Related Manuals for PerkinElmer Clarus SQ 8 MS Series
Summary of Contents for PerkinElmer Clarus SQ 8 MS Series
- Page 1 GAS CHROMATOGRA CHROMATOGRAPHY LARUS LARUS SQ 8 MS SQ 8 MS Hardware Guide Hardware Guide...
- Page 3 Clarus SQ 8 MS Clarus SQ 8 MS Hardware Guide Hardware Guide...
- Page 4 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 Except as specifically set forth in its terms and conditions of sale, PerkinElmer makes no...
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Page 5: Table Of Contents
Electromagnetic Compatibility (EMC) ............13 Regulatory Information ................. 13 United States (FCC) ................13 Europe ....................13 Electrical Symbols Used on Clarus SQ 8 MS Series ......14 Label Location and Content ..............15 Clarus MS Safety Practices ................18 Generic Warnings .................. 18 Moving the Clarus SQ 8 MS .............. - Page 6 Clarus SQ 8 MS Hardware Guide PC Requirements ................... 34 Operating System .................. 35 Software ....................35 Instrument Firmware Versions .............. 35 Printer ....................35 Pre-Installation Checklist................36 Introduc Introduction ........tion ..................37 ..........37 Preface ......................39 System Overview................... 39 Summary of this Guide ................
- Page 7 Contents Removing the Source ................71 Returning the Source ................74 Changing a Column ..................75 Tools and Items Required: ..............75 Physical Measurement Outside the SQ 8MS ......... 76 Alignment Using the 10 mm Positioning Gauge Tool ......79 Optical Column Alignment Using the Optional Plug Handle and Sight .....................
- Page 8 Clarus SQ 8 MS Hardware Guide Communications Related ..............147 Forepump Related ................148 Message Dialogs ..................151 Index ................Index ....................15 ....155 5 Index ......................157...
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Page 9: Warnings And Safety Warnings And Safety Informat Information
Warnings and Safety Information... -
Page 11: Conventions Used In This Manual
Bold 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 12 Clarus SQ 8 MS Hardware Guide We use the term WARNING to inform you about situations that could result in personal injury personal injury to yourself or other persons. Details about these circumstances are in a box like this one. WARNING WARNING Warning (Warnung)
- Page 13 Warnings and Safety Information We use the term CAUTION to inform you about situations that could CAUTION CAUTION result in serious damage serious damage to the instrument to the instrument or other equipment. Details about these circumstances are in a box like this one. Caution (Achtung) Bedeutet, daß...
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Page 14: Customer Service
Clarus SQ 8 MS Hardware Guide Customer Service Company Name and Address: PerkinElmer 710 Bridgeport Avenue Shelton, Connecticut 06484-4794 USA Tel: (800) 762-4000 or (203) 762-4000... -
Page 15: Electromagnetic Compatibility (Emc)
Operation of this equipment in a residential area is likely to cause harmful interference in which user will be required to correct the interference at their own expense. NOTE: Changes or modifications not expressly approved by PerkinElmer could cause the NOTE: instrument to violate FCC (U.S. Federal Communications Commission) emission regulations, and because of this violation could void the user’s authority to operate... -
Page 16: Electrical Symbols Used On Clarus Sq 8 Ms Series
Clarus SQ 8 MS Hardware Guide Electrical Symbols Used on Clarus SQ 8 MS Series Alternating current. Protective conductor terminal. Ground Off position of the main power switch. On position of the main power switch. Warning: Risk of electric shock. -
Page 17: Label Location And Content
Warnings and Safety Information Label Location and Content Figure 1 Front View of Clarus SQ 8 T. Figure 1 Front View of Clarus SQ 8 T. - Page 18 Clarus SQ 8 MS Hardware Guide Figure 2 Figure 2 Rear View of Rear View of the Clarus SQ 8 the Clarus SQ 8 T. T.
- Page 19 Warnings and Safety Information Figure 3 Figure 3 Rear View of the Clarus SQ 8 S compa Rear View of the Clarus SQ 8 S compatible with the Clarus 580 GC tible with the Clarus 580 GC and Clarus 680 GC. and Clarus 680 GC.
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Page 20: Clarus Ms Safety Practices
Clarus SQ 8 MS Hardware Guide Clarus MS Safety Practices NOTE: NOTE: This equipment requires no specified inspection or preventive maintenance to ensure the continuous functioning of its safety features. The Clarus SQ 8 Mass Spectrometer should be used in accordance with the instructions provided in the hardware and software user’s guides and tutorial supplied with the instrument. - Page 21 Lethal voltages are present at certain areas within the instrument. Internal maintenance of the instrument should only be performed by a PerkinElmer service engineer or similarly authorized and trained person. When the instrument i When the instrument is connected to line...
