Waters GCT Premier Operator's Manual

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Waters GCT Premier

Mass Spectrometer

Operator's Guide

71500109202/Revision B

Table of Contents

Troubleshooting

Summary of Contents for Waters GCT Premier

Page 2 Corporation assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Waters Corporation be liable for incidental or consequential damages in connection with, or arising from, its use.
Page 3: Safety Information
The Waters GCT Premier Mass Spectrometer conforms to European standard EN61010-1:2001, Safety requirements for electrical equipment for measurement, control, and laboratory use - Part 1: General requirements.
Page 4: High Temperature Hazard
The reference reservoir inlet and GC interface shown in Figure titled “GCT Premier high temperature hazard:” on page 1-iv can be hot. GCT Premier high temperature hazard: GC interface Reference reservoir inlet Warning: To avoid burn injuries, take care when working with the...
Page 5: High Voltage Hazard
Warnings in this guide or on the instrument must be observed during all phases of service, repair, installation, and operation of the instrument. Waters Corporation assumes no liability for the failure of those who install, repair, or operate its instruments to comply with these requirements.
Page 6: Consignes De Sécurité
Tout usage détourné du GCT Premier risquerait d’endommager l’instrument et invaliderait sa garantie. Le spectromètre de masse GCT Premier de Waters est conforme à la norme européenne EN61010-1:2001, Règles de sécurité pour appareils électriques de mesurage, de régulation et de laboratoire - Partie 1: Prescriptions générales.
Page 7: Risques De Brûlure
à la conception et à l’usage prévu de l’instrument. Waters Corporation ne saurait voir sa responsabilité engagée en cas de manquement de l’utilisateur à respecter les consignes de sécurité.
Page 8: Gct Premier Mass Spectrometer Information
éviter de l’endommager et ainsi nuire à son fonctionnement. GCT Premier mass spectrometer information Intended use The Waters GCT Premier Mass Spectrometer can be used as a research tool to deliver authenticated exact mass measurement; it is not for use in diagnostic procedures. viii...
Page 9: Calibration
Calibration Follow acceptable methods of calibration with pure standards to calibrate. Use a minimum of five standards to generate a standard curve. The concentration range should cover the entire range of quality-control samples, typical specimens, and atypical specimens.
Page 11: Table Of Contents
Risques biologiques..................... vi Risques chimiques ....................vi Risques de brûlure .................... vii Risques d’électrocution ..................vii Pictogrammes de sécurité................. vii GCT Premier mass spectrometer information ........... viii Intended use..................... viii Calibration ......................ix 1 Instrument Description ................ 1-1 Introduction ....................... 1-2 Ion source ......................
Page 12 Reference reservoir inlet ................1-7 Vacuum system ....................1-7 MassLynx control system ................1-8 Controls and indicators on the instruments’ front panel ....... 1-9 Status display ....................1-9 Controls on the instruments’ top panel ............. 1-11 Controls and connectors on instruments’ rear panel ......1-12 Signal connections ..................
Page 13 Setting up for CI tuning ................3-27 Tuning CI gas peaks ..................3-28 Obtaining a beam in positive CI mode ............3-28 Turning off CI gas ..................3-30 Tuning the instrument for negative CI ............. 3-30 Tuning for negative CI mode operation............3-31 Obtaining a beam in negative CI mode ............
Page 14 Setting up DRE mode ..................4-15 5 Calibration ....................5-1 Calibrating the instrument ................5-2 Setting up the instrument for calibration ............5-2 Lock mass correction ..................5-3 Using the Calibration wizard ................. 5-4 Accepting a calibration ..................5-9 Manually correcting a calibration..............5-11 Using calibrations for subsequent acquisitions ........
Page 15 Installing the GC column ................6-9 Configuring the GC and autosampler ............6-11 Removing the GC interface ................6-11 7 The Direct Insertion Probe ..............7-1 Introduction ....................... 7-2 Installing the probe insertion lock ............... 7-2 Inserting and removing the DI probe ............7-4 Loading sample into the DI probe..............
Page 16 9 FI/FD Operation ..................9-1 Introduction ....................... 9-2 Preparing the instrument for FI/FD Operation ........9-2 Choosing an emitter for the FI/FD inner source ..........9-2 Setting-up for FI/FD operation ..............9-3 Changing the FI/FD outer source assembly ........... 9-3 Changing the FI/FD inner source assembly...........
Page 17 10 Routine Maintenance ................ 10-1 Maintenance schedule ................... 10-2 Safety and handling ..................10-3 Rotary pump oil ....................10-4 Oil quality....................... 10-4 Oil color ......................10-4 Gas ballast control ..................10-4 Rotary pump maintenance ................10-5 Gas-ballasting the rotary pump..............10-5 Checking the rotary pump oil ...............
Page 18 Spare parts ....................... 11-2 Safety and handling ..................11-2 System troubleshooting ................. 11-2 Component hardware troubleshooting ............. 11-3 Contacting Waters ..................11-14 A Starting-up and Shutting-down the Instrument ......A-1 Starting-up the instrument ................A-2 Shutting-down the instrument ..............A-3 Emergency instrument shutdown..............
Page 19 Monitoring the instrument vacuum..............B-9 The Tune window Settings menu ............... B-10 Configuring the Tune setup parameters ............B-10 Configuring the TDC settings ............... B-11 Low Mass Cut-Off ..................B-16 Conditioning the detector ................B-16 Ramping the probe temperature..............B-18 Viewing the status of, and rebooting, the instrument’s embedded PC..
Page 20 Setting up nominal mass ................B-47 Setting up resolution for dead time correction manually ....B-48 Dead time correction ..................B-49 Effects of saturation on peak shape ............B-51 C Calibration Reference Information ..........C-1 Overview ......................C-2 Editing a calibration reference file ............. C-2 Calibration reference file ................
Page 21 Typical lock mass values ................C-8 D External Connections ................D-1 Safety Considerations ..................D-2 GCT Premier system external wiring ............D-3 GCT Premier system vacuum connections ..........D-4 E Status Display Vacuum LED .............. E-1 Vacuum LED: displays for normal instrument operation ....... E-2 Vacuum LED: displays for instrument faults ..........
Page 22 General considerations for tuning .............. G-6 Low mass cut-off ....................G-8 DRE mode ......................G-10 Multiple peak stitching ................G-12 Gain drop monitoring ................... G-13 xxii Table of Contents...
Page 23 Instrument Description This chapter describes the instrument, including its controls, gas, and electrical connections. Contents: Topic Page Introduction Inner source assembly Inlets Reference reservoir inlet Vacuum system MassLynx control system Controls and indicators on the instruments’ front panel Controls on the instruments’ top panel 1-11 Controls and connectors on instruments’...
Page 24: Instrument Description
Introduction The GCT Premier is a high-performance, bench-top, orthogonal acceleration/time-of-flight (oa-TOF) mass spectrometer. To identify volatile sample components, the instrument is coupled to a gas chromatograph (GC). To identify nonvolatile components, it operates as a standalone instrument that receives sample through a direct insertion (DI) or direct chemical ionization (DCI) probe.
Page 25: Ion Source
at a given moment, regardless of how rapidly the sample composition is changing. See also: Appendix G Theory and Principles of Operation for details of the electron ionization (EI), chemical ionization (CI) field ionization (FI), and field desorption ionization (FD) techniques, and the ion optics in the instrument. Ion source The outer ion source consists of two assemblies: •...
Page 26: Inner Source Assembly
nner source assembly The inner source assembly comprises a handle that is attached to a shaft supporting the source. Separate inner source assemblies are provided for EI, CI, DCI, FI, and FD. The source type is identified on the handle. The inner source assembly is secured to the outer source by means of two ®...
Page 27 DCI inner source assembly: Source type identifier Shaft Handle Thumbscrews DCI source The FI/FD inner source consists of a removable probe holding the FI/FD emitter. The emitter consists of a tungsten wire on which there are carbon microneedles. FI/FD inner source assembly: Rotational Isolation valve Micrometer...
Page 28: Inlets
Inlets GC interface for EI/CI The GC interface provides a heated transfer line between the GC (gas chromatograph) and the ion source. The transfer line ensures even heating which prevents the sample from condensing in the GC column before it reaches the ion source.
Page 29: Reference Reservoir Inlet
See also: Vacuum system The GCT Premier vacuum system incorporates two vacuum systems: fore pumping and fine pumping. Before the fine pumping can be operated, the region to be pumped has to be fore pumped. Fore pumping can achieve a vacuum level of approximately 1e-3 kPa (1e-2 mbar, 1.45e-4 psi) inside the...
Page 30: Masslynx Control System
B-9. MassLynx control system PC based MassLynx software controls the GCT Premier, GC system, and the autosampler. A second PC–the "embedded" PC (EPC)–occupies a place next to the GCT Premier. The EPC acquires and processes data and directly controls the instrument’s electronics.
Page 31: Controls And Indicators On The Instruments' Front Panel
Controls and indicators on the instruments’ front panel Front view of the instrument: Vacuum LED Operate LED Inner source handle Status display The Vacuum and Operate light-emitting diodes (LEDs) are at the left of the instrument’s front panel. The Vacuum LED indicates the instrument’s vacuum status. See also: Table titled “Vacuum LED display:”...
Page 32 See also: • Table titled “Vacuum LED: displays for normal instrument operation” on page E-2. • Table titled “Vacuum LED: displays for instrument faults” on page E-5. • Contacting Waters on page 11-14. 1-10 Instrument Description...
Page 33: Controls On The Instruments' Top Panel
Controls on the instruments’ top panel The reference reservoir pump valve and reference inlet are located on the top of the instrument. Reference reservoir pump valve and reference inlet: Reference reservoir pump valve Reference inlet To avoid burn injuries, take care when using the reference Warning: inlet;...
Page 34: Controls And Connectors On Instruments' Rear Panel
Controls and connectors on instruments’ rear panel Warning: All electrical connections to the rear panel must be separated from hazardous voltages by double or reinforced insulation [safety extra low voltage (SELV)]. Examples of circuits that are typically SELV include contact closure inputs and outputs for auto-samplers and, FID, TDC, ECD, PID for GC/MS products.
Page 35: Signal Connections
Analyzer Valve Sense Backing Pirani Connection to the fore pump Pirani gauge. Signal Out Time-to-digital converter (TDC) signal to the EPC. Figure titled “GCT Premier system external wiring:” on page D-3. See also: Trigger Out TDC trigger signal to the EPC.
Page 36 Analyzer Valve Sense Connection to the PVPK valve on the fore pump. See also: GCT Premier system vacuum connections: on page D-4. Analog Inputs, Contact Closure Inputs, and Contact Closure Event Out outputs: Event Out connections Event Out selector switches...
Page 37 Analog Inputs To avoid electric shock and damage to the instrument, do not Warning: apply more than 16 V to any of the analog input connections. Four analog input channels are available for acquiring simultaneous data, such as a flame ionization detector output. The input differential voltage must not exceed one volt.
Page 38 SIP, fiber-optic and power inlet connections: ESD Earth Fiber-optic connections Power switch Power fuse Power ESD Earth For engineers’ use only. Scan-in-progress connection to the EPC. See also: Figure titled “GCT Premier system external wiring:” on page D-3. 1-16 Instrument Description...
Page 39 In and Out fiber-optic connections Blue (In) and gray (Out) fiber optic connections to the EPC. See also: Figure titled “GCT Premier system external wiring:” on page D-3. Power switch You switch the instrument on and off using this switch.
Page 40: Vacuum And Gas Inlet Connections
To avoid toxic vapors, a suitable exhaust line must be fitted to the fore pump. There are two vacuum connections to the fore pump; one connection from the analyzer and one from the outer source. See also: Figure titled “GCT Premier system vacuum connections:” on page D-4. 1-18 Instrument Description...
Page 41: Gas Inlet Connections
Set the air pressure to 80 psi. Analyser PVPK Compressed air connection to the analyzer backing isolation PVPK valve located on the head of the rotary pump. Figure titled “GCT Premier system vacuum connections:” on See also: page D-4.
Page 42: Epc Power Switch
EPC power switch The EPC power switch is on the front of embedded PC (EPC). The EPC is a separate PC located next to the GCT Premier. The switch is used to power up, power down, and reboot the EPC.
Page 43 Preparing the instrument for EI/CI operation This chapter describes how to prepare the instrument for operation, including how to install and remove the inner and outer source options for electron ionization (EI) and chemical ionization (CI). Note: For details about preparing the instrument for FI/FD operation, including how to install and remove the FI/FD inner and outer source options, see Chapter 9 FI/FD...
Page 44: Preparing The Instrument For Ei/Ci Operation
Changing the EI/CI inner source assembly If the GC column is installed, to avoid damaging the GC Caution: column and inner source chamber assembly, the source components must be removed in the order shown in the Figure titled “Removing the source components:” on page 2-2.
Page 45: Removing The Ei/Ci Inner Source
Removing the EI/CI inner source To remove the inner source: In the MassLynx Tune window, click and confirm that the instrument operate status indicator shows red. See also: Figure titled “The MassLynx Tune window:” on page B-3. In the MassLynx Tune window, click Vacuum > Vent Source. Click the Engineer tab.
Page 46: Installing The Ei/Ci Inner Source
Inner source: Thumbscrew The inner source is hot. To avoid burn injuries, take Warning: care when withdrawing the inner source assembly. Caution: When removing the inner source, take great care not to knock the filament or ion chamber assembly, for they can be damaged.
Page 47 Ensure that you are about to install the correct inner source. See also: Inner source assembly on page 1-4. On the inner source assembly, verify that the O-rings: • Sit correctly in the groove. • Are in good condition. • Are clean and free from dust.
Page 48: Changing The Ei/Ci Outer Source Assembly
Changing the EI/CI outer source assembly Removing the EI/CI outer source from the instrument The source component scan be contaminated with Warning: toxic and biohazardous materials. Wear chemical-resistant, powder-free gloves at all times while handling the components. The source is hot and can cause burn injuries to Warning: the skin.
Page 49 Loosen the two thumbscrews that retains the GC interface, and pull the interface approximately 2 cm back on its support rods. To avoid burn injuries, allow the outer source lid Warning: assembly to cool before handling it. Lift the top cover from the back, and pull forward to remove. Outer source lid assembly cover...
Page 50: Fitting The Ei/Ci Outer Source To The Instrument
Outer source lid assembly: Reference sample reservoir Pump valve Wing nut Reference reservoir heater connection Source electrical Handle connectors CI gas Outer source connector lid assembly Tip: A second heater connection is behind the reference reservoir. Disconnect the red CI gas connector. Disconnect the electrical and heater connectors.
Page 51 Fit the top cover to the instrument. Fit the inner source. See also: Installing the EI/CI inner source on page 2-4. Push the GC interface into place, and tighten the two thumbscrews. Open the reference reservoir valve. If required, fit the GC column to the instrument. See also: Installing the GC column on page 6-9.
Page 52 2-10 Preparing the instrument for EI/CI operation...
Page 53: Tuning The Instrument
Tuning the Instrument This chapter describes how to prepare and tune the instrument (that is, adjust the instrument’s parameters to achieve maximum performance). Note: • Tuning is not the same as instrument calibration, which ensures that the peaks displayed in a spectrum are in their correct locations. •...
Page 54: Preparing The Instrument For Operation
