reagents in the Same Run In some demanding applications, it may be desirable to change CI reagents within a single chromatographic acquisition. This is done by time programming the GC/MS Method so that the correct External Events are opened during the corresponding MS acquisition time for each CI reagent.
  • Page 101 Then, while Segment 2 is highlighted, click the Add twice to create two additional Segments. Segment 2 is left as an acetonitrile CI segment ending at 10 minutes. Segment 3 parameters are changed in the Ionization Mode tab dialog to those for methanol CI and the end time is set for 20 minutes.

  • Page 102: Mci Module Maintenance

    In a complex method such as this, it is always advisable to review the MS Method to assure that the segment times and acquisition parameters have been entered correctly. Switching Times Between Reagents If one is interested in switching CI reagents on consecutive runs, the foreline pump clears residual reagent from the MCI Module lines effectively between runs.

  • Page 103: Handling And Storage Of Ci Liquids In Reservoir Bulbs

    Handling and Storage of CI Liquids in Reservoir Bulbs Use the procedure Filling/Refilling the Liquid CI Reservoir Bulb to fill the reservoir bulbs (03-920270- 00) with liquid. If you wish to replace a liquid reagent with a different liquid, you may use a vial cap (03-949870-04) from the MCI Module Accessory Kit to cap the reservoir and store it in the laboratory refrigerator in the Reservoir Stand (03- 930073-01) supplied with the Kit.
  • Page 104 adapter fitting and the long restrictor (03-930597-01). The long restrictor was connected between the pneumatics manifold and the gas shut off valve before the MCI module was installed. Protect the ends of the restrictors to prevent contamination and plugging, when working on the assembly. The MCI Module must have all of its ports connected for proper operation.

  • Page 105: Changing A Channel From Gas To Liquid Operation

    15. Do not turn on the filament or multiplier for about 2-3 minutes after opening the CI valves. A convenient way to verify that air and water have been removed sufficiently is to check the ion gauge pressure with the CI valves open. Verify that the pressure has returned to less than 35 x 10 Torr before turning on the Filament and Multiplier.

  • Page 106: Leak Checking

    for more than 20 seconds. After a few seconds, return the valve setting to ½ open or their previous setting (approximately 7 turns). 14. Do not turn on the filament or multiplier for about 2-3 minutes after opening the CI valves. A convenient way to verify that air and water have been removed sufficiently is to check the ion gauge pressure with the CI valves open.

  • Page 107: Hints For Successful Operation Of The Mci Module

    Hints for Successful Operation of the MCI Module 1. Acquisition with each CI reagent using the MCI Module requires a unique GC/MS method. The GC section method MUST contain External Events programming (done in the Sample Delivery section) to select the CI reagent in Channel A, B, or C.

  • Page 108: System Start-Up And Shutdown

    System Start-up and Shutdown Diffusion Pump Shutdown NOTE: During the SHUTDOWN procedure, the GC and MS temperature zones are reduced (<80 °C). The system is manually vented to atmosphere when the trap temperature is less than 80 °C. From the System Control click on Shutdown tab. The display of the Shutdown program appears and click on Shutdown.
  • Page 109 This represents a group of error messages indicating that the diffusion pump has been shut down. To precisely identify the problem, the USER should go to the Diagnostics tab, check “System Test and Run to Completion.”. Fault messages may appear on startup or during operation. •...

  • Page 110: Diffusion Pump Startup

    Diffusion Pump Startup NOTE: The Diffusion Pump System Startup sequence takes at least 30 minutes. First, the Peltier Baffle cooler is turned on while the pump heater is left off. This step lasts 15 minutes and allows the cooler to drop in temperature before any pump vapors are created.
  • Page 111 System Start-up and Shutdown 2000 MS Hardware Maintenance...

  • Page 112: Mass Spectrometer Maintenance

    Mass Spectrometer Maintenance Periodic Maintenance To ensure the Saturn GC/MS peak-performance, you will have to perform periodic maintenance on the vacuum and cooling systems. The following table identifies relevant maintenance intervals. Procedure Interval Check the foreline pump oil level and condition Weekly Purge foreline pump oil Weekly...