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Page 22: Contamination
Clarus GC Installation Guide (P/N 09936590 or 09936779) . Servicing of electrical components within the mass spectrometer should be • performed only only by a PerkinElmer Service Representative. Servicing of the incoming AC power line components in your laboratory • should be performed only only by a licensed electrician. -
Page 23: Decontamination
Decontamination Before using any cleaning or decontamination methods except those specified by PerkinElmer, users should check with PerkinElmer that the proposed method will not damage the equipment. Customers wishing to return instrumentation and/or associated materials to PerkinElmer for repair, maintenance, warranty or trade-in purposes are advised that all returned goods must be certified as clean and free from contamination. -
Page 24: Compressed Gases
Clarus SQ 8 MS Hardware Guide Compressed Gases Explosive hazard. Cylinders (tanks) of compressed gases should Explosive hazard. be handled with extreme care. Gas cylinders can be hazardous if mishandled. WARNING WARNING Avoid banging the valves and ensure that the correct valves and gauges are installed. Gas cylinders should be stored (and placed) outside the laboratory and connected to the instrument through specially cleaned copper tubing. -
Page 25: Heated Zones
Warnings and Safety Information To ensure adequate cooling of the instrument electronics, do not obstruct the gap at the base of the Clarus MS/Clarus GC, in the system (for example, the TurboMatrix ATD or and if practical, leave a minimum 6-inch clearance between each instrument Headspace). -
Page 26: Using Ammonia Gas
Clarus SQ 8 MS Hardware Guide Using Ammonia Gas Hazardous gas vapors. . When using ammonia gas while running in the Hazardous gas vapors chemical ionization (CI) mode, it is necessary to vent the mass spectrometer effluent from the forepump exhaust into a fume hood or charcoal trap. -
Page 27: Definitions In Warning For Hazardous Chemicals
Warnings and Safety Information When using toxic samples, the mechanical pump oil is toxic waste. WARNING WARNING Some chemicals used with the Mass Spectrometer may be hazardous or may become hazardous after completion of an analysis. The responsible person (for example, the Lab Manager) must WARNING WARNING take the necessary precautions to ensure that operators and... -
Page 28: Temperature, Humidity, And Environment
Clarus SQ 8 MS Hardware Guide Temperature, Humidity, and Environment Operating Conditions The Clarus SQ 8 MS is designed for indoor use only. CAUTION CAUTION CAUTION CAUTION Do not operate the mass spectrometer in a Cold Room or a refrigerated area. -
Page 29: General Laboratory Safety
Exterior surfaces of the MS may be cleaned with a soft cloth, dampened with a mild detergent and water solution. Do not not use abrasive cleaners or solvents. Before using any cleaning or decontamination methods except those specified by PerkinElmer, users should check with PerkinElmer that the proposed method will not damage the instrument. -
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 Size Weight Weight Clarus SQ 8 T, C, and S 32 cm (13 in.) wide x 50 cm 46.8 kg (102 lb) (20 in.) high x 77 cm (30 in.) deep Clarus 580 GC 32 cm (13 in.) wide x 46 cm 48 kg (105 lb) -
Page 32: Environmental Requirements
Clarus SQ 8 MS Hardware Guide Bench Space The laboratory bench should be sturdy enough to support the full weight of the GC/MS as well as additional equipment (for example, computer and/or printer). Expect the total weight of the GC/MS and accessory equipment to weigh at least 159 kg (350 lb). -
Page 33: Power Requirements
Warnings and Safety Information Power Requirements Power Consumption Clarus MS: 1000 VA (volt-amps) Clarus GC: 2400 VA (volt-amps) Add 100 VA for the computer and 108 VA for a printer. Power Consumption See below listing for the Clarus 580/680. Add 100 VA for the (with optional oven computer and 108 VA for the printer. -
Page 34: Gas Requirements
Clarus SQ 8 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 The gas delivery pressure required is 15 psi (103 kPa) to the bulkhead fitting (1/8 in. Swagelok) on the mass spectrometer. If ammonia is used for chemical ionization, all fittings and tubing Ammonia must be stainless steel to avoid corrosion. A single-stage regulator is Methane required for ammonia, rated for corrosive service. -
Page 36: Computer And System Software Requirements
PC Requirements The TurboMass software is installed at PerkinElmer prior to shipment and tested using the following minimum PC system specifications. If you need to reinstall the software, verify that the PC meets the following minimum requirements: •... -
Page 37: Operating System
Warnings and Safety Information • Integrated video, Intel® GMA4500 • Hard disk with 2.0 GB free space • 1 RS-232 port • 2 RJ-45 10/100Base-T ports • Lenovo USB Keyboard and Lenovo USB optical mouse with scroll Operating System Windows 7 Professional Software TurboMass Software. -
Page 38: Pre-Installation Checklist
Clarus SQ 8 MS Hardware Guide Pre-Installation Checklist __________________________ _____________________ MODEL: DATE: __________________________________ CUSTOMER: __________________________________ SPO#: Requirements Requirements Needs Prior Needs Prior To To Installation Installation Customer Responsibility Lab Space Requirements Power Requirements Gas Requirements Environmental Requirements Safety Requirements Preparation of Samples (Customer Responsibility) Computer Configuration Customer Experience... -
Page 39: Introduc Introduction
Introduction... -
Page 41: 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 7 computer. -
Page 42: Summary Of This Guide
Introduction Summary of this Guide Thoroughly read and understand the Safety and Regulatory Information chapter before using the mass spectrometer. Warnings and Safety Information Chapter 1: Contains all of the safety information and topics to comply with EN/IEC 61010. Introduction Chapter 2: Provides an instrument overview and the references to related documentation. -
Page 43: Supplies, Accessories And Replacement Parts
Supplies, Accessories and Replacement Parts Supplies, accessories, and replacement parts can be ordered directly from PerkinElmer using the eight-digit part numbers provided in this manual. To place an order for supplies and many replacement parts, request a free catalog, or ask for information visit our website. - Page 44 Clarus SQ 8 MS Hardware Guide...