Preparing the instrument for operation Tuning the instrument for operation requires you to perform certain procedures. During the tuning procedure the tuning parameters are optimized so that the optimum resolution and sensitivity can be achieved before acquiring data. To prepare the instrument for operation: Ensure that the power is connected to the instrument, and the fore pump is turned on.
Page 55: Obtaining An Ion Beam
Obtaining an ion beam To obtain an ion beam: In the MassLynx Tune window, click In the TDC Settings dialog box, clear the Low Mass Cut-Off check box. Low Mass Cut-Off on page B-16. See also: In the Tune window, click Confirm that the instrument status indicator displays green.
Page 56 Tuning Setup dialog box: In the Tuning Setup dialog box, Time pane, set the Scan Time (s) to 0.9. In the Time pane, set the Inter Scan Delay (s) to 0.1. In the Data Format pane, click Continuum in the Data Format list. 10.
Page 57 Tune window showing low mass peaks: The low mass peaks are displayed as: • Carbon dioxide = m/z 44 • Nitrogen = m/z 28 • Water = m/z 18 Obtaining an ion beam...
Page 58: Introducing The Reference Sample
Introducing the reference sample To introduce the reference sample: Ensure the reference reservoir valve is closed. Use a septum-piercing syringe, inject approximately 0.2 µL of heptacosa into the reference reservoir inlet cap. Introducing the reference compound into the reference reservoir inlet cap: Reference reservoir...
Page 59 Tune window with peak display: The peak at m/z 28 is air (nitrogen). The peak at m/z 219 is the heptacosa reference sample. The aim of tuning the instrument is to maximize the sample signal while keeping the nitrogen peak as small as possible. To accomplish this, you can increase or decrease the beam steering and focus lens values.
Page 60: Setting Up The Instrument Automatically
The intensity of the signal is highlighted in the example shown in Figure titled “Tune window with peak display:” on page 3-7. See also: Effects of saturation on peak shape on page B-51. Setting up the instrument automatically Using the Instrument Setup Wizard you can automatically setup the instrument so that is it ready to be tuned for accurate mass data acquisition.
Page 61 If there are insufficient ions detected, you may have to inject more Tip: reference sample. If there is too much sample and the detector becomes saturated, open the reference reservoir value to release some sample. Aim to have about 1000 counts per second in continuum. Note: When the wizard is complete, the infused solution can be used as the lock mass.
Page 62 Instrument Setup Wizard Introduction: Click Next. The Instrument Setup Wizard Lock mass Compound window appears. Instrument Setup Wizard Lock Mass Compound: 3-10 Tuning the Instrument...
Page 63 10. From the Reference list, click the reference compound file for the sample that has been injected into the instrument. Note: Click the User specified value check box to tune using a specific mass value. 11. Click Next. The Instrument Setup Wizard Nominal Mass window appears. Instrument Setup Wizard Nominal Mass: The wizard automatically calculates the Veff setting required to adjust the peak position so that the correct nominal mass is assigned.
Page 64 Instrument Setup Wizard Detector Setup: The wizard automatically calculates the detector setting that is required to detect more than 90% of all the ions produced. During the procedure the detector voltage is set so that the intensity of the signal no longer increases as the detector voltage is increased. To ensure optimum sensitivity and mass accuracy, check this value periodically.
Page 65 Instrument Setup Wizard DDTC Setup: The wizard automatically determines the resolution and sets the Np Multiplier setting to compensate for dead time. See also: Setting up resolution for dead time correction manually on page B-48 Dead time correction on page B-49.
Page 66 Instrument Setup Wizard Lock Mass Setup: The wizard automatically sets the Lock Mass by checking a specific mass and intensity. To achieve the best mass accuracy a lock mass is necessary to correct the mass scale for the thermal drift factors. See also: Configuring the TDC settings on page B-11 Lock mass...
Page 67 Lock Mass is too intense: If the Lock Mass is too low, inject more reference sample into the reference reservoir to increase the intensity of the signal. Lock Mass is too weak: Setting up the instrument automatically 3-15...
Page 68 The Instrument Setup Wizard Lock Mass check is complete window appears. Instrument Setup Wizard Lock Mass check is complete: 12. Ensure that the reference reservoir valve is closed. If you have injected more sample or backed sample out using the reference reservoir valve, the signal can overshoot and appear too intense or too weak.
Page 69 Instrument Setup DRE Magnification Factor Setup: 15. From the Reference File list, click the reference compound file for the sample that has been injected into the instrument. Ensure you are using the correct file for the reference compound Note: sample and the ion mode selected. 16.
Page 70 DRE Magnification Factor: The wizard automatically determines several magnification factors across the mass range required to enable Dynamic Range Enhancement. The DRE Magnification Factor value can be edited manually on the Tune window DRE tab. See also: The DRE tab on page B-43.
Page 71: Tuning The Instrument For Ei
Instrument Setup Complete: 17. Click Finish Tuning the instrument for EI Use the following methods to introduce samples in EI mode: DI probe, the DCI probe, the gas chromatograph, or the reference inlet system. The example procedure in this chapter specifies tris (trifluoromethyl) Tip: triazine as the infused sample.
Page 72 In the EI Tune tab, adjust beam steering in increments of 0.1 V. Result: The intensity of the air peak changes. Optimize beam steering so that the peak at m/z 28 is minimized while the peak at m/z 285 is maintained. 3-20 Tuning the Instrument...
Page 73 Steering Voltage -1.5 V: Steering voltage -3.4 V: Steering voltage -0.5 V: Steering Voltage +1.0 V: Tuning the instrument for EI 3-21...
Page 74 As beam steering is increased from -3.4 V, the air peak at m/z 28 drops in intensity. However, the sample peak reaches a maximum at around -0.5 V, and then drops off again as the voltage is increased to +1.0 V. In this example, a steering voltage of about -0.5 V is optimum.
Page 75: General Tips For Tuning
General tips for tuning A strong beam (more than 2000 counts per second in continuum) can become saturated and distorted due to the dead time effect. Aim for 1000 counts per second in continuum for your lock mass. See also: •...
Page 76: Tuning The Instrument For Best Resolution In Ei
FWHM is Full Width Half Maximum of the peak. Resolution for the peak at 614 Da of heptacosa should be equal to or more than 7000 counts per second on the GCT Premier. To tune for best resolution adjust the pusher bias and grid 2 parameters which are found on the Engineers tab.
Page 77: Tuning The Instrument For Positive Ci
Tuning the instrument for positive CI Use the following methods to introduce samples in CI mode: DI probe, the DCI probe, the gas chromatograph, or the reference inlet system. In CI mode, you can introduce reference samples in one of the following ways: •...
Page 78: Introducing Ci Reagent Gas
Setting up and purging the CI gas lines Before introducing the CI reagent gas, the internal CI reagent gas lines must be purged of air. To set up and purge the CI gas line: Ensure the CI inner source is correctly installed. Installing the EI/CI inner source on page 2-4.
Page 79: Setting Up For Ci Tuning
Setting up for CI tuning To setup for CI tuning: Ensure that the instrument is pumped down (evacuated) with an analyser pressure of less than 3e-6 mbar (3e-7 kPa, 4.35e-8 psi) and that the MCP detector has been conditioned. Detector maintenance on page 10-50.
Page 80: Tuning Ci Gas Peaks
Right-click in the peak display and click Intensity > Normalize Data. Result: The peak display is scaled to the value of the intensity of the highest peak. Tuning CI gas peaks To tune CI gas peaks: From the Tune window, clear Low Mass Cut Off check box in the TDC Settings dialog box.
Page 81 Table titled “Recommended Tuning starting values:” on See also: page 3-3. Ensure the Limit Rhenium Filament Current check box is selected. Tip: The rhenium filament is provided with the instrument. However, if you have fitted a Tungsten filament, then ensure the Limit Rhenium Filament Current check box is cleared.
Page 82: Turning Off Ci Gas
Tips: • The near-absence of m/z 285 indicates good CI conditions. • It might be necessary to adjust the level of the reference compound to fall below saturation of the TDC. Effects of saturation on peak shape on page B-51. See also: To adjust the level of reference compound, open the pump-out valve on the reference reservoir slowly.
Page 83: Tuning For Negative Ci Mode Operation
During electron ionization (EI), negatively charged ions form in addition to positively charged ions. Normally, the negative ions remain undetected because the ion source and focusing potentials allow only the extraction of positive ions. There are limitations to the analytical usefulness of negative ions formed by electron ionization.
Page 84: Obtaining A Beam In Negative Ci Mode
In the Tune window, click Increase the detector and the TOF flight tube voltages to the previously determined operating voltage over a period of 20 seconds. Doing so minimizes the risk of discharge and possible damage to the detector. Purging the CI gas lines Before introducing the CI reagent gas, the internal gas lines must be purged of air.
Page 85: Turning Off Ci Gas
In the TDC Settings dialog box Data pane, set the Veff value to display the correct mass in the peak display. See also: Setting up nominal mass on page B-47. To obtain the best intensity of the m/z 451.97 ion, retune the following parameters in the Tune window, CI Tune tab, Beam Steering, Focus1, Focus2, and, Focus3.
Page 86: Managing Tune Parameters
Managing tune parameters Printing tune information To print a report of the peak information displayed in the Tune window (including a record of each parameter setting), click Restriction: You cannot configure the report. Storing tune parameters MassLynx stores tuning parameters with each data file as part of the experimental record.
Page 87 To recall a saved set of parameters: In the Tune window, click Select the required tuning parameter file by typing its name or by selecting it from the displayed list. Click Open. Result: The *.ipr file opens. Managing tune parameters 3-35...
Page 88 3-36 Tuning the Instrument...
Page 89: Acquiring Data
Acquiring Data This chapter describes how to acquire data and set up the function list. Note: To acquire accurate mass data you must first tune the instrument (see Chapter 3) and then calibrate it (see Chapter Contents: Topic Page Starting data acquisition Setting up an MS Method Setting up an MS Scan 4-12...
Page 90: Starting Data Acquisition
• Acquire multiple sample sequences. To start a single sample acquisition: In the Tune window, click In the GCT Premier Tune Acquire dialog box, specify the required parameters. See also: Table titled “GCT Premier Tune Acquire dialog box parameters:” on page 4-3.
Page 91 GCT Premier Tune Acquire dialog box: GCT Premier Tune Acquire dialog box parameters: Parameter Description File Name Type the name of the data file to be created in this text box. If the file already exists on the disk, then MassLynx prompts you to rename the file or over- write the existing one.
Page 92 GCT Premier Tune Acquire dialog box parameters: (Continued) Parameter Description Format Specifies the data type (Centroid or Continuum) to be collected and stored on disk. Centroid format is recommended for collecting data, except when checking data resolution. See also: Types of data acquisition on page 4-14.
Page 93: Starting A Multiple-Sample Data Acquisition
GCT Premier Tune Acquire dialog box parameters: (Continued) Parameter Description Close Closes the dialog box. Tip: MassLynx does not retain the current settings when the dialog box is next opened. Starting a multiple-sample data acquisition The MassLynx window includes a sample list that defines how to acquire multiple samples on the instrument.
Page 94: Adding A Function To The List
Experiment Setup editor: Adding a function to the list To add a function to the list: Click In the TOF MS Scan Editor, make the required changes to the parameters. See also: Figure titled “Full Scan Function Editor:” on page 4-12.
Page 95: Modifying An Existing Function In The List
Modifying an existing function in the list To modify an existing function in the list: In the Function List, select the function. Click Double-click the function. Alternative: In the TOF MS Scan Editor, make the required changes to the parameters. Click OK.
Page 96: Changing The Order Of Functions In The List
Changing the order of functions in the list To change the order of functions in the list: Select the required function. Repeatedly click until the function is in the required position. Functions appear in ascending order according to their start and Note: end time and the order cannot be changed.
Page 97: Selecting The Run Time For The Experiment
Selecting the run time for the experiment The run time, or duration, of the experiment should be long Requirement: enough to identify all the mass peaks eluting from the chromatographic column. To select the run time for the experiment: In the Experiment Setup window MS method, specify the run-time value, in the Total Run Time text box.
Page 98: Acquiring Analog Data
Solvent Delay dialog box: MassLynx does not store data during the solvent delay period. Also, MassLynx turns off the source filament during that period. Therefore, solvent peaks that would normally appear as eluting on the TIC (Total Ion Count) chromatogram no longer appear. The delay time depends on the solvent used.
Page 99 The external channel is read at the end of each scan and stored with the data for that scan. The resolution of the chromatography for an analog channel therefore depends on the analog samples. Analog Data dialog box: To store data for an analog channel: In the MS Method Editor, click Options >...
Page 100: Setting Up An Ms Scan
Setting up an MS Scan The TOF MS Scan Function Editor sets up centroid and continuum functions. Full Scan Function Editor: To set up a full scan function: In the MS Method Editor, click Click Functions > MS Scan. Alternative: In the Full Scan Function Editor, type the required parameters.
Page 101 Full Scan function editor parameters: Parameter Description Start The mass at which the scan starts. The mass at which the scan stops. The Start mass must be less Requirement: than the End mass. Use DRE Acquires data in DRE mode. Doing so increases the dynamic range to over four orders of magnitude.
Page 102: Types Of Data Acquisition
Full Scan function editor parameters: (Continued) Parameter Description The retention time (in minutes) at which the scan stops. Use Probe When selected, you can enter the name of a Ramping Method Probe Ramp Method file (*.prf) in the adja- cent text box; alternatively, click Browse to search for a file.
Page 103: Setting Up Dre Mode
Setting up DRE mode Dynamic Range Enhancement (DRE) mode increases the dynamic range of the GCT Premier, permitting the analysis of strong samples that produce intense signals. In DRE mode, the instrument acquires alternate high and low intensity scan data and then uses the low intensity data to provide the mass and intensity of peaks that saturate in high-intensity data streams.
Page 104 Set z-focus to 40 and z-lens steering to 0. Tune the instrument in EI with heptacosa or any other reference compound. In the Tuning Setup dialog box, set Data Format to Centroid. See also: Tuning the instrument for EI on page 3-19.
Page 105 peak intensity in high intensity mode ---------------------------------------------------------------------------------------- magnification factor peak intensity in low intensity mode Requirements: • If the instrument was tuned in negative ion mode, use the mass values shown in the Table titled “Mass values and example magnification factor results for methyltriazine in EI and CI positive ion mode:”...
Page 106 14. On the MassLynx Tune window DRE tab, specify the values of Mass and Magnification factor in the table. Tip: The ideal magnification factor is 40 and you should aim for values between 20 and 60. The magnification factor must always be greater than 10.
Page 107: Calibration
Calibration This chapter describes how to calibrate the mass scale of the instrument (that is, to ensure that the peaks displayed in a spectrum are in their correct locations). Notes: The figures in this chapter show indicative parameter values only. Contents: Topic Page...
Page 108: Calibrating The Instrument
Calibrating the instrument To obtain exact mass measurements, you must calibrate the instrument’s mass scale. When nominal mass is set up, the masses will be correct to within m/z 0.5. Using the calibration routine produces more accurate mass measurements. To obtain exact mass measurement (within 5 ppm RMS), use a lock mass as well as a calibration file.
Page 109: Lock Mass Correction
Instrument Setup wizard Ensure that the Instrument Setup wizard has been successfully run, or all the appropriate parameters are set up manually. Obtaining an ion beam on page 3-3. See also: Tune Window parameters Ensure that none of the parameters are changed since the Instrument Setup wizard was run.