  • Page 113: Purging Foreline Pump Oil

    Foreline Clamping Ring Seal Inlet Gas Ballast Valve Drain Plug Oil Level Sight Glass Filler Plug Exhaust Foreline Pump Purging Foreline Pump Oil Condensable vapors accumulate in the foreline pump oil during routine operation. These condensates will reduce pump efficiency and shorten the life of the oil.

  • Page 114: Changing Foreline Pump Oil

    Changing Foreline Pump Oil To ensure peak performance and maximum pump lifetime, change the pump oil whenever the oil becomes thick, dark in color and has a burnt smell; or at least every six months. The oil change must be performed while the oil is warm. To change the pump oil: 1.

  • Page 115: Flushing

    If the paper is sucked toward the fan guard, the fan is working. • If it is not, the fan is broken. Contact your Varian Customer Support Representative to arrange for a replacement. 3. Check the second fan in the same manner.
  • Page 116 Saturn 2000 GC/MS, Front View Main Power Switch (rear Cal Gas Vial panel) Service Switch Vent Valve Transfer Line Heater RF Coil Trap Heater RF Coil Adjustment Screw Manifold Heater Transfer Line Turbomolecular Pump Pneumatics Manifold Cooling Fans CI Cal Gas Adjust...

  • Page 117: How To Replace The Turbomolecular Pump

    • If the noise stops, it is coming from the electronics compartment fan. 4. Contact a Varian Customer Support Representative to arrange for replacement of the broken fan. How to Replace the Turbomolecular Pump To replace the turbomolecular pump, proceed as follows: 1.
  • Page 118 • Take care not to completely unscrew the two inner clamping screws. (If you should unscrew them, restart the screws after you have removed the turbomolecular pump from the instrument.) 12. Remove the outside bottom clamping screw. 13. Remove the bottom clamp as you hold the turbomolecular pump in place. 14.

  • Page 119: Check Cooling Fans Diffusion Pump System

    Check Cooling Fans Diffusion Pump System CAUTION To prevent electronics overheating and diffusion pump failure, do not block air intakes or remove covers. Cooling fans perform two important functions in the Saturn GC/MS. They prolong the lifetime of temperature sensitive electronic components by maintaining optimal temperatures within the electronics compartments and they provide the airflow required by the air cooled diffusion pump and Peltier baffle.

  • Page 120: Checking The Diffusion Pump Fluid Level And Condition

    • If not, the fan is broken and should be replaced. Contact your Varian Customer Support Representative to arrange for a replacement. 9. Zone 3: Diffusion pump compartment. The Zone 3 fan is located in the lower left corner of the rear panel. Failure of this fan will cause the diffusion pump to overheat.

  • Page 121: Turning Off The Diffusion Pumped Mass Spectrometer

    Diffusion Pump Compartment Thermocouple Gauge Exhaust Clamp Elbow Diffusion Pump Controller (behind cover) Pneumatics Exhaust Inlet Clamp Tube Diffusion Pump Turning Off the Diffusion Pumped Mass Spectrometer WARNING: BURN HAZARD Allow diffusion pump and other heated zones to cool before disassembly. To turn off the MS: 1.

  • Page 122: Replacing The Diffusion Pump Thermocouple Gauge

    Replacing the Diffusion Pump Thermocouple Gauge The thermocouple gauge will need replacing if its filament has burned out or its thermocouple has become detached. This will be indicated in the Diagnostics report. To replace the thermocouple gauge: 1. Turn off the MS as described in the Start-up and Shutdown section. 2.

  • Page 123: Replacing The Diffusion Pump Peltier Baffle

    24. Reinstall the clamp by pushing it onto the joined exhaust flanges. 25. Rotate the clamp 180° and install the screw from the left side. 26. Thread the wing nut onto the screw. 27. Rotate the clamp as far to the left as possible, while still allowing room to turn the wing nut.

  • Page 124: Cleaning The Diffusion Pump Peltier Baffle

    9. Ensure the new seal and sealing surfaces are clean and free of particles and fibers. 10. Fit the new seal to the Peltier baffle and lower the baffle into position on the manifold. Do not allow the seal to twist. 11.

