SCIEX TripleTOF 5600 Plus System User's Manual
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SCIEX TripleTOF 5600 Plus System User's Manual

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TripleTOF
5600/5600+ System
System User Guide
RUO-IDV-05-7040-B
January 2018

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Summary of Contents for SCIEX TripleTOF 5600 Plus

  • Page 1 ® TripleTOF 5600/5600+ System System User Guide RUO-IDV-05-7040-B January 2018...
  • Page 2 SCIEX warranties are limited to those express warranties provided at the time of sale or license of its products and are SCIEX s sole and exclusive representations, warranties, and obligations.

  • Page 3: Table Of Contents

    Contents 1 Operational Precautions and Limitations....................7 General Safety Information..............................7 Regulatory Compliance..............................7 Australia and New Zealand............................7 Canada..................................8 Europe..................................8 United States................................8 International................................9 Electrical Precautions.................................9 AC Mains Supply................................9 Protective Earth Conductor............................10 Chemical Precautions...............................10 Ventilation Precautions..............................11 Environmental Precautions..............................12 Electromagnetic Environment............................13 Decommissioning and Disposal..........................14 Qualified Personnel................................14 Laboratory Conditions..............................14 Operating Conditions..............................14 Performance Specifications............................15...
  • Page 4 Contents 5 Operating Instructions Hardware Profiles and Projects..............34 Hardware Profiles................................34 Create a Hardware Profile............................34 Add Devices to a Hardware Profile..........................39 Troubleshoot Hardware Profile Activation.........................41 Projects and Subprojects..............................42 Create Projects and Subprojects..........................42 Create Subprojects..............................44 Copy Subprojects...............................44 Switch Between Projects and Subprojects........................44 Installed Project Folders.............................45 Back Up the API Instrument Folder..........................46 Recover the API Instrument Folder..........................46...
  • Page 5 Contents Queue States................................70 View Instrument and Device Status Icons........................71 Queue Right-click Menu.............................72 9 Operating Instructions Analyze and Explore Data.................74 Open Data Files................................74 Navigate Between Samples in a Data File........................75 View Experimental Conditions............................75 Show Data in Tables................................76 Show ADC Data................................78 Show Basic Quantitative Data............................79 Chromatograms................................79 Show TICs from a Spectrum.............................80 Show a Spectrum from a TIC............................81...
  • Page 6 Contents A Recommended Calibration Ions......................110 B Exact Masses and Chemical Formulas....................113 C Toolbar Icons............................116 D Glossary of Symbols..........................125 E Glossary of Warnings...........................130 ® TripleTOF 5600/5600+ System System User Guide 6 / 131 RUO-IDV-05-7040-B...

  • Page 7: Operational Precautions And Limitations

    Operational Precautions and Limitations Note: Before operating the system, carefully read all of the sections of this guide. This section contains general safety-related information and provides regulatory compliance information. It also describes potential hazards and associated warnings for the system and the precautions that should be taken to minimize the hazards.

  • Page 8: Canada

    Operational Precautions and Limitations • Safety: AS/NZ 61010-1 and IEC 61010-2-061 Canada • Electromagnetic Interference (EMI): CAN/CSA CISPR11. This ISM device complies with Canadian ICES-001. Refer to Electromagnetic Interference on page • Safety: • CAN/CSA C22.2 No. 61010-1 • CAN/CSA C22.2 No 61010-2-061 Europe •...

  • Page 9: International

    The covers need not be removed for routine maintenance, inspection, or adjustment. Contact a SCIEX Field Service Employee (FSE) for repairs that require the covers to be removed. • Follow required electrical safe work practices.

  • Page 10: Protective Earth Conductor

    (grounding cable) is connected between the sample loop and an appropriate grounding point at the ion source. This supplementary grounding will reinforce the safety configuration specified by SCIEX. Chemical Precautions WARNING! Ionizing Radiation Hazard, Biohazard, or Toxic Chemical Hazard.

  • Page 11: Ventilation Precautions

    • Determine which chemicals have been used in the system prior to service and regular maintenance. Refer to the Safety Data Sheets for the health and safety precautions that must be followed with chemicals. SCIEX Safety Data Sheets can be found at sciex.com/tech-regulatory.

  • Page 12: Environmental Precautions

    WARNING! Puncture Hazard, Ionizing Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Discontinue use of the ion source if the ion source window is cracked or broken and then contact a SCIEX Field Service Employee (FSE). Any toxic or injurious materials introduced into the equipment will be present in the source exhaust output.