Page 110: Using The Calibration Wizard
Lock mass intensity When using the lock mass in experiments the lock mass compound is continually introduced to the source from the reference reservoir throughout the experiment. Before starting an acquisition using lock mass, make sure that there is a constant signal of lock mass compound at the mass specified in the TDC settings window and that the intensity is appropriate.
Page 111 The Calibration Wizard Introduction window appears. Calibration Wizard Introduction: Click Next. The Calibration Wizard Reference Setup window appears. Using the Calibration wizard...
Page 112 Calibration Wizard Reference Setup: Click Next. Calibration Wizard Reference Setup: Calibration...
Page 113 In the Calibration Wizard Reference Setup page, click Browse, to select the appropriate reference file for the reference sample that you are using for the calibration. When the reference file is selected, the reference file information is Tip: displayed in the Calibration Wizard Reference Setup window. In the Calibration Wizard Acquisition Setup page, specify a Start Mass and an End Mass or use the wizard defaults.
Page 114 Calibration Wizard Acquisition Setup parameters: (Continued) Parameter Description Reference Window Is the size of the window in Da used to search for the peak in the reference file for initial peak matching. Auto Polynomial When selected, the order the wizard attempts to select the polynomial order that fits the data best.
Page 115: Accepting A Calibration
Calibration Wizard Acquiring Data: The calibration process takes several minutes to acquire the necessary data if the reference sample is weak. An error may occur if the beam is too strong or too weak. When the calibration wizard finishes the Calibration Graph window appears.
Page 116 Calibration Graph window: The Calibration report window comprises four sections: • Data file: The data selected for calibration. • Reference file: The spectrum of the selected reference file. • Residuals: The software will have attempted to produce a calibration that corrects the acquired data so that the reference peaks are at the correct expected mass.
Page 117: Manually Correcting A Calibration
Manually correcting a calibration Caution: If the Calibration Parameters dialog box is opened and then closed with the Perform auto peak matching option selected, the spectrum is automatically recalibrated. Any manual corrections are lost. See also: Editing the calibration parameters on page 5-13.
Page 118 To manually adjust the large residual error peaks: Left-click and drag across a mass region of a mismatched peak to zoom the mass region. Tip: Click Display > Default to zoom out. In the reference spectrum pane, right-click the mismatched reference peak.
Page 119 Editing the calibration parameters For any type of experiment, you can edit the calibration parameters in the Calibration Parameters dialog box. In the Calibration report window, select Edit > Calibration Parameters. Calibration Parameters dialog box: Calibration Parameters dialog box parameters: Parameter Description Perform auto peak...
Page 120 Calibration Parameters dialog box parameters: (Continued) Parameter Description Peak window +/- Specifies the maximum mass difference between the reference peaks and the expected position of the corresponding peaks in the acquired calibration spectrum. The normal operating range for this parameter is 0.3 to 1.5 Da.
Page 121: Using Calibrations For Subsequent Acquisitions
Using calibrations for subsequent acquisitions Using calibrations When acquiring data via the Tune window or from the Sample List, the last calibration file produced using the calibration wizard or manually produced calibration can be used. The calibration file that is currently being used is displayed on the Tune window Calibration tab.
Page 122: Removing A Calibration File
The calibration filename and path appear separately on the Result: Calibration tab. Click OK. Note: The calibration wizard automatically sets the current calibration file when it finishes. Removing a calibration file When a calibration file is created using the Calibration wizard, the file appears in the Tune window and is used in all subsequent acquisitions.
Page 123 Double-click at the top of the Spectrum window. In the Header Editor, click Spectrum QTOF in the Group list. Click Temp Correction in the Element list. Click OK. Result: The current temperature inside the instrument is displayed in Spectrum window. Repeat the same acquisition later in the day under the same conditions and when the room temperature has changed by up to 3°C.
Page 124: Calibrating The Instrument In Ci
Calibrating the instrument in CI The instrument can be calibrated in CI ion mode in a similar way as you calibrate EI ion mode. In CI positive ion mode the calibration is performed using a reference sample, such as heptacosa or tris (trifluoromethyl) triazine without CI gas, to reproduce the EI spectrum.
Page 125: Manual Calibration
• Using heptacosa or FC70 the reagent gas can be left at CI+ pressure and calibrated under CI+ conditions. Tune the system in CI mode with CI gas in. See also: Tuning the instrument for positive CI on page 3-25. Set up the nominal mass.
Page 126 Extended and normal dynamic range acquisitions can use the same calibration file. To turn Dynamic Range Enhancement off when acquiring data for calibration: In the GCT Premier Tune Acquire dialog box, ensure that Use DRE is clear. Click Calibration. To manually calibrate the instrument: In the TDC Settings dialog box, Centroiding Parameters pane, set Lock Mass to 0.
Page 127 In the Tune window, click GCT Premier Tune Acquire dialog box: In the GCT Premier Tune Acquire dialog box Data pane Format list, click Centroid. In the Mass pane, set Start Mass to 50 and Set End Mass to 650.
Page 128: Creating A Calibration File
11. Monitor the acquisition and acquire 3 minutes of data. See also: Chapter Acquiring Data. Creating a calibration file To create a calibration file: In the Chromatogram window, click Process > Combine Spectra. In the Combine Spectrum dialog box, ensure the Peak separation parameter is set to 0.05.
Page 129 Make new calibration dialog box: Click OK. Result: When processing is complete, the Calibration report window opens. Manual calibration 5-23...
Page 130 Manual calibration report: To save the calibration: In the Calibration report window, click File > Save As. Save the file with an appropriate name with the extension .scl. To convert the calibration file: In the Tune window Calibration tab, click Open Calibration. Browse to the calibration file that you have created with the .scl extension.
Page 131: Calibrating The Instrument In Ci- Mode
Calibrating the instrument in CI- mode The procedure for calibrating in CI- mode is similar to the procedure for calibrating in CI+ mode except use heptacosa as the reference sample with a small amount of CI gas, heptaneg.ref as the reference file and acquire over a mass range up to 700 Da.
Page 132 5-26 Calibration...
Page 133 The GC Interface This chapter describes installing, configuring, and removing of the GC interface. Contents: Topic Page The GC interface Installing the GC interface Installing the GC column Configuring the GC and autosampler 6-11 Removing the GC interface 6-11...
Page 134: The Gc Interface
The GC interface To avoid burn injuries, take care when working with the GC Warning: interface and GC. They operate at high temperatures. The GC interface provides a heated transfer line between the GC) and the ion source. The transfer line ensures even heating in this region, which prevents the sample condensing in the GC column before it reaches the ion source, reducing chromatographic peak quality.
Page 135: Installing The Gc Interface
Installing the GC interface The GC interface can be heated to a temperature of 350 °C. It incorporates a spring-loaded tip at the source end of the column transfer line. The tip ensures that the interface remains in contact with the outer source block (to maintain reagent gas pressure for CI operation) and accommodates thermal expansion of the transfer line.
Page 136 Blanking plate: Retaining screws Blanking plate Source housing ® Remove the 1/16-inch nut and graphitized Vespel ferrule from the column transfer line. The outside diameter of the column, and therefore the ferrule Note: required, can vary depending on the column type used. GC interface: Interface body 1/4-inch retaining nut...
Page 137 Caution: Be careful not to damage the transfer line shaft when removing the graphitized Vespel ferrule with wire cutting pliers. Doing so can cause air leaks. Remove the 1/4-inch graphitized Vespel ferrule by cutting part of it away with wire cutting pliers. If the 1/4-inch ferrule has been removed by cutting, Requirement: replace it.
Page 138: Reinstallation Of The Gc Interface
11. Ensuring that the heater connection on the interface flange is at the bottom of the assembly. Then fit the GC interface to the instrument, and secure it using the two retaining screws. 12. The GC column can now be installed, or the transfer line blanked, to allow source housing pumping.
Page 139 GC interface and interface fitting tool as supplied: Interface fitting tool Interface flange Replace the interface fitting tool, then place this and the GC interface upright on the bench. Ensure that the fitting tool fits evenly over the locating ring and interface flange. Installing the GC interface...
Page 140 GC interface with fitting tool attached for checking the tip position: Interface body Interface flange Holes for adjustment screws Interface fitting tool Indent Look through the slot in the side of the interface fitting tool and assess the alignment of the tip; the tip should be central to the indentation in the interface fitting tool.
Page 141: Installing The Gc Column
When the tip is in the correct position, tighten the 1/4-inch retaining nut, taking care not to change the position of the transfer line and tip. Fit the 1/16-inch nut and graphitized Vespel ferrule to the transfer line. Remove the GC interface from the interface fitting tool. Changing the position of the heater tube To change the position of the heater tube: Slacken the lock nuts on the three adjustment screws.
Page 142 Insert the GC column through the GC interface transfer line until the end of the column is approximately 5 mm from the center line of the source. To determine the correct position, look into the inner source probe Tip: port from the front with the inner source removed. The end of the GC column will be visible as it enters the source housing, as shown in the following figure.
Page 143: Configuring The Gc And Autosampler
B-8. Configuring the GC and autosampler The GC and autosampler must be configured before using the GCT Premier. Configuration is carried out using the MassLynx Inlet Configuration Wizard. See also: The MassLynx Inlet Control Guide for details.
Page 144 Remove the two GC interface retaining thumbscrews. 10. Remove the GC interface. 6-12 The GC Interface...
Page 145: The Direct Insertion Probe
The Direct Insertion Probe This chapter describes the Direct Insertion (DI) probe and its operation. Contents: Topic Page Introduction Installing the probe insertion lock Inserting and removing the DI probe Controlling the DI probe temperature 7-10...
Page 146: Introduction
Introduction The direct insertion (DI) probe is designed to admit solid samples, or liquid samples not sufficiently volatile to inject via the reference inlet, into the ion source. The DI probe is inserted into the instrument source via the probe insertion lock, which must be fitted to the instrument prior to using the probe.
Page 147 Probe insertion lock: Probe retaining knob Probe lock guide rod and microswitch contact Thumbscrews Threaded probe collar PROBE electrical connector Probe lock insertion valve (shown closed) Pump probe VAC button The Pump probe button is labelled VAC on the instrument. Tip: Ensure that the Viton O-ring is present in the insertion lock retaining flange groove.
Page 148: Inserting And Removing The Di Probe
Inserting and removing the DI probe This section explains the following tasks: • Loading sample into the probe. • Inserting the probe. • Removing the probe. Loading sample into the DI probe Warning: To avoid contamination with samples wear chemical-resistant, powder-free gloves at all times when handling the probe.
Page 149 Direct insertion probe sample cups: Sample cup (type D) Heating element and capillary cooling tube Probe tip Tungsten strip Sample cup (type C) To load sample into the DI probe: Push the sample cup firmly into the probe tip to ensure good thermal contact with the heater element.
Page 150: Inserting The Di Probe Into The Insertion Lock
Sample cup holder: Any solvent used in loading can be evaporated by placing the sample cup(s) in a warm place, for example on top of the GC oven. To avoid solvent vapor blowing the sample out of the cup, be careful not to heat the cup too quickly. To remove the sample cup after use: Gently tap the sample cup out, or unscrew the tip of the DI probe to allow easy access to the cup.
Page 151 The instrument has a microswitch to prevent the probe heater being Tip: activated if the probe is not fully inserted. Inserting the DI probe: Probe retaining knob Probe cable Insertion lock First stop Guide rod Cooling water tubes Connect the cooling water tubes to the water chiller or other suitable water cooling system.
Page 152: Removing The Di Probe From The Probe Insertion Lock
Wait until the green light in the center of the VAC button illuminates. Rationale: The light indicates that the inlet pressure has fallen below the trip level set on the Pirani gauge. If it fails to illuminate check the insertion lock for leaks and the insertion lock O-ring for damage. Open the probe lock insertion valve.
Page 153 Pull back the spring-loaded probe retaining knob (located on the probe insertion lock). Withdraw the probe from the probe insertion lock. Inserting and removing the DI probe...
Page 154: Controlling The Di Probe Temperature
Controlling the DI probe temperature Source temperature is often sufficient to evaporate the sample, particularly if the shallow sample cup is used. If the sample fails to evaporate, or if a more controlled evaporation is required, MassLynx can ramp the probe temperature during acquisition.
Page 155: Ramping The Probe Temperature Automatically
The temperature readback should rise to match the set temperature. Note: A temperature readback of 850 °C indicates that the probe cable has not been correctly connected. Ramping the probe temperature automatically The Probe Control dialog box automatically ramps the probe temperature. To open the Probe Control dialog box: In the MassLynx Tune window toolbar, click Alternative:...
Page 156 Probe Control dialog box Options tab parameters: Parameter Description Use Ramps Enables probe ramp control. Use Base Peak Enables probe temperature regulation based on the base peak intensity. The base peak is the most intense peak within the scanned mass range. Use TIC control Enables probe temperature regulation based on the Total Ion Current (TIC).
Page 157 Probe Control dialog box Options tab toolbar buttons: Button Description Allows creation of a new probe ramping method file. Allows an existing probe ramping method file to be opened. Saves the probe ramping method file. See also: Use Probe Ramping Method on page 4-4 Probe Ramping Method on page 4-14.
Page 158: Probe Control Dialog Box Ramps Tab
Probe Control dialog box Ramps tab You set multiple probe ramps in the Ramps tab. Probe Control dialog box Ramps tab: Probe Control Ramps tab parameters: Parameter Description Ramp The ramp identifying number. Rate The rate of the ramp, in units of °C/minute for the DI and A/minute for the DCI probe.
Page 159 To create probe ramping data: Type the required initial ramp value in the Value field, then press Enter. Result: The value is entered in the field, and the focus moves to the Hold field. Type the required start time for the ramp in the Hold field, then press Enter.
Page 160: Probe Control Dialog Box
Probe Control dialog box In the Control tab of the Probe Control dialog box, you manually run probe ramp methods. The tab also visually represents ramping method as it runs. Probe Control dialog box Control tab: Probe Control dialog box Control tab: Parameter Description Ramps Display...
Page 161: Ramping The Probe During A Acquisition
Probe Control dialog box Control tab toolbar buttons: Button Description Starts the active probe ramping method. Stops the active probe ramping method. Pauses the active probe ramping method. Ramping the probe during a acquisition A probe ramp can be saved as a .prf file and run from a Tune window acquisition or via the Sample list.
Page 162 7-18 The Direct Insertion Probe...
Page 163 The Direct Chemical Ionization (DCI) Probe This chapter describes the Direct Chemical Ionization (DCI) probe and its operation. Contents: Topic Page Introduction Installing the probe insertion lock Inserting and removing the DCI probe Controlling the DCI probe current...
Page 164: The Direct Chemical Ionization (Dci) Probe