  • Page 125: Removing The Diffusion Pump

    Removing the Diffusion Pump 1. Turn off the MS. 2. Carefully separate the MS from the GC by approximately 250 mm (10"). Be careful not to break the GC column. 3. Remove the top cover. 4. Remove the transfer line. 5.

  • Page 126: Topping Off The Diffusion Pump Fluid Level

    14. Grip the pump with your right hand, tilt towards you until the inlet flange clears the manifold flange. CAUTION Be careful not to scratch or damage sealing surfaces. 15. Pull the pump out to the full extent of its cable. 16.

  • Page 127: Cleaning The Diffusion Pump

    Cleaning the Diffusion Pump Diffusion Pump Circlip Heater Assembly Inlet Baffle Harness Clamp Centering Plate & Spring Insulation Disk Jet Assembly Insulation Exhaust Baffle & Circlip Over temperature Switch Sight Glass Assembly Inlet Port Body Exhaust Port Retaining Plate Ejector Stage Base Plate Hazardous chemicals may be present.
  • Page 128 4. Using a pair of circlip pliers, remove the circlip that holds the exhaust baffle in the exhaust port. Place the circlip on the towels. CAUTION Be careful not to scratch or damage sealing surfaces. 5. Withdraw the baffle and place it on the towels. 6.

  • Page 129: Changing The Diffusion Pump Heater

    CAUTION Be careful not to scratch or damage sealing surfaces. 21. Pour the diffusion pump fluid (03-930639-01) through one of the holes in the diffusion pump’s inlet baffle. Part Number 03-930639-01 contains 40 cm . This is a full charge, plus an allowance for fluid that remains on the walls of the container.

  • Page 130: Reinstalling The Diffusion Pump

    e. If the heater does not pull out freely, a second application of penetrating oil may be necessary. 9. Apply the anti-seize compound to the new heater and install it in the base. 10. Refit the insulating pad, retaining plate, harness clamp, ground wire, nuts, base plate, and retaining screws.
  • Page 131 10. Inspect the exhaust seal. Replace if it is worn or damaged (27-402536-00). 11. Wipe the exhaust seal clean with a lint free cloth, and refit to the exhaust port. 12. Lower the elbow onto the diffusion pump exhaust port. CAUTION Take care not to dislodge the seal.

  • Page 132: Turning On The Mass Spectrometer

    Inlet Clamp Exhaust Clamp Manifold Elbow Exhaust Diffusion Pump Relative positions of the manifold, diffusion pump, elbow and clamps as viewed from above. NOTE: The manifold and elbow are shown as outlines for clarity. Turning on the Mass Spectrometer 1. Make sure the power switch on the rear panel is in its OFF position. 2.

  • Page 133: How To Service The Ion Trap

    How to Service the Ion Trap NOTE: The Saturn 2000 Maintenance Tutorial on CD-ROM provides viewing maintenance procedures on computer screen. Refer to MS Maintenance Section. You will need to service the ion trap if it needs to be cleaned or requires replacement of the filaments or multiplier.

  • Page 134: Turn Off The Mass Spectrometer

    Turn off the Mass Spectrometer WARNING: BURN HAZARD Allow heated zones to cool before disassembly. Turn off the mass spectrometer by invoking the Shutdown procedure. Refer to chapter on system Start-up and Shutdown. 1. Shut off the turbomolecular pump, foreline pump, and all electronics by turning off the main power switch on the back panel.

  • Page 135: Remove The Analyzer Assembly

    Heating Cable O-ring Boot Transfer Line Tip Heating Cable Slot Ferrule Nose Clip Tool Bayonet Mount Nose Analyzer Assembly Tongue Nose Hole Analyzer Assembly Lock-Down Tabs Transfer Line Assembly Remove the Analyzer Assembly Retract transfer line before removing analyzer assembly. NOTE: Be sure the transfer line is retracted.
  • Page 136 NOTE: Some Saturn systems have a transfer line removal flap warning that will block the locking tabs. If such a flap is present, tip it out of the way during the procedure and return it to its original position once the analyzer is replaced. 6.

  • Page 137: Replace The Electron Multiplier

    Replace the Electron Multiplier When positioned to collect ions, the electron multiplier sits as close as possible to the ion trap. The electron multiplier grid should never be in contact with the trap. To remove the electron multiplier, proceed as follows: 1.