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Page 45: About The Clarus Gc/Ms System
About the Clarus GC/MS System... -
Page 47: About The Clarus Sq 8 Ms System
About the Clarus SQ 8 MS System About the Clarus SQ 8 MS System The Clarus SQ 8 mass spectrometers (MS) are compact benchtop instruments that produce positive identification and quantitation of compounds separated by the Clarus 580 and 680 series gas chromatographs, respectively. Even if the compounds coelute, the mass spectrometer can still positively identify and quantitate each compound based on spectral data. - Page 48 Clarus SQ 8 MS Hardware Guide Figure 5 Figure 5 Clarus SQ Clarus SQ 8 Mass 8 Mass Spectrometer. Spectrometer. A high-performance, research-grade analytical quadrupole mass analyzer with a quadrupole prefilter assembly transmits only those ions having your selected mass- to-charge ratio.
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Page 49: Clarus 580/680 Series Gc
About the Clarus GC/MS System Clarus 580/680 Series GC The Clarus 580/680 Series Gas Chromatograph is a dual-channel, temperature- programmable gas chromatograph (GC). It is available in many configurations, such as with or without, an autosampler, programmable pneumatic control (PPC), and a variety of injector/detector combinations to provide you with total GC flexibility. -
Page 50: Gc Interface (Transfer Line)
Clarus SQ 8 MS Hardware Guide autosampler can run up to 15 injections per vial from as many as 108 vials and one priority vial using one or two autosampler programs (if not under TurboMass control). In the latter case, a different GC method can be used by each program if desired. PPC provides real-time digital readouts to simplify setting carrier gas pressures and flows. -
Page 51: Ion Optics Path
About the Clarus GC/MS System Ion Optics Path The Clarus MS ion source consists of a removable ion source. The Ion Source Ion Source Clarus SQ 8 C also supports a CI source. In the EI source, molecules exit the column where they are bombarded by electrons from the filament and ionized into positive and negative ions as well as neutral species. -
Page 52: Vacuum System
Clarus SQ 8 MS Hardware Guide Vacuum System The source, ion optics, analyzer, and detector are fitted inside a cast aluminum chamber. Vacuum is applied to the chamber using a rotary pump and a turbomolecular pump. The vacuum is monitored through a wide range gauge. The rotary pump sits on the floor and a turbomolecular high vacuum pump is inside the instrument. -
Page 53: Vacuum Pump Options
About the Clarus GC/MS System The AC line cord for the rotary vane pump must be plugged into the designated receptacle on the back of the Clarus MS. The pump is controlled by the TurboMass software. CAUTION CAUTION Connecting the vacuum hose to the exhaust connection of the rotary pump will severely contaminate the Clarus MS. - Page 54 Clarus SQ 8 MS Hardware Guide Vacuum Gauge The single wide range vacuum gauge monitors the system pressure from atmosphere down to 10 Torr using a combined Pirani/Inverted Magnetron ionization sensor. Normal operating pressure with 1 mL/min helium for the 255 L/sec turbomolecular pump is between 9x10 Torr and 2x10 Torr after pump-down and ion source bake-...
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Page 55: Turbomass Software
About the Clarus GC/MS System 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 56: 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 57: 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 58: Pre-Operational Checklist
Clarus SQ 8 MS Hardware Guide Pre-Operational Checklist This checklist provides you with a list of items to check to make sure everything is in working order before you begin to use Clarus. Item 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 59: Maintenan Maintenance
Maintenance... -
Page 61: Overview
Overview High electrical voltage is High electrical voltage is present inside the mass spec present inside the mass spectrometer. trometer. To prevent the risk of electrical shock or injury from high voltage, unplug the AC line cord from the AC outlet and wait at least one minute before opening or removing an instrument panel. - Page 62 Clarus SQ 8 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. NEVER Before reassembling and replacing dismantled components, inspect O-rings and •...