The desorption yields a high abundance of the molecular ion [M+H]+. On the GCT Premier mass spectrometer, the sample is loaded onto the DCI probe tip and, once inserted in the source, desorbed by ramping the probe tip current. The DCI probe is inserted into the source via the probe insertion lock, which must be fitted to the instrument prior to using the probe.
Page 165: Inserting And Removing The Dci Probe
Figure titled “Probe insertion lock:” on page 7-3. See also: Ensure that the Viton O-ring is present in the insertion lock retaining flange groove. Attach the probe insertion lock to the source housing. Tighten the two thumb screws that secure the probe insertion lock to the source housing.
Page 166: Inserting The Dci Probe Into The Insertion Lock
Warning: To avoid contamination from samples, wear chemical-resistant, powder-free gloves at all times when handling the probe. To load sample into the DCI probe: The wire filament at the end of the DCI probe tip is Caution: fragile. Be careful not to damage the tip when handling it. Push the DCI tip onto the end of the DCI probe.
Page 167 Lubricate the probe shaft with molybdenum disulphide to ensure Tip: smooth travel when inserting it into the probe lock. Caution: • Do not use Santovac oil as a lubricant on the probe shaft, it causes a contamination. • The wire filament at the end of the DCI probe tip is fragile. Be careful not to damage the tip when handling it.
Page 168: Removing The Dci Probe From The Probe Insertion Lock
The light indicates that the inlet pressure has fallen below Rationale: the trip level set on the Pirani gauge. If it fails to illuminate, check the insertion lock for leaks and the insertion lock O-ring for damage. Open the probe insertion lock valve. Pull back the sprung-loaded probe retaining knob (located on the probe insertion lock).
Page 169: Controlling The Dci Probe Current
Pull back the spring-loaded probe retaining knob (located on the probe insertion lock). Caution: • Ensure the probe tip is not knocked during removal, as it is easily damaged. • To avoid damage to the probe filament, do not pass a current through the probe tip when the tip is in air.
Page 170: Ramping The Probe Current Automatically
Tune window Inlet tab: Press Enter. Alternative: Use the slider control to select the required current. Tip: For safety reasons, the current is set to 0 at the start of an acquisition. Once the acquisition has started, you can manually ramp the probe current using this control.
Page 171: Fi/Fd Operation
FI/FD Operation This chapter describes how to prepare the instrument for operation, including how to install and remove the inner and outer source options for Field Ionization (FI) and Field Desorption (FD). Contents: Topic Page Introduction Preparing the instrument for FI/FD Operation Setting-up for FI/FD operation Tuning in FI mode 9-20...
Page 172: Introduction
Introduction In field ionization (FI/FD), sample molecules pass close to the tips of a mass of carbon micro-needles on the emitter. Extraction rods maintained at high voltage produce a very high electric field around the needles. This causes ionization by quantum tunnelling of a valence electron. The process is very 'soft' often producing spectra with little or no fragmentation.
Page 173: Setting-Up For Fi/Fd Operation
Setting-up for FI/FD operation When using the FI/FD inner source probe fit the blank Recommendation: flange or the GC interface to the instrument. When using the FI/FD inner source probe with the DI probe, fit the FI/FD inner source direct insertion probe flange.
Page 174 Top cover Reference reservoir pump valve Remove the EI/CI outer source assembly from the instrument. See also: Removing the EI/CI outer source from the instrument on page 2-6. Carefully lower the FI/FD outer source lid assembly vertically into the outer source enclosure using the two studs to ensure correct alignment. FI/FD Operation...
Page 175 FI/FD outer source: Reference reservoir Reference pump valve inlet Lifting handle Wing nut OA source housing connector FI lens supply connector Clear viewing port EXT voltage connectors Tighten the two wing nuts on the top of the outer source lid assembly. Connect the two cables to the extraction voltage (EXT voltage) connectors.
Page 176 Removing the FI/FD outer source The source components can be contaminated with Warning: toxic and biohazardous materials. Wear chemical-resistant, powder-free gloves at all times while handling the components. Warning: The source is hot and can cause burn injuries to the skin. Allow the source to cool before handling it. To remove the FI/FD outer source: In the MassLynx Tune window, click Vacuum >...
Page 177: Changing The Fi/Fd Inner Source Assembly
Changing the FI/FD inner source assembly Installing the FI/FD inner source lock assembly To install the FI/FD inner source lock assembly: Caution: To avoid damaging the GC column, ensure the GC column is retracted before installing the FI/FD inner source assembly.
Page 178 FI/FD inner source lock assembly: Source isolation valve (closed position) Hex-head retaining screw (captive) Vent Valve Ensure that the source isolation valve is closed. When the outer source and the inner source lock assembly has been fitted you can pump the instrument down. Open the reference reservoir valve.
Page 179: Installing The Fi/Fd Inner Source Direct Insertion Probe Only Flange
Removing the FI/FD inner source lock assembly To remove the FI/FD lock assembly: In the Tune window, click Click Vacuum > Vent Source. A message confirms the vent command. Click OK. The turbomolecular pump is turned off. When the turbomolecular pump has run down to half normal operating speed, the vent valve is opened and the instrument is automatically vented.
Page 180 FI/FD inner source direct insertion probe flange: Thumbscrews FI/FD inner source direct insertion probe flange with probe: 9-10 FI/FD Operation...
Page 181 Inserting the FI/FD inner source probe When the inner source lock assembly has been fitted, you can insert the FI/FD inner source probe with either an FI or FD emitter fitted. The FI/FD inner source probe can be fitted and removed without venting the source chamber by using inner source lock assembly.
Page 182 Fasten the two clips at each side of the FI/FD inner source probe. Caution: Do not leave the FI/FD inner source probe in the retracted position when not in use. Remove the probe from the instrument. Ensure that the vent valve is closed (fully clockwise). Press the VAC button on the right side of the instrument.
Page 183 FI/FD inner source inserted: Source isolation valve (open position) Hex head bolts Clips Micrometer Depth stop rings Vent valve Rotational Adjustment Knob Probe retaining stopper Removing the FI/FD inner source To remove the FI/FD inner source: In MassLynx Tune window, click , to switch the instrument into Standby.
Page 184: Changing The Fi/Fd Gc Interface
Unfasten the two clips at each side of the FI/FD inner source probe. Warning: To avoid burn injuries, do not touch the FI/FD tip. Allow the tip to cool before handling. Pull the inner source probe away from the lock assembly. Caution: To avoid damage when removing the inner source assembly, be careful not to knock the emitter.
Page 185 GC interface: Interface body 1/4-inch retaining nut Column transfer line 1/16-inch nut 1/4-inch graphitized Vespel ferrule Graphitized Vespel ferrule Ensure the ceramic tip is screwed securely in place, is clean and not cracked. Note: The ceramic tip helps to minimize the disturbance of the electrical field close to the emitter.
Page 186 GC interface tip: Locating ring Interface flange Heater connection Ceramic tip Heater tube Lock nut Interface body Adjustment screw Adjust the position of the tip to approximately 5 mm from the rod. Figure titled “GC-FI column position:” on page 9-20. Ensure that the two Viton O-rings: •...
Page 187 GC interface fitted: GC interface flange Thumbscrews VAC button GC heater connection Probe connection Removing the FI/FD GC interface To remove the FI/FD GC interface In the Tune window, click to switch the instrument into Standby. Click Vacuum > Vent Source. Wait for the Vacuum Status LED to display steady yellow.
Page 188: Positioning The Gc Column For Fi Operation
Turn the black knobs on the side of the GC plinth. Result: The two GC plinth stops are released. Push the GC away from the GC interface. Disconnect the GC interface heater connection. 10. Remove the two GC interface retaining thumbscrews. 11.
Page 189 Probe depth stop: Depth stop rings Position the emitter so that it is in line with or fractionally in front of the end of the GC column. Note: Use the clear viewing port on the top of the source lid to view position of the emitter and ensure that the emitter wire does not touch the extraction rods.
Page 190: Tuning In Fi Mode
GC-FI column position: Reference Extraction reservoir GC column rods re-entrant 2 mm Emitter GC-FI transfer line 5 mm 12 mm Inner source shaft Tuning in FI mode When using the instrument in FI mode, sample is ionized by passing close to the very high field generated around the emitter by the voltage on the extraction rods.
Page 191: Introducing The Reference Sample
Caution: Do not close the Tune window in FI mode with the instrument in operate. If you do, the emitter is damaged the next time you open the Tune window. To avoid damaging the emitter if you do close the Tune window while the instrument is in operate, pull the emitter back into the lock, to protect it when you open the Tune window.
Page 192 In the Tuning Setup dialog box, Time pane set the Scan Time(s) to 1.2 and the Inter Scan Delay (s) to 0.2 In Data pane, click Continuum from the Data Format list. Increase the Extraction Voltage in increments of 2000 V to a maximum of 12,000 V.
Page 193: General Considerations For Tuning In Fi Mode
14. Use a septum-piercing syringe, to inject approximately 5 µL chloropentafluorobenzene into the reference reservoir. See also: Introducing the reference sample on page 9-21. 15. Adjust the peak display to mass range 198 to 204 amu. 16. Right-click the peak display and click Intensity > Normalize Data. 17.
Page 194: Setting Up And Calibrating The Instrument
Changes in the Focus Voltage can also result in changes in beam steering voltage. The focus lenses should be optimized in conjunction with this steering lens. if the beam steering lens optimizes at more or less than ±4 V, the lens should be returned to zero and the micrometer used to re-optimize the beam.
Page 195: Optimization Of Fi Calibration
Compounds and relative amount by volume: (Continued) Compound name % by volume Expected masses Chloropentafluorobenzene 201.9609 Xylene 106.0783s These proportions can be adjusted to produce a more balanced spectra if Tip: required. The sample should be kept in a sealed vial, out of direct light and in a cool place.
Page 196: Running Samples
Running samples Running MS samples in GC FI mode You must set a use solvent delay at the beginning of an acquisition when running in GC FI mode. See also: Setting a solvent delay on page 4-9. The solvent delay is set so that the solvent front has completely eluted before the end of the solvent delay time.
Page 197: Tuning In Fd Mode
Tuning in FD mode When working in FD mode, you must first obtain a beam using the reference sample, and tune the ion source. Once the instrument is tuned, you can introduce the sample onto the emitter. Using the probe ramp, the emitter current is ramped and you can run an experiment.
Page 198: Introducing The Sample
Increase the Extraction Voltage in increments of 2000 V to a maximum of 12,000 V, while monitoring the current leakage. Using the system with an excessive leakage current can Caution: result in poor mass measurement, unstable signals and the risk of high voltage flash overs in the outer source, which could blow the emitter.
Page 199: Calibration And Setup In Fd
Increase the Extraction Voltage to 12,000 V in increments of 2000 V, while monitoring the leakage current. Do not enable the Flash Off or raise the Emitter Caution: Current above 0 at this stage. Introduce acetone into the reference reservoir until the source pressure reaches 1e-5 mbar.
Page 200: Running An Fd Experiment Using The Probe Ramp
Set up the manual experiment as required, ensuring data is collected in continuum because signals are normally leak in FD.. In the MassLynx Tune window FD tab, increase the Emitter Current This will gradually warm up the emitter and desorb the sample. As it is desorbed the sample will ionize on the emitter.
Page 201 way whether you are using the DCI, DI, or FI/FD probe. The only difference is the units and values that are used in the Probe Control dialog box. See also: Ramping the probe temperature automatically on page 7-11. Probe Control Ramp tab Table titled “Probe Control Ramp tab:”...
Page 202: Loading The Fd Inner Source Probe With Sample
Probe Control Control tab The Control tab shows a graphical representation of the probe current ramp. Probe Control Control tab Probe Control dialog box on page 7-16. See also: Loading the FD inner source probe with sample Sample concentration in the range of 500 ng/µL to 20 µg/µL should be used. Higher concentrations of sample may sputter off the emitter, causing a discontinuous spectrum and, sometimes, arcing, which can damage the emitter.
Page 203 To load the FD probe with sample: Remove the FI/FD inner source probe from the instrument. See also: Removing the FI/FD inner source on page 9-13. Place the FI/FD inner source probe on a flat work surface. Rotate the FI/FD inner source probe shaft so that the emitter is horizontal.
Page 204 9-34 FI/FD Operation...
Page 205: Routine Maintenance
Routine Maintenance This chapter provides maintenance guidelines and procedures required to maintain the instrument’s performance. Keep to the maintenance schedule and perform maintenance as required and described in this chapter. Contents: Topic Page Maintenance schedule 10-2 Safety and handling 10-3 Rotary pump oil 10-4 Rotary pump maintenance...
Page 206: Maintenance Schedule
Maintenance schedule The following table lists periodic maintenance schedules that ensure optimum instrument performance. The maintenance frequencies shown apply to instruments that normally receive moderate use. Maintenance schedule: Procedure Frequency Gas-ballast the rotary pump. Weekly. Inspect and adjust the rotary pump Weekly.
Page 207: Safety And Handling
Safety and handling Remember the following safety considerations when performing maintenance procedures. Warning: To avoid electric shock, do not remove the instrument panels. There are no user-serviceable items inside. Warning: To avoid electric shock, ensure that the instrument is in standby mode before commencing any maintenance.
Page 208: Rotary Pump Oil
Should a fault occur soon after a particular part of the system has been repaired or otherwise disturbed, first ensure that the part is correctly refitted and /or adjusted. Then determine whether adjacent components have not been inadvertently disturbed. Rotary pump oil Oil quality It is important that the recommended oil type is used for the associated rotary pump and vacuum conditions.
Page 209: Rotary Pump Maintenance
Rotary pump maintenance Rotary pump: Oil filler plugs Gas-ballast Inlet port Power switch control Oil level sight glass Oil drain plug Gas-ballasting the rotary pump When the rotary vacuum pump draws large quantities of solvent vapors, the vapors tend to condense in the pump oil and reduce pump efficiency. Gas-ballasting purges condensed contaminants from the oil.
Page 210: Checking The Rotary Pump Oil
To gas-ballast the rotary vacuum pump: To avoid burn injuries, be careful while working with Warning: the rotary pump; it can be hot. Caution: • Failure to routinely gas-ballast a rotary pump shortens oil life and consequently shortens pump life. •...
Page 211: Changing The Rotary Pump Oil
Changing the rotary pump oil Change the rotary pump oil every 3 to 4 months, or earlier, if it becomes noticeably discolored. Required materials • Chemical-resistant, powder-free gloves. • Flat-blade screwdriver. • Container to catch used oil. • Funnel. • Vacuum pump oil [use only Ultragrade19 or Inland Q45 (Edwards 45) vacuum pump oil].
Page 212: Replacing The Oil Mist And Odor Filter Elements
Allow the pump to cool enough to handle it. Warning: The pump is heavy for one person to lift. Follow the instructions in the Edwards Rotary Pump Instruction manual. Raise the pump 6 to 8 inches (150 to 200 mm) above the floor, if necessary.
Page 213 To replace the oil mist and odor filter elements: Warning: To avoid burn injuries, be careful while working with the rotary pump; it can be hot. Warning: The rotary pump oil can be contaminated with toxic and biohazardous materials. Wear chemical-resistant, powder-free gloves at all times while handling the oil, and ensure that the waste oil is disposed of according to local environmental regulations.
Page 214 This exposes the oil filter element and odor filter element. Odor filter element Oil filter element Lift out the element(s) you are replacing. Wipe clean the insides of the upper and lower body assemblies. 10-10 Routine Maintenance...
Page 215: Foreline Trap Maintenance
10. Ensure that the oil filter element O-ring is in position on the lower body assembly. O-ring 11. Fit the new filter elements to the lower body assembly, ensuring that the foam sealing rings are correctly seated on the top and bottom of the elements.