  • Page 138: Replace The Filament(S)

    Replace the Filament(s) To replace the filament(s), proceed as follows: 1. Orient the trap so the filament assembly is facing you. 2. Disconnect the filament connectors from the flange-feedthrough pins by gently pulling each pin connector up until the wires are free from the pins. 3.

  • Page 139: Remove The Ion Trap Oven

    Remove the Ion Trap Oven Using gloves to remove the ion trap oven, proceed as follows: 1. Remove the electron multiplier and place it on its side. 2. Disconnect the filament wires from the flange feed-through pins (labeled 1, 2, C) by gently pulling each pin connector up until all wires are free of the flange.

  • Page 140: Clean The Trap Components

    Screw, 6/32, 4 places Wave Washer Clamping Plate Gate Conductor Exit End Cap Trap Oven, “T” is located this side. Quartz or Silica Coated Spacer, 2 places Filament Assembly RF Ring Electrode Filament Clip Filament End Cap Screw Electron Gate Ion Trap Assembly Clean the Trap Components To clean the ion trap parts, you will...
  • Page 141 2. After you clean a part, hold it under running water and use a clean applicator to remove the last visible traces of aluminum oxide. 3. Immediately place the clean part in a beaker containing a solution of detergent and warm water. NOTE: Do not let the slurry dry on the metal.

  • Page 142: Clean Silchrom Ion Trap Electrodes

    Clean SilChrom Ion Trap Electrodes The silica top surface of the SilChrom Ion Trap Electrode is a very thin (only about 1 µm), but durable layer which is strongly bonded. However, abrasives such as alumina powder must not be used to clean the trap parts because this will definitely destroy the silica layer! Strongly acidic or strongly basic laboratory cleaners must not be used to clean the trap parts because they will also remove the silica layer!

  • Page 143: Re-Install The Trap Oven

    NOTE: The orientation of the trap components is important. Make sure that all parts are free of particles, lint, etc. 1. Replace the gate conductor, tab-down into position. 2. Replace the wavy washer on the gate conductor. The washer orientation is not important.

  • Page 144: Reposition The Electron Multiplier

    5. Replace and tighten the nut until it is snug. 6. Attach filament wires 1, 2, and C to the flange feed-through pins. Reposition the Electron Multiplier To install the electron multiplier, proceed as follows: 1. Slide the electron multiplier forward along its track. 2.

  • Page 145: Close The Vent

    3. Orient the assembly so that the heating cable fits inside the shell slot. 4. Rotate the nose so that the nose holes line up with the small slots in the shell. These holes will be found at the 4:00 and 10:00 positions. 5.

  • Page 146: Check Ion Trap Operation

    Check Ion Trap Operation To check the ion trap operation, proceed as follows: 1. Once bake out is finished, re-establish the analysis temperature in the trap for at least 2 hours to achieve thermal equilibrium. • The manifold temperature should be below 50 °C. 2.
  • Page 147 Mass Spectrometer Maintenance 2000 MS Hardware Maintenance...

  • Page 148: Gc Maintenance

    Varian service representative. For maintenance problems where mechanical or electrical assemblies need to be repaired or replaced please call your local Varian service center. There are certain maintenance tasks that should be carried out on a routine basis.

  • Page 149: General Gc Maintenance

    General GC Maintenance The common general GC maintenance tasks are checking and changing gas supply cylinders, leak checking, and changing gas purifier filters. These should be performed at the frequency suggested above. The following procedures are critical to the successful long-term operation of a Gas Chromatograph. It is very important to leak check the system on a routine basis and to ensure the quality of gas supplies, particularly the carrier gas.

  • Page 150: Gas Purifier Replacement

    Locate leaks with an electronic leak detector or leak detection fluid. An electronic helium leak detector is available from Varian (01-900153-01). This device can detect helium concentration in the air as low as 2 ppm and is very effective at identifying the precise location of a helium leak from a GC system.
  • Page 151 The moisture trap should also be changed immediately when it changes color to prevent breakthrough of moisture to the oxygen trap. The filters supplies by Varian are mounted either on the rear panel of the instrument or on a filter stand, depending on when the instrument was purchased.