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Page 63: 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 64: Monthly
Clarus SQ 8 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 analyzer prequadrupole. Clean if necessary. •... -
Page 65: 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: Ensure that all connections are made to the mass spectrometer. Set the GC split flow to 50 mL/min by pressing the PSSI injector icon on the Clarus GC touch screen. - Page 66 Clarus SQ 8 MS Hardware Guide Display the TunePage dialog by clicking The TunePage dialog is displayed. Make sure the Tune parameters are similar to the values displayed. NOTE: NOTE: The inlet and source temperatures should be less than 100°C only when venting the system.
- Page 67 Maintenance The indicator box color changes to green and the name of the button changes to Press for Standby. Select Pump Pump from the Options Options menu. This starts the forepump and the turbomolecular pump. Watch the vacuum gauge readout and allow time for the gauge to achieve 4 x 10-5 Torr. Observe the displayed masses.
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Page 68: Tuning The Clarus Ms
Clarus SQ 8 MS Hardware Guide Tuning the Clarus MS After determining that no leaks exist and before acquiring data, you may need to check the mass spectrometer tuning conditions and, if necessary, modify one or more of the tuning parameters. Clarus MS can be tuned either manually or automatically from the Tune window. - Page 69 Maintenance To display the Tune page: While displaying TurboMass sample list screen click The TunePage displays. Turn on the filament and high voltages by clicking Press for Operate Press for Operate at the bottom right of the window. The indicator box turns green to indicate that it is on. Select UltraTune/Custom (AutoTune) UltraTune/Custom (AutoTune) from the Options Options menu, then click...
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Page 70: Preparing Clarus Ms For Hardware Maintenance
Clarus SQ 8 MS Hardware Guide Save this new Tune Tune of the instrument by selecting Save As Save As from the File menu and entering a name for this tune in the File name File name field. A way to keep track of the tunes is to use dates for the file names. Click Save Save... - Page 71 Maintenance Cool the Transfer Line, GC Column Oven, and the Source The transfer line, GC oven, and source are HOT HOT . Touching them can cause serious burns. To prevent personal injury, wait until the oven and transfer line reach the lower setpoint temperature before touching them.
- Page 72 Clarus SQ 8 MS Hardware Guide Vent the System Once both the Inlet Line and Source temperatures have dropped below 100 °C, select Vent/Vacuum System Off Vent/Vacuum System Off from the Options Options menu. The Vent Pump dialog appears. All pumps are turned off. Click Observe the Vacuum Pressure Gauges status on the Tune window.
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Page 73: Removing And Returning The Source
Maintenance Removing and Returning the Source To prevent contamination of the mass spectrometer, always wear clean, lint-free, powder-free nitrile , nylon, or PVC gloves before touching, removing or replacing parts. Hold the source by its handle only. Never CAUTION CAUTION touch these parts with ungloved (bare) fingers, as this will introduce contaminants into the system. - Page 74 Clarus SQ 8 MS Hardware Guide Inner Transfer Tube Inner Transfer Tube Pull Back Pull Back Column Column 1/4-inch Nut 1/4-inch Nut Figure 9 Figure 9 Pulling back the inner transfer tube. Pulling back the inner transfer tube. Open the Clarus SQ 8 MS access door. Hold the source by the edge and rotate it counter clockwise.
- Page 75 Maintenance Figure 11 Figure 11 Removing Removing the source. the source. Place the source on a clean surface. Preferably place the handle end on a flat surface so that the source stands in an upright position. Figure 12 Figure 12 The source placed in The source placed in an upright position.
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Page 76: Returning The Source
Clarus SQ 8 MS Hardware Guide Returning the Source To prevent contamination of the mass spectrometer, always wear clean, lint-free, powder-free nitrile , nylon, or PVC gloves before touching, removing or replacing parts. Hold the source by its handle only. Never CAUTION CAUTION touch these parts with ungloved (bare) fingers, as this will introduce... -
Page 77: Changing A Column
Maintenance Changing a Column This procedure outlines the steps required to properly position the end of the column in the Source and connect the column to the MS Transfer Line tube fitting inside the GC oven. To prevent contamination of the mass spectrometer, always wear clean, CAUTION CAUTION lint-free, powder-free nitrile , nylon, or PVC gloves when handling the... -
Page 78: Physical Measurement Outside The Sq 8Ms
Clarus SQ 8 MS Hardware Guide Prior to removing the source from the Clarus SQ 8 MS instrument (for example, to change a filament or clean the source), the column must be pulled back from CAUTION CAUTION its placement inside the source. This is conveniently achieved by loosening the large nut on the Transfer Line tube assembly so that the entire Transfer Line tube assembly can be pulled back from the source. - Page 79 Maintenance Graphite/Vespel Graphite/V espel Ferrule Ferrule Septum Septum Column Nut Column Nut Figure 14 Figure 14 Location of septum Location of septum on capillary column. on capillary column. Slide a 1/16 inch column nut over the outlet end of the column. With the tapered end facing towards the column nut, slide a graphite/vespel ferrule over the outlet end of the column.