Page 216 cast aluminium body. The metal basket is held in place by a knurled nut, a lid, and a spring. An absorbent material (activated alumina balls with a strong affinity towards oil vapor) is contained in the metal basket to absorb any oil that back migrates from the pump.
Page 217 The lid comprises a flange and a disk, which has a strong spring Tip: pushing against it. Spring Remove the spring and the basket holding the alumina balls from the foreline trap casing. Basket Clean the casing. If the inside of the foreline trap casing appears oily or dirty, wash it with isopropyl or ethyl alcohol, and then dry it thoroughly.
Page 218 Remove the wing nut, washer and end casing from the basket. Wing nut End casing Remove the washer and short compression spring from the inside of the basket. 10-14 Routine Maintenance...
Page 219 Washer Short compression spring Remove the perforated end disk from the inside of the basket. Perforated end disk Activated alumina, a desiccant, can absorb Warning: materials from the samples run through the mass spectrometer. Ensure that the alumina is disposed of according to local environmental regulations.
Page 220: Reference Reservoir Maintenance
10. Fill the basket with fresh alumina balls up to the maximum fill level marker, and refit the perforated disk, smooth side down, to avoid abrading the balls. The perforated disk should align with the maximum fill level Tip: marker. Tap the basket gently to settle the alumina, and add or remove balls if necessary.
Page 221 Reference reservoir: Reference inlet cap Reference reservoir pump valve To renew the reference reservoir septum: Warning: The reference reservoir components can be contaminated with toxic and biohazardous materials. Wear lint-free cotton gloves at all times while handling the components. Warning: To avoid burn injuries, take care when working with the reference reservoir;...
Page 222: Ei/Ci Inner Source Maintenance
Fit the new septum to the inlet cap with the grey Teflon side facing downwards, and the yellow rubber side facing upwards. Refit and loosely tighten the inlet cap. Push a septum-piercing syringe needle through the septum. 10. Finger tighten the inlet cap. 11.
Page 223 EI inner source assembly: Support plate Filament contacts Repeller contact Ceramic insulator Spacing tube Tungsten filament Locating rod Ion chamber 3.2 mm (M1.6) hex nut 3.2 mm (M1.6) washer Repeller Trap contact Screws 6 mm ceramic insulator 11 mm ceramic insulator 2 mm ceramic insulator Trap Ion exit plate (EI)
Page 224: Cleaning The Inner Source Components
Cleaning the inner source components Identify the following components for cleaning: • Ion exit plate (see Cleaning the ion exit plate on page 10-22). • Repeller (see Cleaning the trap and repeller on page 10-23). • Trap (see Cleaning the trap and repeller on page 10-23).
Page 225: Ultrasonically Cleaning The Inner Source Components
Where no specific cleaning procedure is given, fine abrasives should be used to remove dirt from metal components. Recommended abrasives are: • 1200-grade wet/dry paper. • Lapping paper (produced by 3M®). • Polaris powder. After cleaning with abrasives, wash all metal components in suitable solvents to remove all traces of grease and oil.
Page 226: Cleaning The Ion Exit Plate
Place the vessel in the ultrasonic bath for 30 minutes. Tip: Depending on the nature of the contamination, Waters recommends that steps 1 and 2 be repeated with various solvents to thoroughly clean the components. To avoid re-contaminating the ion source components...
Page 227: Cleaning The Trap And Repeller
Ion exit slit To clean the ion exit plate: Using 1200-grade wet/dry paper, rub all the ion exit plate surfaces, including the ion exit slit edges, until they are free of visible ion burn. Using 9-micron lapping paper, polish all the ion exit plate surfaces, including the ion exit slit edges.
Page 228 Inner source assembly Grub screw Ion block assembly Remove two screws that secure the ion block assembly to the inner source assembly brass support. Unscrew and remove the two screws that secure the two threaded support rods to the ion block. Lift off the ion block assembly so that the two threaded support rods come out from the bottom of the ion block.
Page 229 Filament securing screw Unscrew and remove the filament securing screw. The filament is fragile. To avoid damaging it, handle Caution: with care. Remove the filament from the inner source. EI/CI inner source maintenance 10-25...
Page 230 Trap contact Repeller contact 10. Remove the repeller and trap contacts, Trap/repeller ceramic isolator, and associated ceramic spacers. 10-26 Routine Maintenance...
Page 231 When removing the trap and repeller, take care not to Caution: lose the ceramic spacers. 11. Push out the trap and ceramic spacers from underneath the ion block. 12. Push out the repeller and ceramic spacers from underneath the ion block.
Page 232 To clean the trap and repeller: Using 1200-grade wet/dry paper, rub the trap edge and end surfaces until they are free of visible ion burn. Using 9-micron lapping paper, polish the trap edges and end surfaces. Using 1200-grade wet/dry paper laid on a flat surface, in a figure-of-eight motion, rub the repeller’s flat surface until it is free of visible ion burn.
Page 233 Fit the trap and ceramic spacers in the ion block. Fit two ceramics on the rear of the ion block, one on the repeller and the other on the trap. Fit the trap contact to the trap. Fit the trap/repeller ceramic isolator to the repeller. Fit the repeller contact to the repeller.
Page 234 Fit and tighten the two contact securing nuts. Caution: The filament is fragile. To avoid damaging it, handle with care. 10. Fit the filament to the ion block. 11. Align the center of the filament wire with the hole in the ion chamber. Filament wire alignment: Filament 12.
Page 235 16. Fit and tighten the two screws that secure the two threaded support rods to the ion block. 17. Fit and tighten the four screws that secure the ion block assembly to the inner source assembly brass support. 18. Insert the spring into the ion block support tube. 19.
Page 236: Renewing The Filament
Renewing the filament The filament is fragile. To avoid damaging it, handle with Caution: care. To renew the filament: Using a jeweller’s screwdriver, unscrew the single screw securing the filament to the ion chamber assembly. Remove the filament. Use a jeweller’s screwdriver to transfer the filament contact blocks to the new filament.
Page 237: Changing An Emitter
To extend the lifetime of the emitter: Store the emitter under vacuum or in an atmosphere of dry nitrogen. Changing an emitter You must replace the emitter if it is damaged or broken. The sensitivity of the emitter is significantly compromised when a dirty, damaged or broken emitter is used.
Page 238 FI emitter: Emitter wire Ceramic bead Legs Carefully hold the FI inner source on its side and carefully install the emitter bead into the end of the probe. Use the tweezers to gently touch the ceramic bead pushing the emitter onto the probe, taking care not to touch the emitter wire.
Page 239: Ei/Ci Outer Source Maintenance
A dirty outer source can cause loss of sensitivity, poor stability, or it can even affect the resolution of the GCT Premier. As the beam goes through the source it passes through collimating slits, on the EI/CI outer source, which are only 0.25 mm wide.
Page 240 Screw securing the collimating slits Lift the collimating slits assembly out of the outer source lid assembly. Collimating slits assembly Disassemble the collimating slits assembly by unscrewing and removing the screw securing each slit to the alignment block and removing the slits.
Page 241: Cleaning The Complete Outer Source
Ultrasonically clean the slits in a suitable solvent to remove any remaining grease. See also: Ultrasonically cleaning the inner source components on page 10-21. To refit the collimating slits: Assemble the collimating slits assembly in the reverse order to which you disassembled it.
Page 242 Outer source lid Front support plate Securing screw Unscrew and remove the four screws that secure the front support plate to the metal rods. Securing screws Metal rod Remove the front support plate. Remove each lens plate and its associated spacers from the outer source assembly in turn.
Page 243 You can to access the lenses from the opposite end of the Alternative: outer source lid assembly, avoiding the need to remove the washers and the spacers around the inner source contacts. To clean the lens plates: Rub each side and the inner aperture of each lens plate with 1200-grade wet/dry paper to remove any visible ion burn.
Page 244 Assembled outer source (1): Heater wires Thermocouple 10-40 Routine Maintenance...
Page 245: Assembling The Ion Chamber
Assembled outer source (2): CI gas tube (top) Reference gas tube (bottom) Assembling the ion chamber To fit the source magnets: Fit the first magnet to the ion block. Fit the stainless steel cap to the inner end of the magnet. Use a 1.5-mm hex (Allen) key to fit the and tighten the grub screw securing the magnet to the ion block.
Page 246: Fi/Fd Outer Source Maintenance
A dirty outer source can cause loss of sensitivity, poor stability, or it can even affect the instrument resolution of the GCT Premier. As the beam goes through the source it passes through collimating slits, which are only 0.5 mm wide.
Page 247 To remove the extraction rod assembly: Warning: Cleaning the various parts of the source requires solvents and other chemicals that can be flammable and hazardous to health. Close the isolation valve to isolate the source housing. Remove the outer source from the instrument. Removing the FI/FD outer source on page 9-6.
Page 248 The surface of the rods should appear highly polished with no scratches or sharp points. Ultrasonically clean the rods in a suitable solvent to remove any remaining grease or sample particles. See also: Ultrasonically cleaning the inner source components on page 10-21.
Page 249: Cleaning The Source Ceramic And Focus Plates
Cleaning the source ceramic and focus plates During use, sample builds up on the source ceramics and on the focus plates causing the leakage of extraction voltage and adversely affecting mass accuracy and sensitivity. If voltage leakage occurs, the source must be removed from the source lid assembly, disassembled, and the dirty components individually cleaned.
Page 250 Front support plate Securing screws Outer source lid Hex-head screw Unscrew and remove the four screws that secure the front support plate to the metal rods. Remove the front support plate. 10. Remove each lens plate and its associated spacers from the outer source assembly in turn.
Page 251 Sonicate the lens plates in a suitable solvent to remove any remaining grease. See also: Ultrasonically cleaning the inner source components on page 10-21. Removing the collimating slits The two collimating slits are 0.25 mm wide and can be removed from the outer source when using FI or FD ion mode.
Page 252: Checking For Leaks After Source Maintenance
Sonicate the slit in a suitable solvent to remove any remaining grease. See also: Ultrasonically cleaning the inner source components on page 10-21. To assemble the outer source: Assemble the outer source in the reverse order to which you disassembled it, consulting the diagrams prepared during disassembly. Checking for leaks after source maintenance Leaks normally occur when components have recently been removed for cleaning and/or refitted.
Page 253 When the CI purge button is clicked, the internal CI solenoid valves open and the source’s pneumatic (PVPK) valve closes. If the GC is connected, the source pressure will rise because the helium cannot be backed away. If a large source pressure rise occurs when you click CI Purge in the Inlet tab, reduce the GC helium flow or remove the GC.
Page 254: Detector Maintenance
Connect the CI gas supply to the CI gas connector on the rear of the instrument. See also: Gas inlet connections on page 1-19. Allow the backing pirani read back to reach 1.00e-2 mbar. If this cannot be achieved note the read back. (Sometimes a minor amount of condensation within the line prevents attaining the required pressure.) In the Tune window Inlet tab, click CI purge.
Page 255 Note: Waters recommends that you condition the detector for 10 hours when the analyzer has been vented to air. If the analyzer has been vented to dry gas and not exposed to air, conditioning can be reduced to 60 minutes.
Page 256: Setting The Optimum Gain For The Detector
Setting the optimum gain for the detector The optimum gain for the detector is determined automatically when the Instrument Setup wizard runs. Using the procedure described to determine the gain of the detector manually. Note: Before setting the optimum gain for the detector, ensure you conditioned the detector.
Page 257 10 mV and return to step 2. If you have set the TDC signal threshold to less than 10 mV the MCP, detector may need renewing. Contact Waters for advice. See also: Contacting Waters on page 11-14. Detector maintenance 10-53...
Page 258 10-54 Routine Maintenance...
Page 259: Troubleshooting
Troubleshooting This chapter describes how to troubleshoot the GCT Premier mass spectrometer with the help of recommended troubleshooting procedures. Contents: Topic Page Spare parts 11-2 Safety and handling 11-2 System troubleshooting 11-2 Component hardware troubleshooting 11-3 Contacting Waters 11-14 11-1...
Page 260: Spare Parts
Spare parts Waters recommends you replace only the parts mentioned in this document. Safety and handling When troubleshooting the GCT Premier, keep the following safety considerations in mind. To prevent injury, always observe good Warning: laboratory practices when handling solvents, changing tubing, or operating the GCT Premier.
Page 261: Component Hardware Troubleshooting
If the fuses fail continually, isolate the instrument from the power supply and contact Waters for advice. See also: • Contacting Waters on page 11-14.
Page 262 No peaks in the Tune window (no ion beam): (Continued) Possible cause Corrective action The instrument is not in Operate. In the MassLynx Tune window, click Tip: When in Operate, the instru- ment status icon is green. MCP is set to zero. Set-up the MCP gain.
Page 263 No peaks in the Tune window (no ion beam): (Continued) Possible cause Corrective action Communication failure. Ascertain the status of the embedded PC. If necessary, reboot the embedded PC using the embedded PC’s power switch. See also: Viewing the status of, and rebooting, the instrument’s embedded PC on page B-18.
Page 264 Unsteady or low intensity peaks (ion beam): (Continued) Possible cause Corrective action The source components have been Ensure that the source voltage read- incorrectly assembled. backs vary with the Tune window setting. If any of these voltages are absent, disassemble and correctly reassemble the source assembly.
Page 265 Insufficient vacuum: (Continued) Possible cause Corrective action Scroll pump not operating correctly. Contact Waters for advice. See also: Contacting Waters on page 11-14. Leak in a vacuum backing line. Inspect the vacuum hoses for cracks or vacuum leaks. Restriction in the vacuum pump Inspect the exhaust lines for exhaust tubing.
Page 266 Source heater not working: Possible cause Corrective action The source heater has failed. Inspect the Tune window EI tab Source Temp (°C) readback. A readback of 503 indicates that the source heater is disconnected. Check the integrity of the heater connections.
Page 267 Possible cause Corrective action No filament current. Indicates the power supply for the current has failed. See also: Contacting Waters on page 11-14. No Filament current, Trap current maximum or Emission current zero: Possible cause Corrective action Particle, or general contamination in...
Page 268 Ion repeller inactive in EI mode: Possible cause Corrective action Poor contact to the ion repeller from Use tweezers to adjust the spring the spring contacts on the outer contacts on the outer source to source. improve contact. Tunes with repeller more than 5 V: Possible cause Corrective action Dirty inner source.
Page 269 Emission: Trap ratio is greater than 10:1: Possible cause Corrective action Outer source magnets have been Remove the outer source magnets fitted incorrectly. and reassembly with opposite poles facing each other. Cleaning the complete See also: outer source on page 10-37.
Page 270 No Beam or Emitter current (in FI source): Possible cause Corrective action Probe is incorrectly position. Determine whether the position of the emitter is correct. Using the emitter probe, adjust the knob. Inserting the FI/FD inner See also: source probe on page 9-11.
Page 271 Excessive leakage current (in FI source): (Continued) Possible cause Corrective action Leakage between the extraction rods Withdraw the emitter by 5 to 10 mm and the emitter. from the extraction rods. Remove the ion source, and clean the extraction rods. Removing the FI/FD outer See also: source on page 9-6...
Page 272: Contacting Waters
10-37. Contacting Waters Most operational problems that arise with the GCT Premier are easily correctable. However, if you cannot correct the problem, you must contact Waters. Customers in the USA and Canada should report maintenance problems they cannot resolve to Waters Technical Service (800 252-4752).
Page 273 • The GCT Premier serial number. Depending on the nature of the fault, it can also be useful to have the following information available: • Details of the flow rate, GC conditions, and sample concentrations. • The Tune window settings.