  • Page 152: Injector Maintenance

    6. Mark the date of installation on the calendar in the filter label with a felt tip pen. NOTE: Review the instructions supplied with the replacement filters. The following are the stand-alone gas purifiers available from Varian. Purifier Part Number...

  • Page 153: 1079 Injector

    Use the following procedure to change a septum on any Varian injector: 1. Cool the column oven and injector oven to 50 °C. This ensures safe handling of injector parts and protects the column from elevated temperatures while it is exposed to air.

  • Page 154: Remove The Glass Insert

    Refer to the figure below when removing and/or replacing the glass insert. Injector Nut Septum Septum Purge Septum Support Graphite Ferrule Carrier Gas Inlet Split Vent Glass Insert Fused Silica Column 10 Capillary Column Nut 11 Vespel® Ferrule 12 Point of Injection Tools Required Tweezers or septum pick (72-000084-00)

  • Page 155: Replace The Glass Insert

    NOTE: If the GC is equipped with an 8200 AutoSampler, to access the injector nut, push the carrousel release button (back left) and swing the carrousel out. 2. With tweezers or septum pick, lift the edge of the septum (Item 2). Remove the septum.

  • Page 156: Clean The Glass Insert

    2. Position the tool as shown above on a flat, clean surface. Use clean laboratory tissue on the surface. Tighten the septum support finger-tight. Holding the tool with a 5/8″ wrench, give the septum support an extra 1/3 to 1/2 turn past finger-tight. Now unscrew the septum support, which now has the ferrule and insert seated in it.

  • Page 157: Deactivate The Glass Insert

    NOTE: Rinsing the glass inserts with strong acids or bases or heating to a high temperature will remove the deactivation coating on the glass inserts. Rinsing the glass inserts with solvents or mixed solvents will not remove the deactivation coating. Deactivate the Glass Insert Follow these steps to deactivate the glass insert in the 1079 Injector.

  • Page 158: How To Remove The Capillary Column From The System

    WARNING: FIRE HAZARD Use proper eye and skin protection. Methanol and acetone are toxic and flammable chemicals. Exercise appropriate precautions when these chemicals are used. 4. Remove the injector nut, septum, and septum support, with ferrule and insert attached. 5. Moisten a cotton swab and a stick with methanol and gently swab center of the injector body.
  • Page 159 NOTE: Avoid contamination of the transfer line, injector, and capillary column by using clean tools and wearing clean lint-free Nylon gloves. As you remove parts, place them on a clean, lint-free, unpainted surface. 4. Use the alignment tool and a 5/16-in. wrench to loosen the brass nut on the end of the transfer line.

  • Page 160: How To Install A New Capillary Column In The System

    How to Install a New Capillary Column in the System To install a new capillary column in the mass spectrometer, proceed as follows: 1. Unwind about 60 cm (24 in.) of the mass spectrometer end of the column from the support cage. 2.
  • Page 161 19. Gently push the transfer line toward the manifold, and rotate the collar in the clockwise direction until the bayonet lock engages. 20. Reconnect the transfer line heating cable to the mass spectrometer. 21. Gently push the mass spectrometer toward the GC, until the transfer line boot fits snugly over the collar on the side of the GC oven.

  • Page 162: Troubleshooting

    Troubleshooting How to Isolate a GC or Mass Spectrometer Problem In general, whenever you attempt to isolate a Saturn GC/MS problem, you will check the system in the following order: • Data System • Gas Chromatograph (GC) • Mass Spectrometer Checking the Data System Please refer to the Saturn GC/MS software release notes for relevant software troubleshooting procedures.

  • Page 163: How To Troubleshoot Problems With Spectra

    There are two procedures for isolating problems associated with the Mass Spectrometer. Running the Auto Tune routine from System Control will provide you with information about system performance. Running the diagnostics program will initiate a hardware test. These tests may be used to isolate simple ion trap problems, e.g., air leaks, burned-out filaments, high contamination levels, etc.