- Page 80 Clarus SQ 8 MS Hardware Guide Insert the column into the MS Transfer Line tube and carefully slide it partially toward the source. Be careful not to move the septum. With the column partially inserted, engage the threaded column nut onto the Transfer Line tube fitting until it is just finger-tight.
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Page 81: Alignment Using The 10 Mm Positioning Gauge Tool
Maintenance The column is now installed the MS may be pumped down. Confirm that the proper vacuum level is reached (on the TurboMass software Tune Page). After initially heating the GC oven through one or two analysis cycles, the column nut may loosen. Re-tighten the column nut. After re-tightening, the column nut should not loosen any more. - Page 82 Clarus SQ 8 MS Hardware Guide With the column partially inserted, engage the threaded column nut onto the Transfer Line tube fitting until it is finger-tight. Carefully continue inserting the column into the Transfer Line tube until it hits the far side of the source. Be careful to avoid forcefully jamming the column into the side of the source.
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Page 83: Optical Column Alignment Using The Optional Plug Handle And Sight
Maintenance Optical Column Alignment Using the Optional Plug Handle and Sight To prevent contamination of the mass spectrometer, always wear clean, CAUTION CAUTION lint-free, powder-free nitrile , nylon, or PVC gloves when handling the part of the capillary column that will be inserted into the MS Transfer Line. - Page 84 Clarus SQ 8 MS Hardware Guide Re-insert the Transfer Line tube assembly and tighten the large nut. Slide a 1/16 inch column nut over the outlet end of the column. With the tapered end facing towards the column nut, slide a graphite/vespel ferrule over the outlet end of the column.
- Page 85 Maintenance Carefully continue inserting the column into the Transfer Line tube until it becomes visible inside the Plug Handle and Sight. Be careful to avoid inserting the column so far that it hits the far side of the MS vacuum chamber. Position the outlet end of the column so it aligns with the edge of the engraved circle on the tip of the Plug Handle and Sight.
- Page 86 Clarus SQ 8 MS Hardware Guide Loosen the large ¼ inch nut on the Transfer Line tube assembly using the 9/16 inch wrench and pull back the Transfer Line tube approximately 1 to 2 inches. See Figure 9. Turn the Plug Handle and Sight counterclockwise to the unlock symbol on the instrument and remove it from the Clarus SQ 8 MS instrument.
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Page 87: Refilling The Reference Gas Vial
Maintenance 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 88 Clarus SQ 8 MS Hardware Guide Reference Gas Vial Reference Gas Vial Knurled Fitting Knurled Fitting Figure 22 Figure 22 Reference gas Reference gas vial and knu vial and knurled fitting. rled fitting. The toxicity of the FC-43 calibrant is uncertain. Take appropriate precautions to avoid getting the calibrant on your skin or in your eyes.
- Page 89 Maintenance Gas Tight Gas Tight Syringe Syringe Reference Reference Gas Vial Gas Vial 50 µL max 50 µL max Figure 23 Figure 23 Filling the Filling the reference gas vi reference gas vial. Re-insert the reference gas vial into the knurled fitting. Make sure the O-ring is still present and the tapered end of the ferrule faces the mass spectrometer.
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Page 90: Replacing A Filament
Clarus SQ 8 MS Hardware Guide Replacing a Filament This procedure is the same for both an EI or CI source. Make sure you are wearing lint-free, powder-free nitrile , nylon, or CAUTION CAUTION PVC gloves, and that you wipe each part with a methanol dampened Kimwipe. - Page 91 Maintenance Filament Filament Filament Filament Retaining Clip Retaining Clip Move the Ceramic Move the Ceramic Insulating Connector Insulating Connector Assembly Down Assembly Down Figure 24 Figure 24 Moving the ceram Moving the ceramic insulating connector ic insulating connector assembly down. assembly down.
- Page 92 Clarus SQ 8 MS Hardware Guide Filament Filament Figure 25 Figure 25 Removing the defec Removing the defective filament assem tive filament assembly. bly. Position the new filament assembly with the filament side up. Position the new filament assembly with the coiled filament wire facing and centered in the orifice in the ion volume and the white ceramic rests on the tab.
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Page 93: Ei Source Maintenance
Maintenance Source Maintenance NOTE: NOTE: Before beginning this procedure, you may want to have on hand the following source component kits; Rebuild Kit Part No. N6480080 and N6480081. To ensure that the mass spectrometer remains contamination free, wear CAUTION CAUTION lint-free, powder-free nitrile , nylon, or PVC gloves while performing this procedure. - Page 94 Clarus SQ 8 MS Hardware Guide The filament assembly will fall out of place, so carefully hold or catch it with your other hand. As you remove the source parts, note their placement and position in CAUTION CAUTION the source so that you can reassemble the source correctly. There is only ONE way to replace the parts in the source.