Page 274 11-16 Troubleshooting...
Page 275 Starting-up and Shutting-down the Instrument This appendix describes how to start-up and shut-down the GCT Premier Mass Spectrometer. Contents: Topic Page Starting-up the instrument Shutting-down the instrument...
Page 276: A Starting-Up And Shutting-Down The Instrument
Yes, steps 13 to 15 are completed automatically. Waters recommends that you condition the detector for 10 hours Tip: when the analyzer has been vented to air. If the analyzer has been vented to dry gas and not exposed to air, conditioning can be reduced to 60 minutes.
Page 277: Shutting-Down The Instrument
14. In the Tune window, click and confirm that the instrument status indicator shows red. 15. Condition the MCP detector. Conditioning the detector on page 10-50. See also: 16. Leave the instrument in Operate for at least one hour to warm up and stabilize before calibration or acquiring data.
Page 278: Complete Shutdown
In the Tune window CI tab, turn off the CI gas. Complete shutdown To shut down the instrument completely: In the Tune window, click and confirm that the instrument status indicator shows red. Click Vacuum > Vent Instrument. A message confirms the vent command. Click OK.
Page 279: B The Masslynx Tune Window
The MassLynx Tune window This appendix describes the MassLynx Tune window. Note: For the highest mass accuracy, tune and calibrate the instrument using a suitable reference compound before sample data are acquired (see Preparing the instrument for operation on page 3-2 Calibrating the instrument on page 5-2).
Page 280: Opening The Masslynx Tune Window
Opening the MassLynx Tune window Click in the MassLynx window Instrument shortcut bar. Result: The Tune window opens. TheFigure titled “The MassLynx Tune window:” on page B-3 summarizes the Tune window layout. The MassLynx Tune window...
Page 281 The MassLynx Tune window: Open vacuum Save current instrument Start Pause/restart monitor window parameters acquisition acquisition settings Create a new instrument Copy peak parameter file display Open an existing Print current Peak Probe Stop instrument Tune display ramping acquisition parameter file window setup parameters...
Page 282: The Tune Window Toolbar
The Tune window toolbar The following table details the Tune window toolbar buttons. Toolbar buttons: Tool Equivalent menu item Function File > New Creates a new set of default instrument parameters in the Tune window. File > Open Opens an existing instrument parameter file (.ipr).
Page 283: The Tune Window File Menu
Toolbar buttons: (Continued) Tool Equivalent menu item Function Settings > Probe Opens the Probe Control dialog box. This Ramping is used to automatically ramp the probe temperature or current. Ramping the probe tempera- See also: ture automatically on page 7-11. Starts an acquisition.
Page 284 To save an instrument parameter file: Click File > Save. Result: Saves all the instrument parameters in the current Tune window into the current instrument parameter file (which is indicated in the Tune window title bar). This option is available only if changes have been made to Tune window Tip: parameters since opening the instrument parameter file.
Page 285: The Tune Window Ion Mode Menu
The Tune window Ion Mode menu The Ion Mode menu is used to select the required ionization mode and update the Tune window Source tab to that mode. You cannot change the ion mode while the instrument is in operate. Note: Before changing the ion mode, switch the instrument to standby.
Page 286: Pumping/Venting The Instrument
Pumping/venting the instrument To pump the instrument: open the reference reservoir pump value. In the MassLynx Tune window, click Vacuum > Pump Instrument. The analyzer begins to pump (evacuate). When the pneumatic valve opens, you should hear a small hiss. When the analyzer is pumped down, the source begins to pump down.
Page 287: Monitoring The Instrument Vacuum
To vent the source: In the MassLynx Tune window, click Vacuum > Vent Source. Wait for the Vacuum Status LED to display steady yellow. Status display on page 1-9. See also: Result: The source is now vented. Monitoring the instrument vacuum The instrument’s vacuum status appears in the Vacuum Monitor window, in mbar.
Page 288: The Tune Window Settings Menu
The Tune window Settings menu The Settings menu is used to: • Configure the Tune setup parameters. • Configure the TDC settings. • Viewing Calibration parameters. • Condition the detector. • Ramp the probe temperature. • View the status of the instrument’s embedded PC. •...
Page 289: Configuring The Tdc Settings
Tuning Setup parameters Parameter Description Data Format Lists data formats on the Data Format drop-down list. See also: Types of data acquisition on page 4-14. Scan Time (s) Specifies the duration of each scan. Inter Scan Delay (s) Specifies the time between the scans. The minimum value is 0.01s (10 ms).
Page 290 TDC Settings dialog box: In the TDC Settings dialog box, set the TDC trigger Threshold parameter value to 350, or to a previously saved value. Set the TDC Threshold parameter value to 40, or to a previously specified value. Observe a beam of the reference compound. See also: Tuning the instrument for EI on page 3-19.
Page 291 TDC Settings dialog box parameters: Parameter Description Trigger Threshold Sets the trigger pulse level that triggers the TDC. (mV) Specify 350 mV, or the level set at instrument instal- lation, if different. If peak splitting is seen, change the value to another within the range of 200 to 700 until peak splitting is no longer seen.
Page 292 TDC Settings dialog box parameters: (Continued) Parameter Description Drift (PPM/°C) Set the size of the correction to be applied to mass measurements to compensate for the effect of temper- ature drift. Setting the DXC drift value on page 5-16. See also: Data pane Veff Sets the instrument nominal mass scale.
Page 293 TDC Settings dialog box parameters: (Continued) Parameter Description Lock Mass When acquiring in centroid mode each spectrum is corrected by setting the mass of a known peak to an exact mass entered in this field. Lock mass correction on page 5-3.
Page 294: Low Mass Cut-Off
Low Mass Cut-Off The low mass cut-off prevents low masses from reaching the detector by cutting off the beam at a set time before the push. This saves the detector from becoming saturated with data or burning out, which can occur if exposed to high signal intensities of background ions that are not ions of regularly required, such as air, water, CI gas, or helium.
Page 295 Detector Conditioning dialog box: Detector Conditioning parameters: Parameter Description Start (V) The voltage at which the detector conditioning starts. Set this voltage to 0. Stop (V) The voltage at which the detector conditioning stops. Set this voltage to 2700. Duration (mins) The number of minutes it will take to ramp the voltage from the start voltage to the stop voltage.
Page 296: Ramping The Probe Temperature
Ramping the probe temperature Click Settings > Probe Ramping to open the Probe Control dialog box, which is used to ramp the instrument’s probe temperature during tuning or data acquisition. See also: Ramping the probe temperature automatically on page 7-11. Viewing the status of, and rebooting, the instrument’s embedded To view the current status of the instrument’s embedded PC: Click Settings >...
Page 297: The Tune Window View Menu
The Tune window View menu The View menu is used to: • Copy an image of the peak display. • Hide/display the tuning parameters. • Hide/display the engineer parameters. • Hide/display the peak display. • Hide/display the readback display. Copying an image of the peak display To copy an image of the peak display to the clipboard: Click Alternative:...
Page 298: Hide/Display The Multiple Peak Displays
Hide/display the multiple peak displays To hide/display the multiple peak displays: Click View > Show Peak Display 2 to show a second peak display. Click View > Show Peak Display 3 to show a third peak display. A check mark is displayed beside the menu item when the peak display is Tip: displayed.
Page 299: The Tune Window Tuning Controls
The Tune window tuning controls In the tuning control tabs you set the parameters used to tune the instrument. Five tabs are provided: • Source tab • Inlet tab • DRE tab • Calibration tab • Engineer tab Tip: The tuning control tabs can be hidden by clicking View > Tuning Parameters.
Page 300 The EI Tune tab EI Tune tab: EI Tune tab parameters: Parameter Description Detector Voltage Sets the voltage across the detector. The default value is 2700 V, which provides a beam. However, for accurate mass this value must be set correctly. Setting the optimum gain for the See also: detector on page...
Page 301 EI Tune tab parameters: (Continued) Parameter Description Source Temperature The temperature of the source in °C. the normal setting is between 180 and 200 °C which suits most samples. For certain applications–for example, high temperature GC–this can be increased to a maximum of 350 °C. Using a lower temperature can reduce fragmenta- tion.
Page 302 EI Tune tab parameters: (Continued) Parameter Description Filament Off Click the button to switch the filament on and off. This enables you to leave the instrument for a long time without the filament burning out or sagging. In filament save mode (Filament Off), the button changes to Reset Filament.
Page 303 EI Tune tab parameters: (Continued) Parameter Description Beam Steering The beam steering applies a voltage to one side of the focus lens and reduces voltage on the lens’ other side. This redistribution of voltage to change the lens angle effectively steer a beam left or right. The readback from one side of the focus 1 lens appears in the left field of the two Beam Steering fields.
Page 304 The CI Tune tab CI Tune tab: CI Tune tab parameters: Parameter Description Detector Voltage Sets the voltage across the detector. The default value is 2700 V, which provides a beam. However, for accurate mass this value must be set correctly.
Page 305 CI Tune tab parameters: (Continued) Parameter Description Source Temperature The temperature of the source in °C is normally set at 100 to 150 °C, which suits most samples. Using a lower temperature may reduce fragmen- tation. However, this is likely to allow compounds with a high boiling point to condense in the source, which can reduces sensitivity over time.
Page 306 CI Tune tab parameters: (Continued) Parameter Description Outer Source pane Beam Steering The beam steering applies a voltage to one side of the focus lens and reduces voltage on the lens’ other side. This redistribution of voltage to change the lens angle effectively steer a beam left or right.
Page 307 The FI Tune tab FI Tune tab: FI Tune tab parameters: Parameter Description Detector Voltage Sets the voltage across the detector. The default value is 2700 V, which provides a beam. However, for accurate mass this value must be set correctly. Setting the optimum gain for the See also: detector on page...
Page 308 FI Tune tab parameters: (Continued) Parameter Description Set Maximum Emitter Opens the Emitter Current Control dialog box. Current button You can specify the maximum emitter current to be used. For FI mode, use 10 mA. Emitter Current The current that is passed through the emitter during an acquisition or tuning.
Page 309 FI Tune tab parameters: (Continued) Parameter Description Extraction Voltage This is the high voltage applied to the extraction rods. Normally the extraction voltage is 12000 V. The voltage and leakage current are shown as readbacks. The voltage should be increased from zero to 12000 V manually in increments of 2000 V.
Page 310 The FD Tune tab FD Tune tab: FD Tune tab parameters: Parameter Description Detector Voltage Sets the voltage across the detector. The default value is 2700 V, which provides a beam. However, for accurate mass this value must be set correctly. See also: Setting the optimum gain for the detector on page...
Page 311 FD Tune tab parameters: (Continued) Parameter Description Set Maximum Emitter Opens the Emitter Current Control dialog box. Current button You can specify the maximum emitter current to be used. For FD mode, use 100 mA. Emitter Current (mA) The current that is passed through the emitter during an acquisition or tuning.
Page 312: The Inlet Tab
FD Tune tab parameters: (Continued) Parameter Description Beam Steering The beam steering is a voltage added to one side of Focus 3 lens and taken off the other side of Focus 3 lens. This has the effect of steering the beam to the left or right.
Page 313 Inlets tab: Inlets tab parameters : Parameter Description Use DCI mode When selected, the parameters displayed change to reflect the DCI probe. Solids Probe The temperature of the solids probe in °C. If the readback value of the probe shows 850, the probe cable has not been correctly connected.
Page 314 Inlets tab parameters (Continued): Parameter Description DCI Probe The current of the DCI probe. See also: Ramping the probe current manually on page 8-7. Tip: For safety reasons, the current is set to 0 at the start of an acquisition. Once the acqui- sition has started, you can manually ramp the probe current using this control.
Page 315 Inlets tab parameters (Continued): Parameter Description CI Gas Flow% Regulates the amount of CI gas going into the source (from 1 to 100%). Tip: 100% equals approximately 1 mL/min of methane or ammonia. The Tune window tuning controls B-37...
Page 316: Calibration Tab
Calibration tab The Calibration tab allows you to associate a previously created calibration file to a new calibration. You can also remove calibration files and convert SCL files to CAL files from this tab. Calibration tab: Calibration tab parameters: Parameter Description Filename Shows the path and file name of the calibration...
Page 317: The Engineer Tab
Calibration tab buttons Button Description Remove Calibration Replaces the current calibration file with the Uncal.cal file, an uncalibrated file. Convert SCL to CAL Converts a manual calibration file (.scl) to a cali- bration file (.cal) which can be used for subsequent acquisitions from the Tune window and Sample List.
Page 318 Engineer tab: Engineer tab parameters: Parameter Description Entrance The voltage of the analyzer entrance slit. Set the value to between 38 and 43 V. Pushout Voltage The voltage of the pulser plate that pushes ions down the flight tube. Set the value to between 960 and 970 V.
Page 319 Engineer tab parameters: (Continued) Parameter Description Pusher Interval Sets the frequency of the pusher pulse. Set the value to between 33 and 250 µsec. The default value is 40, but this can be increased to accommodate higher masses. To achieve good resolution, you Requirement: need to retune the Pusher Bias and the Grid 2 parameters if the pusher interval is changed.
Page 320 When the source is pumped down (evacuated) the value should be between 95 and 100%. A value below 90% indicates a cooling fault. See also: Contacting Waters on page 11-14. Analyser Turbo The speed at which the analyser turbo operates.
Page 321: The Dre Tab
The DRE tab DRE tab: DRE tab parameters : Parameter Description High Sensitivity When the parameter is selected, the instrument operates in high-sensi- tivity mode for the z-focus and the z-lens steering. When the parameter is cleared, the instrument operates in low-sensitivity mode for the z-focus and the z-lens steering.
Page 322 DRE tab parameters (Continued): Parameter Description z-focus The voltage applied to the z-focus. For high-sensitivity work the voltage is set to approximately 42. For low-sensitivity work the voltage is set to approximately 250. z-lens steering Steers the beam up and down using the DRE lenses.
Page 323: The Tune Window Peak Display
The Tune window peak display Customizing the peak display Opening the peak display menu Use the peak display menu to customize the peak display. To open the peak display menu: In the MassLynx Tune window, right-click in the peak display window. Customizing the colors and numbers of displayed traces To change the color of the background and traces and the number of traces displayed, on the Peak Display menu, click Customise >...
Page 324 To change the number of displayed traces: In the Customise Plot Appearance dialog box, type the required value in the Visible traces box, within the range 2 to 20. Customizing the peak trace line appearance You can customize the peak trace line appearance using the Trace command in the Peak Display menu.
Page 325: Setting Up Nominal Mass
Setting up nominal mass The instrument’s mass scale is set up to provide nominal mass measurement without calibration. This specifies a Veff (effective potential) value on installation. The Veff value must be routinely evaluated and changed. See also: Table titled “TDC Settings dialog box parameters:” on page B-13.
Page 326: Setting Up Resolution For Dead Time Correction Manually
Instrument Setup Wizard Nominal Mass: on page 3-11 See also: To set up Veff manually: Introduce a known standard compound into the reference reservoir (for example, heptacosa). Reduce the amount of sample using the reference reservoir value so that the intensity of the signal is less than 1000 counts per second in continuum mode to avoid saturation effects.
Page 327: Dead Time Correction