  • Page 164: Check For An Open Filament

    Check for an Open Filament Diagnostics will determine is one or both filaments are open. If only one filament is open, enter System Control. Click on Set Points. Under Filament Selection, select the other filament. If both filaments are open, shut down the instrument. Then check the filament continuity and wire connections after you have removed the ion trap assembly from the manifold.

  • Page 165: Check The Assembly Of The Trap

    If the electron multiplier voltage in the Diagnostics is only a few volts, the multiplier is shorted to ground. Shut down the system, and replace the electron multiplier or call a Varian Customer Support Representative. Check the Electronics Check whether there is an electronics problem, proceeding as follows: 1.

  • Page 166: What To Do If You Experience A Loss Of High Mass Peaks

    NOTE: If, after performing these tests, you are still unable to isolate the cause of the problem, contact your Varian Customer Support Representative. What To Do If You Experience a Loss of High Mass Peaks The loss of high mass peaks maybe due to: •...

  • Page 167: Check The Rf Storage Level

    NOTE: If, after performing these tests, you are still unable to isolate the cause of the problem, contact your Varian Customer Support Representative. What To Do If the Resolution is Poor But the Air and Water Levels are Acceptable...

  • Page 168: Check The Axial Modulation Setting

    6. If oven is properly assembled and axial modulation is out of range, contact your Varian Customer Support Representative. What To Do If There is a High Baseline at High Masses...

  • Page 169: What To Do If The Trap Function Calibration Fails After The Calibration Ions Have Been Correctly Identified

    What To Do If the Trap Function Calibration Fails After the Calibration Ions Have Been Correctly Identified If the trap function calibration fails after the calibration ions have been correctly identified, you should investigate the following possible causes: • The electron multiplier voltage is too low. •...
  • Page 170 CAUTION Often, major air leaks are accompanied by a hissing sound. These leaks may be due to extremely loose fittings, improperly seated O-rings, or open valves. If you suspect a major leak, do not turn on the electron multiplier, RF voltage, or filament.
  • Page 171 Air/water Spectrum from a System with a Very High Water Vapor Background Troubleshooting 2000 MS Hardware Maintenance...
  • Page 172 Air/water Spectrum from a System with Excess Water Vapor and a Relatively Small Air Leak • If the ratio of the height of the peak of mass 18 (H ) to mass 19 (H is about 10:1, there is little water vapor in your system. •...
  • Page 173 100% value 18:28 ratio 19:18 ratio 28 width <100 <1000 ~ 1:1 10 to 15% < 1 m/z 7. Spectra observed if there is an air leak in your system. An Air/Water Spectrum Obtained from a System with a Small Air Leak and Little Water Vapor as Indicated by: •...

  • Page 174: How To Fix High Water Levels

    An Air/Water Spectrum Obtained from a System with a Large Air Leak and Little Water Vapor as Indicated by: • The peak at mass 32 is the base (highest) peak. • The peaks at masses 18, 19, and 28 are broadened. As a leak increases, all peaks broaden and eventually become undifferentiated.

  • Page 175: How To Fix A Large Air Leak

    be sure to wait until all GC zones are cool before beginning. If the leak is coming from the transfer line connection, you will have to shutdown the GC/MS system and vent the system before fixing it. NOTE: Set the mass range from 35 to 50 if you will be using an argon leak- detection gas, or from 80 to 110 if you will be using a Freon leak-detection gas.

  • Page 176: How To Fix A Small-To-Moderate Air Leak

    The brass nut on the transfer line is not tight enough, recheck the system. Do not over tighten the fittings. Otherwise, you may generate an even larger leak. If you cannot eliminate the leak, vent the system, and check the O-ring on the manifold and transfer line for particles.

  • Page 177: How To Troubleshoot The Gc

    How to Troubleshoot the GC NOTE: Please refer to the GC Operator’s Manual for information about GC troubleshooting and diagnostics procedures not described in this section. This section describes chromatographic troubleshooting, with particular emphasis on GC/MS applications. You will be able to see most of the problems addressed in this section by running the COLTEST mixture (03-920273-00).

  • Page 178: Set Up The Transfer-Line And Trap-Temperature Conditions

    Set Up the Transfer-Line and Trap-Temperature Conditions 1. Set the transfer line temperature to 260 °C. 2. Set the trap temperature to 150 °C. 3. Set the manifold temperature to 35 °C. Set Up the Mass Spectrometer Acquisition Method To set up the mass spectrometer acquisition method with: 1.