- Page 95 Maintenance Cleaning NOTE: NOTE: You can do the following cleaning method of aluminum oxide paste to polish the flat surfaces of the parts. For either cleaning method, the final step you must must sonicate the parts in an ultrasonic bath of methanol for at least five minutes. Dry off the parts using lint-free tissue and/or clean compressed Nitrogen gas to prevent solvents from drying on these parts and leaving a residue Mix together aluminum oxide and de-ionized water and a few drops of...
- Page 96 Clarus SQ 8 MS Hardware Guide Reassembling Replace the source parts into the source as shown below. Remember to insert Remember to insert the parts into the source only as positioned below. the parts into the source only as positioned below. You may want to insert the trap insulator and trap before you insert the repeller.
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Page 97: Mass Analyzer Maintenance (Advanced Users Only)
Maintenance Mass Analyzer Maintenance (Advanced Users Only) This procedure is intended for advanced users only advanced users only that have been properly trained. WARNING WARNING 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. -
Page 98: Removing And Returning The Ion Optics Assembly
Clarus SQ 8 MS Hardware Guide • 8000 Grade Micro Mesh (Part No. N9303421) • 600 grit aluminum oxide in DI Water with a few drops of methanol to make a paste • Acetone Methanol • When cleaning internal components it is important to maintain the quality of the surface finish. - Page 99 Maintenance Make sure to vent the instrument and turn the power off and unplug the mass spectrometer from the AC power source. The mass spectrometer contains high voltage. To prevent the risk of shock, unplug the line cord from the AC outlet and wait at least wait at least WARNING WARNING...
- Page 100 Clarus SQ 8 MS Hardware Guide Top Cover Top Cover Top Cover Slot (2) Top Cover Slot (2) Metal Tab on Chassis (2) Metal Tab on Chassis (2) Figure 31 Removing the top cover. Figure 31 Removing the top cover. Place the top cover in a safe location.
- Page 101 Maintenance Use a 5 mm Allen key to loosen the four hex screws that hold the optics assembly in place. See the following figure. Screw Screw Screw Screw Screws Screws Holding the Holding the Front Cover Front Cover Figure 32 Figure 32 Removing the s Removing the screws on the lid and crews on the lid and the front cover.
- Page 102 Clarus SQ 8 MS Hardware Guide Locate the Sliding Lock attachment on the RF Generator Cable connector, then press down on the Sliding Lock attachment to release the lock on the connector. See the following figures. RF Generator Connector RF Generator Connector Sliding Lock attachment Sliding Lock attachment Press Down to...
- Page 103 Maintenance Figure 35 Figure 35 Removing the Removing the RF Generator RF Generator cable. cable. NOTE: NOTE: The metal tube attached to the reference gas vacuum hose has a ferrule on it that may slip off when the nut is removed from the reference gas valve fitting. Be careful Be careful to avoid dropping the ferrule inside the instrument.
- Page 104 Clarus SQ 8 MS Hardware Guide Source Source Connector Connector Nut and Ferrule for Nut and Ferrule for Reference Gas Vacuum Reference Gas Vacuum Hose Hose Fan Cable Fan Cable Reference Gas Valve Reference Gas Valve Cable Connector Cable Connector Figure 36 Figure 36 Disconnecting the ca Disconnecting the cables at the front of...
- Page 105 Maintenance Hold the ion optics assembly by its handles and align the guide pins with the holes in the vacuum manifold. Gently lower the ion optics assembly until it is seated on the vacuum manifold. Ensure that the large o-ring remains in place and does not move out of its groove in the tub.
- Page 106 Clarus SQ 8 MS Hardware Guide RF Generator Box RF Generator Box Figure 38 Figure 38 Reconnecting the RF Reconnecting the RF Generator cable connector Generator cable connector to the receptacle. to the receptacle. Using any Allen key, as shown in the following figure, pull up on the underside of the Sliding Lock attachment to lock the connector into place.
- Page 107 Maintenance NOTE: NOTE: Do not tighten these hex head scr Do not tighten these hex head screws beyond finger-tight. ews beyond finger-tight. The vacuum will pull the ion optics assembly top plate onto the large o-ring to create the seal. Over-tightening these screws may cause the ion optics assembly top plate to warp, which may cause a leak.