To set up resolution parameter manually: Observe a beam of tris (trifluoromethyl) triazine. Use the reference reservoir pump valve to reduce the amount of reference sample until there are less than 1000 ion counts per second in continuum mode to avoid saturation effects. Acquire data in continuum mode and sum up several spectra so there are more than 2000 ion counts peak height viewed in the spectrum.
Page 328 However, MassLynx incorporates digital dead time correction (DDTC™), which compensates for these effects and enables you to achieve accurate mass measurement and quantitation over a large range of ion currents. See also: • Setting the Np multiplier on page B-50 •...
Page 329: Effects Of Saturation On Peak Shape
• If the first isotope maker is above the best fit line compared with the second isotope marker, then too much dead time correction is being applied. Increase Np multiplier by 0.1, and repeat steps 3 through In the spectrum, the first and second isotope peaks of the tris Result: (trifluoromethyl) triazine ion should be within 1 mDa of each other on the residual output.
Page 330 Example E in Figure titled “Schematic diagram of peak shape saturation effects:” on page B-52 displays the effect of dead-time saturation. You can adjust the Np Multiplier and Resolution fields in the TDC Settings dialog box to correct the effect of dead time saturation. Schematic diagram of peak shape saturation effects: A and B show peaks within the...
Page 331 Dead-time saturation on centroid determination shifts the measured mass to a lower value than that calculated from the empirical formula. In the residuals box the calibration, insufficient dead time correction causes a systematic shift of the largest ions in the spectrum (those with the highest degree of dead time saturation) to a position below the line of best fit compared to the smaller ions in the spectrum (those with the least degree of dead time saturation).
Page 332 B-54 The MassLynx Tune window...
Page 333: C Calibration Reference Information
Calibration Reference Information This appendix provides calibration reference file information. Contents: Topic Page Overview Editing a calibration reference file Calibration reference file...
Page 334: Overview
Overview Calibration reference files and DRE file consist of two columns of numbers separated by any number of spaces or characters. The first column contains the reference peak masses (m/z), and the second column contains the reference peak intensities. Most samples can be purchased from the Sigma chemical company. To order them, contact Sigma at http://www.sigma.sial.com.
Page 335: Heptacosa Negative
Heptacos.ref file: (Continued) Calculated Calculated Calculated Intensity Intensity Intensity m/z value m/z value m/z value 99.99358 6.31 168.98877 3.24 230.98560 0.47 113.99669 2.34 175.99350 0.91 263.98705 8.38 118.99199 7.80 180.98877 1.31 313.98386 0.32 325.98386 0.16 425.97748 0.85 537.97112 0.13 375.98067 0.38 463.97429 1.02...
Page 336: Perfluorotripentylamine (Fc70_Ei.ref
Metri.ref: (Continued) Calculated Calculated Calculated Intensity Intensity Intensity m/z value m/z value m/z value 75.998881 189.996568 10 102.00295 265.996448 100 Perfluorotripentylamine (FC70_EI.ref) Use the FC70_EI+.ref file for calibration in EI+. FC70_EI+.ref: Calculated Calculated Calculated Intensity Intensity Intensity m/z value m/z value m/z value 68.9952 100.00...
Page 337: Heptacosa Pci
FC70_PC+.ref: (Continued) Calculated Calculated Calculated Intensity Intensity Intensity m/z value m/z value m/z value 130.9920 36.31 313.9839 0.32 601.9648 0.64 168.9888 3.24 318.9792 0.32 725.9584 0.64 180.9888 1.31 363.9807 0.16 763.9552 0.64 Heptacosa PCI Use the Heptacosa PCI.ref reference file for calibration in CI+. Heptacosa_PCI.ref: Calculated Calculated...
Page 338: Dre Calculation Files
FC70_NCI-.ref: (Continued) Calculated Calculated Calculated Intensity Intensity Intensity m/z value m/z value m/z value 249.9840 532.9695 4.50 682.9600 263.9871 8.38 551.9679 694.9600 268.9824 563.9679 2.32 706.9600 3.14 280.9805 575.9679 1.32 732.9568 4.24 294.9866 582.9663 2.32 744.9568 16.64 313.9839 1.32 594.9663 1.32 782.9536 40.64...
Page 339: Heptacosa Pci Dre
Heptacosa PCI DRE Use the Heptacosa PCI DRE reference file for DRE calculation in CI+. Heptacosa_PCI.drf: Calculated Calculated Calculated Intensity Intensity Intensity m/z value m/z value m/z value 29.0391 0.73 413.97748 1.64 651.96160 0.64 218.98560 38.07 501.97110 1.90 Metri DRE Use the metri.drf reference file for DRE calculations in EI+ and CI+.
Page 340: Heptacosacpfbdreneg.drf
HeptacosacpfbDRENeg.drf Use the HeptacosacpfbDRENeg.drf file for DRE calculations in CI-. HeptacosacpfbDRENeg.drf Calculated Calculated Calculated Intensity Intensity Intensity m/z value m/z value m/z value 201.9609 100.00 513.9711 38.07 632.9632 0.64 451.9743 36.31 594.9663 1.64 Typical lock mass values Typical lock mass values Typical lock mass Mode Calculated value...
Page 341 External Connections This appendix describes the GCT Premier system’s external wiring, which must to be disconnected, then reconnected, if the instrument is moved. Contents: Topic Page Safety Considerations GCT Premier system external wiring...
Page 342: D External Connections
Safety Considerations The GCT Premier is heavy; if you need to move the Warning: instrument, contact Waters. See also: Contacting Waters on page 11-14. External Connections...
Page 343: Gct Premier System External Wiring
GCT Premier system external wiring The electrical connections for a GCT Premier system with a HP6890 GC and autosampler are shown in Figure titled “GCT Premier system external wiring:” on page D-3. GCT Premier system external wiring: Ext Event Modem...
Page 344: Gct Premier System Vacuum Connections
GCT Premier system vacuum connections The vacuum connections for a GCT Premier system are shown in Figure titled “GCT Premier system vacuum connections:” on page D-4. GCT Premier system vacuum connections: Analyser vacuum connection Source vacuum connection Analyser Valve Sense...
Page 345 Status Display Vacuum LED This appendix describes the status display vacuum LEDs for the various instrument states. Contents: Topic Page Vacuum LED: displays for normal instrument operation: Vacuum LED: displays for instrument faults...
Page 346: E Status Display Vacuum Led
Vacuum LED: displays for normal instrument operation Table titled “Vacuum LED display:” on page 1-10. See also: Vacuum LED: displays for normal instrument operation: State Status LED Sub-state Vented Steady red. Vented Analyser Flashing red and Isolation valve closing pumpdown yellow.
Page 347 Vacuum LED: displays for normal instrument operation: (Continued) State Status LED Sub-state Pumped Steady green. CI purge: Analyzer and source backing valves closing CI purge: Backing line stabilizing CI purge: CI gas in and pump-out valves opening CI Purge: CI gas in valve closing CI Purge: CI pump-out valve closing...
Page 348 Vacuum LED: displays for normal instrument operation: (Continued) State Status LED Sub-state Pumped Steady green. Probe Lock Pump: Analyzer and source backing valves opening Probe Lock Pump: Probe lock pumped LED illuminated Pumped Venting to isolated Flashing green Isolation valve closing and yellow.
Page 349: Vacuum Led: Displays For Instrument Faults
Any combination of LED indications not described in Table titled “Vacuum LED: displays for normal instrument operation:” on page E-2 can indicate an instrument normal state or fault; contact Waters for advice. See also: Table titled “Vacuum LED display:” on page 1-10 Contacting Waters on page 11-14.
Page 350 Vacuum LED: displays for instrument faults: (Continued) State Status LED Sub State Time-out in (source Flashing yellow No pump run-down. vent) one second, red Analyzer pump run-down. three seconds. Source pump run-down. Waiting for vent command. Time-out in (instru- Flashing green one No pump run-down.
Page 351 Performance Specifications This appendix details the performance specifications for the instrument. Contents: Topic Page Performance specifications...
Page 352: F Performance Specifications
Performance specifications Mass range 4000 Dalton. Resolution 7000 resolution (FWHM) at m/z 614. Acquisition rate Up to 20 full spectra (to m/z 800) per second in normal mode. Up to 10 full spectra (to m/z 800) per second in DRE extended mode. GC sensitivity EI positive ionization mode 1 pg of hexachlorobenzene (m/z 283.8) will give a peak to peak signal-to-noise...
Page 353: Dynamic Range
For example: In EI positive ionization mode, less than 10 ng of methyl stearate (m/z 298.3) injected onto a capillary column will give, for all peaks above mass 70 and greater than 10% of the base peak intensity, 1.25 mDa RMS error or better, with the 4.0 GHz TDC.
Page 354 Performance Specifications...
Page 355: G Theory And Principles Of Operation
Theory and Principles of Operation This appendix gives a brief overview of the theory and principles of operation of the instrument. Contents: Topic Page GCT Premier functionality Ionization techniques General considerations for tuning Low mass cut-off DRE mode G-10 Multiple peak stitching...
Page 356: Gct Premier Functionality
GCT Premier functionality GCT Premier mass spectrometer schematic diagram (fitted with GC interface): Reflectron Time-of-flight Detector Pusher region mass analyzer Pusher electrode GC oven Ion path Isolation valve Outer source Inner source GC interface Sample is introduced into the inner source, where ions are generated. the ions are accelerated to 40 eV and focused into the pusher region.
Page 357: Ionization Techniques
When the pusher electrode is operated at a repetition frequency of 25 kHz, a full spectrum is recorded every 40 µs. Each spectrum is summed in the Embedded PC (EPC) memory until the completed, histogrammed, spectrum is transferred to the MassLynx PC. Ionization techniques Electron Impact ionization During EI operation, the sample enters the EI inner source via the GC...
Page 358: Chemical Ionization
Electron impact ionization: Electron trap Trap voltage Ion current Ion repeller Repeller voltage Emission current Ion chamber Emission current Electron energy (volts) Filament Filament current Chemical ionization In contrast to EI (where the vaporized sample molecules are ionized by colliding with high energy electrons from the filament), chemical ionization (CI) uses a relatively high-pressure reagent gas (the CI gas) in the ion source to moderate the collision energy.
Page 359: Negative Chemical Ionization
conditions. The filament current is regulated using the total emission current and not the trap current as in EI operation. See also: Tuning the instrument for positive CI on page 3-25. Negative chemical ionization Both positive and negative ions are created in EI and CI sources. Ions of the required polarity are extracted from the source by applying the appropriate polarity potential to the source and focusing lenses.
Page 360: Field Desorption
Figure titled “GC-FI column position:” on page 9-20. See also: The position of the emitter in relation to the center line of the extraction rods is also critical. Small changes to the position can make a large changes in the beam steering voltage being required.
Page 361 In the GCT Premier, the transmission of these ions into the pushout region of the TOF is reduced by restriction slits in the ion source. The primary ion beam exiting the inner source is partially mass-dispersed by a magnetic field.
Page 362: Low Mass Cut-Off
Beam from high and low mass ion: The largest constant low mass background ion should be maintained below the level of saturation of the TDC. See also: This saturation effect is described in Effects of saturation on peak shape on page B-51.
Page 363 However viewing air peaks can provide a good diagnosis of an air leak in the system. It can therefore sometimes be helpful to turn off LMC and look at the air peaks to diagnose leaks. Typically, the air peak at 28Da should be less than 2000 counts/sec in continuum with the GC fitted and <...
Page 364: Dre Mode
Low mass cut-off graph: DRE mode Dynamic range enhancement (DRE) mode increases the range of the GCT Premier. It allows the analysis of strong samples that produce intense signals. DRE is achieved by means of lenses that focus and steer the ion beam in the z-direction.
Page 365 Tune window DRE tab High Sensitivity option. To acquire data in DRE mode, click Use DRE in the GCT Premier Tune Acquire dialog box, or click Use DRE in the MS Method window, Full Scan Function Editor.
Page 366: Multiple Peak Stitching
Setting up DRE mode on page 4-15. Tip: When you acquire data in the DRE mode, Waters recommends that you scan at a rate of at least 5 spectra per second. This gives better peak shapes and more accurate intensity representation.
Page 367: Gain Drop Monitoring
Gain drop monitoring When the detector on the GCT Premier is hit with a very large signal it uses up the available electrons with the result that the detector gain drops until the electrons have been replenished. The effect of this gain drop is that all the peaks in a spectrum are reduced in intensity, and may not be seen at all in an extreme case.
Page 368 Notes: • Gain Drop Monitoring only works in DRE mode. • You must be using a lock mass to use GDM – this is set up in the TDC settings and can be checked because the lock mass will be flagged in the spectrum as a blue peak with a star on top of it.
Page 369 mass within approximately 15 mDa of the lock mass, it can interfere with the lock mass and thus shift all the peaks up or down the mass scale. This will produce mass errors in all the peaks in the spectrum where the lock mass peak is interfered with.
Page 370 G-16 Theory and Principles of Operation...
Page 371 Index a.c. power connection 1-17 calibrating the instrument acquiring in CI 5-18 analog data 4-10 in CI- 5-25 acquisition in CI+ 5-18 starting a multiple-sample calibration starting a single sample manually correcting 5-11 acquisition rate parameters, editing 5-13 air connection 1-19 reference file, editing altering the mass peak of interest...
Page 372 3-31 event out connection 1-15 obtaining a beam 3-32 inputs 1-15 purging the gas line 3-32 contacting Waters 11-14 sensitivity continuum data 4-15 tuning 3-30 copying, existing functions correction calibrating the instrument 5-18 deadtime...
Page 373 4-11 trace line appearance B-46 Calibration Parameters 5-13 cut-off, low mass B-16 Customise Plot Appearance B-45 Detector Conditioning B-17 GCT Premier Tune Acquire 5-21 data acquisition Make new calibration 5-23 starting Probe Control types of 4-14 Control page 7-16 DCI probe...
Page 374 inner source assembly 10-18 power down 1-20 10-19 power switch 1-20 ionization power up 1-20 tab, recommended tuning values rebooting 1-20 B-18 viewing status of B-18 EI techniques equation B-49 ESD Earth connection 1-16 calibration reference file excessive leakage current 11-12 sensitivity existing functions...
Page 375 GC sensitivity maintenance 10-11 GCT Premier mass spectrometer replacing alumina balls 10-12 GCT Premier Tune Acquire dialog box front of the instrument 5-21 Full Scan function editor 4-12 GCT Premier, functionality Full Scan function editor parameters GCT sensitivity...
Page 376 heptacos.ref calibration reference file insertion lock probe, installing installing heptacosa 4-16 DCI probe heptacosa library spectrum 3-23 GC column heptacosa PCI.ref calibration reference inner source file insertion lock probe heptacosacpfbDRENeg.drf calibration installing DI probe reference file instrument heptacosaDREPos.drf calibration calibrating reference file name, selecting B-18...
Page 377 9-21 7-10 obtaining a beam, in CI- mode 3-32 mass accuracy obtaining a beam, in CI+ mode 3-28 mass range oil mist filter element, changing 10-8 mass spectrometer, GCT Premier operate LED Index-7...
Page 378 optimum gain, MCP setting-up 10-52 power outer source assembly connection 1-17 for FI/FD EPC switch 1-20 outer source lid assembly fuse 1-17 outer source maintenance 10-35 preparing for FI/FD operation FI/FD parameter, settings recalling 3-34 preparing for operation parameters printing tune peak information 3-34 Full Scan function editor 4-13...
Page 379 removing DCI probe ramping DI Probe probe temperature automatically DI probe 7-11 FI/FD outer source probe temperature manually GC interface 6-11 7-10 sample cup after use rear of the instrument 1-12 source components rebooting, EPC B-18 source components, order of recalling, parameter settings 3-34 the inner source...
Page 380 saving source components, removing function list source heater not working 11-8 parameter settings 3-34 source housing, pumping region schematic diagram source temperature selecting B-27 instrument name B-18 B-23 run time for an experiment source vacuum connection 1-18 setting spare parts 11-2 B-50 Spectrum window...
Page 381 tris (trifluoromethyl) triazine 3-19 Tune window B-49 File menu troubleshooting 11-1 Ion Mode menu emission current zero 11-9 layout emission trap ration >4:1 11-10 opening 11-11 peak display excessive leakage current 11-12 customizing intensity display hardware 11-3 B-46 high emission current 11-9 menu, opening B-45...
Page 382 1-18 fine fore vacuum system Veff, setting correctly B-47 vent command 9-14 valve 9-14 venting analyzer instrument source venting the instrument 9-14 voltage detector B-22 warm-up instrument Waters, contacting 11-14 windows Spectrum 5-22 wiring, external system Index-12...