  • Page 179: How To Troubleshoot Common Chromatographic Problems

    Typical Chromatogram of COLTEST Text Mixture The following figure demonstrates the resolving power of Saturn for coeluting compounds. Resolution of Saturn for Coeluting Compounds You can also effectively separate the individual components in the mixture for subsequent data manipulation, e.g., library searches and quantitation. For details about plotting single ion chromatograms for ions specific to a single compound, please refer to the SaturnView help or section in the Software Reference manual.

  • Page 180: Correction Of Solvent Tailing Or Broadening Problems

    Correction of Solvent Tailing or Broadening Problems Symptom Solution Poor column installation Reinstall the column in the injector. Check the column seal resulting in dead volume with the insert in the SPI/1079 (on-column). Make sure you in the injector have a good cut on the column by examining the column under magnification.

  • Page 181: Correction Of Leading Sample Peaks (Reverse Tailing)

    Correction of Leading Sample Peaks (Reverse Tailing) Symptom Solution Column overhead due to injection of Dilute the sample, or perform a split injection. excessive amounts of a component Degradation of the stationary phase Change the column. Carrier gas velocity is too low Increase the carrier flow rate.

  • Page 182: Correction Of Peak Splitting (Particularly For Low Boilers)

    Correction of Peak Splitting (Particularly for Low Boilers) Symptom Solution Sample flashing in injector (1077, 1078 Lower the injection temperature, or use a or 1079), simulating two injections SPI/1079 programmed injection. Column temperature programming Increase the initial column hold time until starts before SPI has finished SPI/1079 reaches its maximum temperature, programming...
  • Page 183 Troubleshooting 2000 MS Hardware Maintenance...

  • Page 184: Troubleshooting Of Diffusion Pump System

    Check for large air leaks. Refer to troubleshooting sections on leaks. e. Check the level and condition of the foreline pump oil. Contact Varian Customer Support Representative. 2. Foreline pressure exceeds 500 mTorr (Moderate Air Leak) a. Check the GC column is not broken.

  • Page 185: Problems During Routine Operation

    Contact Varian Customer Support Representative. 3. Peltier Baffle Fan Failure a. Check the fan on the rear panel. b. Contact your Varian Customer Support Representative. 4. Thermocouple Gauge Failure c. Check the cable connections. d. Open filament. Gauge must be replaced.
  • Page 186 Worn or damaged seals must be replaced. g. Contact your Varian Customer Support Representative. 2. CI Gas Settings (must be checked in Diagnostics) a. Pressure Readings should not exceed 350 mTorr. Confirm CI reagent gas head pressure at gas cylinder is set at 5 psi.
  • Page 187 Common Contaminant Compound Possible Source Ions (m/z) 18, 28, 32, 44 O, N , CO Air Leak 69, 131, 219, 264, 414, 464, PFTBA Leaking Calibration Valve 502, 614 31, 32 Methanol Cleaning Solvent 43, 58 Acetone Cleaning Solvent 73, 147, 207, 221, 281, 355, Dimethylpolysiloxane Septum or methyl silicone column coating...

  • Page 188: Miscellaneous Procedures And Instructions

    The repair of such failures is specifically excluded from the standard warranty and service contract coverage. For additional information, please request specific pre-installation support directly through your local Varian Sales/Service Center. Power You are responsible for providing two dedicated fourplex single-phase power sources with earth grounds hard-wired to the main power panel ground.
  • Page 189 equipment, we recommend a separate dedicated power source for their operation. NOTE: Do not use the free outlet for equipment that draws more than 2 amps. Interconnect Diagram for the Saturn GC/MS NOTE: Avoid using power supplies from sources that may be subject to RF interference, such as electric motors and elevators.

  • Page 190: Quality Of Power

    Saturn GC/MS components are as follows: Component Amperes Mass Spectrometer Gas Chromatograph Varian 8200 AutoSampler Computer Monitor Laser Printer NOTE: With a 230V power source, the maximum amperage requirement of each of the above components is one-half of the amperage given above.