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Page 108: Replacing The Electron Multiplier
Clarus SQ 8 MS Hardware Guide Replacing the Electron Multiplier The electron multiplier lifetime is dependent on the number of ions detected. You can increase its life by correctly using the solvent delay settings and minimizing air leaks. To replace an electron multiplier: Remove the ion optics assembly. -
Page 109: Cleaning The Prequads
Maintenance Replace with a new electron multiplier by sliding it forward toward the source and clipping it back into place. Return the ion optics assembly. See Removing and Returning the Ion Optics Assembly on page 96. Cleaning the Prequads To prevent contamination of the mass spectrometer, always wear clean, lint-free, powder-free nitrile , nylon, or PVC gloves before touching, removing or replacing parts. - Page 110 Clarus SQ 8 MS Hardware Guide Blow dry with helium or dry nitrogen. Return the ion optics assembly to the vacuum manifold. See Removing and Returning the Ion Optics Assembly on page 96.
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Page 111: Vacuum System Maintenance
Complete pump instructions are in the instruction manual supplied with the pump. Maintanenace of the Turbomolecular Pump You should never service the turbomolecular pump. Call your PerkinElmer Service Representative for the maintenance and any problems you may have with the pump. -
Page 112: Adding Oil To The Forepump Reservoir
Clarus SQ 8 MS Hardware Guide Determine if the oil level is between the Max Oil Level and Min Oil Level marks next to the window. • If the oil level is closer to the Min Oil Level mark, add oil. Use Edwards 45 oil (Part No. -
Page 113: Replacing The Oil
Maintenance Changing the Oil Warm the oil by running the pump for at least 10 minutes, and then switch off the vacuum system. Unplug the pump from the AC outlet and disconnect it from your vacuum system. Remove one of the oil filler plugs. Filler Plug Max Oil Level Min Oil Level... - Page 114 Clarus SQ 8 MS Hardware Guide If you were running toxic samples, the oil is contaminated as toxic waste. Handle and dispose of waste oil appropriately. WARNING WARNING Remove the drain plug and allow the oil to drain into the container. If the pump oil was contaminated, pour clean oil into the filler hole and allow it to drain until the oil appears clear.
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Page 115: 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 116: Changing From Ei To Ci Mode
Clarus SQ 8 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 vapor Hazardous gas vapors s . - Page 117 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.
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Page 118: Changing To Ci
Clarus SQ 8 MS Hardware Guide ROTARY PUMP ROTARY PUMP Rotary Pump Warning Warning Power POWER IN POWER IN Power In C C H H WATER WATER WATER WATER CI GAS CI GAS VENT VENT Warning 15 psi 15 psi 5 psi 5 psi 50 psi... -
Page 119: Leak Checking
Maintenance In the Vacuum Pressure Gauges Vacuum Pressure Gauges area of the window, observe the Pirani gauge time line and the Penning gauge time line. Wait about 5 minutes until the vacuum gauge achieves about 2.5 x 10-5. Leak Checking Before running in the CI mode, confirm that the column is properly installed and the system is leak-free. -
Page 120: Setting-Up Ci
Clarus SQ 8 MS Hardware Guide The CI source running in the CI mode without reagent gas to produce an EI emission similar to the EI mode but with reduced sensitivity. You will leak-check your system this way. If mass 28 is larger than mass 18, you have a leak. Determine the source of the leak and correct it. - Page 121 Maintenance Set the values as shown in the following table. Parameter: Parameter: CI+ Values Values and and Comments: Comments: Electron energy 30 eV Emission Should be below 200 µA, although 200 to 300 µA is acceptable. (Above 200 mA may cause hydrocarbon “cracking” patterns with methane and isobutane.) Emission measures the real emission current, i.e.
- Page 122 Clarus SQ 8 MS Hardware Guide indicates a leak at the transfer line/inner source connection.) Operate slightly to the low-pressure side of the maximum to minimize gas load on the MS. (The vacuum gauge pressure will be 1.5x10 to 5x10 Torr.) If using ammonia reagent gas, reagent ions at m/z 18 (N1H ) and 35 [(NH...
- Page 123 Maintenance Select CI Gas On from the Gas menu. A check mark appears next to the option. NOTE: NOTE: Always turn on the CI gas before Operate to avoid a pressure surge hitting the filament. Click Press for Operate Press for Operate and monitor the Penning gauge as you adjust the CI gas.
- Page 124 Clarus SQ 8 MS Hardware Guide After you have maximized the peak, slightly decrease the reagent gas by turning the knob clockwise 1/8 turn. Tuning may be optimized on the m/z 69, 219, 414, and 652 ions of the heptacosa reference gas. Click Press for Standby Press for Standby to turn off Operate, followed by the CI gas.
- Page 125 Maintenance Multiplier 1300V to 1600V Source temperature C is standard. Higher temperatures ° keep the source cleaner, but may increase fragmentation. For example, down a little from EI to minimize fragmentation. 120 ° C is the practical lower limit. Ion Energy Approx.
- Page 126 Clarus SQ 8 MS Hardware Guide Make sure the “Use Air Refs” check box is not selected. CAUTION CAUTION Click the Start Start button to display the following dialog box. Click Acquisition Parameters Acquisition Parameters and enter the following values. Click OK to begin calibration.