Waters GCT Premier Operator's Manual

Safety Information

Consignes de Sécurité

GCT Premier Mass Spectrometer Information

1 Instrument Description

Introduction

Ion Source

Inlets

Reference Reservoir Inlet

Vacuum System

Masslynx Control System

Controls and Indicators on the Instruments' Front Panel

Controls on the Instruments' Top Panel

Controls and Connectors on Instruments' Rear Panel

2 Preparing the Instrument for EI/CI Operation

Changing the EI/CI Inner Source Assembly

Changing the EI/CI Outer Source Assembly

3 Tuning the Instrument

Preparing the Instrument for Operation

Obtaining an Ion Beam

Setting up the Instrument Automatically

Tuning the Instrument for EI

Tuning the Instrument for Best Resolution in EI

Tuning the Instrument for Positive CI

Tuning the Instrument for Negative CI

Preparing for FI Operation

Managing Tune Parameters

4 Acquiring Data

Starting Data Acquisition

Setting up an MS Method

Setting up an MS Scan

Setting up DRE Mode

5 Calibration

Calibrating the Instrument

Using the Calibration Wizard

Using Calibrations for Subsequent Acquisitions

Dynamic External Calibration Temperature Compensation

Calibrating the Instrument in CI

Manual Calibration

6 The GC Interface

Installing the GC Interface

Installing the GC Column

Configuring the GC and Autosampler

Removing the GC Interface

7 The Direct Insertion Probe

Introduction

Installing the Probe Insertion Lock

Inserting and Removing the DI Probe

Controlling the DI Probe Temperature

8 The Direct Chemical Ionization (DCI) Probe

Introduction

Installing the Probe Insertion Lock

Inserting and Removing the DCI Probe

Controlling the DCI Probe Current

9 FI/FD Operation

Introduction

Preparing the Instrument for FI/FD Operation

Setting-Up for FI/FD Operation

Tuning in FI Mode

General Considerations for Tuning in FI Mode

Setting up and Calibrating the Instrument

Running Samples

Tuning in FD Mode

10 Routine Maintenance

Maintenance Schedule

Safety and Handling

Rotary Pump Oil

Rotary Pump Maintenance

Foreline Trap Maintenance

Reference Reservoir Maintenance

EI/CI Inner Source Maintenance

FI/FD Inner Source Maintenance

EI/CI Outer Source Maintenance

FI/FD Outer Source Maintenance

Checking for Leaks after Source Maintenance

Detector Maintenance

11 Troubleshooting

Spare Parts

Safety and Handling

System Troubleshooting