  • Page 191: Operating Environment

    High humidity will also block the filters on cooling fans and accelerate wear of the heads in the diskette drives. Varian recommends that your laboratory be equipped with a temperature/humidity monitor. This will ensure that your laboratory is always in conformance with temperature and humidity specifications.

  • Page 192: Exhaust System

    NOTE: The presence of >1 ppm oxygen or water in the carrier gas supply may significantly affect the performance of Saturn, and it damage such components as the capillary column, filaments, and multiplier. Varian recommends that its customers verify that their gas suppliers use controlled tanks; this will ensure that purity standards are maintained.

  • Page 193: Other Gases

    If you are not sure which one of these cryogenic options you ordered, check your purchase order. Other Gases If you ordered an 8200 AutoSampler or automated valves, an independent supply of air or N at 40-60 psig may be required. How to Install Saturn To install the Saturn GC/MS, proceed as follows: 1.

  • Page 194: Parts And Supplies

    3. Open the vent valve lever on the front of the mass spectrometer for ten minutes. 4. Keep an eye on the capillary column inside the GC as you gently slide the mass spectrometer away from the GC. Be sure not to bend or kink the capillary column.

  • Page 195: Trap Components

    03-930109-14 Quad-ring, Viton Manifold 03-930109-18 Quad-ring, Viton Transfer Line Pump Spares, Pumps, Pump Conversion Parts Part Number Description 03-930650-01 Mechanical Pump, 90 L/min, 115/230V, Varian 03-920358-00 Screen, Turbo Pump (V-70) 03-930316-01 Cable, Turbo Controller to turbo 03-930317-91 Turbo Controller 03-920518-00 7’...

  • Page 196: Diffusion Pump Spares

    Diffusion Pump Spares Part Number Description 03-930053-01 Chassis Fan, Electronics Side 03-930645-01 Chassis Fan, Pump Side 03-920510-00 Plastic Nut 03-930109-02 O-ring, Elbow 27-402294-00 O-ring, Diffusion Pump Inlet 27-402536-00 O-ring, Diffusion Pump Exhaust 03-930109-16 O-ring, Peltier Baffle 03-930288-01 PWA Diffusion Pump Controller 27-229907-00 Thermocouple Gauge 03-930640-91...

  • Page 197: Gc Spares

    GC Spares Part Number Description 03-917742-00 Serial I/O PWA 03-925367-31 PWA, CPU, IBDH, 3400 SOC 03-925367-33 PWA, CPU, IBDH, 3600 SOC 03-918332-01 Insert, SPI, High Performance, Glass 03-949551-00 Nut, Capillary Injector 28-694580-01 Ferrule, 0.4 mm ID X 1/16, pkg. 10 28-694581-01 Ferrule, 0.5 mm ID X 1/16, pkg.

  • Page 198: Additional Saturn Spares

    Additional Saturn Spares Part Number Description 03-914763-00 Saturn GC/MS Workstation Hardware Maintenance Manual 03-914764-00 Saturn GC/MS Workstation Software Reference Manual 03-914765-00 Saturn GC/MS Workstation Tutorials Manual 03-930107-02 Solenoid, 3-way, Cal Gas 03-930100-01 Needle Valve, Cal Gas 27-350005-00 Oil Mist Eliminator 03-925677-91 ChromatoProbe Kit CI Parts/Spares...

  • Page 199: Mci Module Accessory Kit

    Part Number Description 12-222006-08 Screw, 6-32 x 1/2, SS 12-222006-05 Screw, 6-32 x 5/16 28-158923-00 Tubing, Vacuum 28-849918-00 Fitting, Tee, Barb 03-930870-02 Cap, Polypro, 1/8 inch 03-930109-10 O-ring, 2-104 03-930109-17 O-ring, 2-108 03-930071-00 Cover, Connector, Harness 03-930068-01 Assembly, Harness, Solenoids, Multi CI 03-930076-01 Label MCI Module Accessory Kit...

  • Page 200: Calling Varian Service

    Calling Varian Service If you have a problem with your Saturn GC/MS that you are unable to resolve using the procedures described, you may want to call a Varian Customer Support Representative. When you call, please be prepared to provide the following information: •...

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