- Page 127 Troubleshooting...
- Page 128 Clarus SQ 8 MS Hardware Guide...
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Page 129: Overview
Troubleshooting Overview The following sources of problems can occur in gas chromatography and mass spectrometry: The operator: 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 130: Spare Components
Clarus SQ 8 MS Hardware Guide Spare Components The following list contains items you should have on hand to help solve problems. New syringes: New syringes: a syringe can break, become plugged or begin leaking. Always • have spare syringes available. Duplicate columns: Duplicate columns: a column does not last forever;... - Page 131 Troubleshooting Change the simplest thing first. For example, if you suspect a gas leak, the easiest change to make is the GC septum instead of replumbing the internal pneumatics. 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.
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Page 132: 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 133 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 134 Clarus SQ 8 MS Hardware Guide Problem Problem Probable Probable Cause Cause Solution 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.
- Page 135 No spectra, not even noise at Loose electrometer cable. Reset the cable. a high multiplier voltage. Defective electrometer Call a PerkinElmer service board. engineer. Multiplier near the end of Replace the multiplier. its lifetime.
- Page 136 Clarus SQ 8 MS Hardware Guide Problem Problem Probable Probable Cause Cause Solution 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.
- Page 137 Troubleshooting Problem Problem Probable Probable Cause Cause Solution 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...
- Page 138 Clarus SQ 8 MS Hardware Guide Problem Problem Probable Probable Cause Cause Solution 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.
- Page 139 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 140 Large air leak. See procedure for leak- status OK. checking. Detector voltage too low. Increase multiplier 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 141 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 142 Clarus SQ 8 MS Hardware Guide Problem Problem Probable Probable Cause Cause Solution Solution Excessive noise. Dirty source. Clean the source. GC and MS on separate power Connect GC and MS together supplies. with the ground strap. Multiplier voltage too high. Run AutoTune.
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Page 143: Chromatography Related
Troubleshooting Chromatography Related Problem Problem Probable Probable Cause Cause Solution 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. - Page 144 Clarus SQ 8 MS Hardware Guide Problem Problem Probable Cause Probable Cause Solution 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 145 Troubleshooting Problem Problem Probable Probable Cause Cause Solution 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.
- Page 146 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.
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Page 147: Spectral Related
Troubleshooting Spectral Related Problem Problem Probable Probable Cause Cause Solution Solution Noisy spectra. Dirty source. Remove and clean the source. Peak detection threshold set too low. Raise the thresholds. Multiplier voltage set too high. Lower the multiplier voltage. Spectrum distortion. Scanning too fast or slow. - Page 148 Clarus SQ 8 MS Hardware Guide Problem Problem Probable Probable Cause Cause Solution 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.
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Page 149: 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 150: Forepump Related
Solution 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 151 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 152 Problem Problem Probable Cause Probable Cause Solution 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.
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Page 153: Message Dialogs
Troubleshooting 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 Icon Meaning Meaning Press this icon to close the message. - Page 154 Press OK OK to close the Gauge gauge. message. Failure Restart the system, if you still have this failure message contact your PerkinElmer service representatives. Pump Press OK OK to close the The vacuum system is off and the failure- message.
- Page 155 If A Vacuum Leak has been the problem continues detected. Please look in the contact your Hardware Guide for additional PerkinElmer service instruction. representatives. Vacuum Gauge The vacuum system is off and the Press OK OK to close the Failure-Safe to system can now be vented.
- Page 156 Clarus SQ 8 MS Hardware Guide Message Title Message Title Icon Icon Message Message Action Action Backing Pump is The system is not in an operating If the transfer line or the state. A vacuum leak or a vacuum source temperatures are gauge failure could have occurred.
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Page 157: Index
Index... -
Page 159: Index
Index Index Aluminum oxide, 93 Hardware maintenance, 68 Caution, 69 Checklist Inline Gas Purifiers, 113 pre-installation, 36 Introduction to TurboMass, 45 pre-operational, 56 Ion source, 49 Chemicals Definitions of Warnings, 25 Hazardous, 24 Labels leak checking, 117 WEEE Instructions, 28 setting parameter values, 118 Leak checking, 63 setting up, 118... - Page 160 Clarus 600 MS Hardware Guide Traps click on connectors, 113 replacement, 113 Pollution degree, 26 Pre-installation checklist, 36 Troubleshooting, 127 Pre-operational checklist, 56 chart, 130 overview, 127 spare components, 128 Tune page, 54 Tuning, 66 Reference Gas Inlet, 48 TurboMass Refilling the reference gas vial, 85 system requirements, 35 TurboMass Software, 53...
- Page 162 PerkinElmer PerkinElmer 710 Bridgeport Avenue Shelton, CT 06484-4794, U.S.A. Internet: http://www.perkinelmer.com email: info@perkinelmer.com PerkinElmer is a registered trademark of PerkinElmer, Inc.