  • Page 13: Electromagnetic Environment

    Operational Precautions and Limitations CAUTION: Potential Mass Shift. Maintain a stable ambient temperature. If the temperature changes by more than 2 °C per hour, then the resolution and mass calibration might be affected. Electromagnetic Environment Electromagnetic Compatibility Basic Electromagnetic Environment: Environment existing at locations characterized by being supplied directly at low voltage from the public mains network.

  • Page 14: Decommissioning And Disposal

    Storage and Handling on page 106. Note: SCIEX will not accept any system returns without a completed Decontamination Form. Contact an FSE to obtain a copy of the form. Do not dispose of system components or subassemblies, including computer parts, as unsorted municipal waste.

  • Page 15: Performance Specifications

    WARNING! Personal Injury Hazard. Use SCIEX-recommended parts only. Use of parts not recommended by SCIEX or use of parts for any purpose other than their intended purpose can put the user at risk of harm or negatively impact system performance.

  • Page 16: Contact Us

    Technical Support SCIEX and its representatives maintain a staff of fully-trained service and technical specialists located throughout the world. They can answer questions about the system or any technical issues that might arise. For more information, visit the SCIEX website at sciex.com.

  • Page 17: Related Documentation

    To find software product documentation, refer to the release notes or software installation guide that comes with the software. Documentation for the hardware products can be found on the Customer Reference DVD that comes with the system or component. For the latest versions of the documentation, visit the SCIEX website at sciex.com. ® System User Guide...

  • Page 18: Principles Of Operation

    Refer to the DuoSpray Ion Source Operator Guide. ® • A SCIEX-supplied computer and monitor with the Analyst TF software for instrument optimization, acquisition method development, and data acquisition. For computer specifications and requirements, refer to the Software ®...
  • Page 19 Adjust the Integrated Syringe Pump Position on page Mass spectrometer status LEDs Refer to Panel Symbols. Communications bulkhead Contact an SCIEX Field Service Employee (FSE). Serial (RS-232) cable connection for the syringe pump Contact an FSE. ® System User Guide TripleTOF...
  • Page 20 Principles of Operation Item Description For more information... USB cable connection for the USB-GPIB card Contact an FSE. InfiniBand cable connection for the TDC card Contact an FSE. Figure 2-2 Left Side View Item Description For more information... Gas and vacuum bulkhead Contact an FSE.

  • Page 21: Panel Symbols

    Principles of Operation Item Description For more information... AUX IO connection. The optional LC system start Contact an FSE. signal connects to this port. External control connection. This port is intended for Contact an FSE. future use. Sources connection. Some ion sources connect to this Contact an FSE.

  • Page 22: Theory Of Operation

    Principles of Operation Table 2-1 Panel Symbols (continued) Color Name Description Green Ready Lit when the system is in the Ready state. The system must be in the Ready state to operate. Fault Lit when the system encounters a system fault. After the system is turned on, all of the LEDs illuminate.

  • Page 23: Data Handling

    Principles of Operation Data Handling ® The Analyst TF software requires a computer running the Windows 7 (32- or 64-bit) operating system or the Windows 10 (64-bit) operating system. The computer and the associated system software work with the system controller and the associated firmware to control the system and data acquisition.

  • Page 24: Operating Instructions Hardware

    WARNING! Personal Injury Hazard. Follow the instructions in the documentation when using the system. The protection provided by the equipment might be impaired if the equipment is used in a manner not specified by SCIEX. Start Up the System WARNING! Electrical Shock Hazard. Make sure that the system can be disconnected from the mains supply outlet in an emergency.

  • Page 25: Shut Down The System

    Operating Instructions Hardware 1. Turn on the roughing pump. 2. Remove the cover on the circuit breaker switch on the left side of the mass spectrometer, when viewed from the front and then turn on the circuit breaker. Refer to Figure 2-2.

  • Page 26: Adjust The Integrated Syringe Pump Position

    Operating Instructions Hardware Note: Leave the ion source installed for proper venting. a. Turn off the roughing pump. Allow the system to vent for 20 minutes. 7. Remove the cover on the circuit breaker switch on the left side of the mass spectrometer and then turn off the circuit breaker.
  • Page 27 Operating Instructions Hardware Figure 3-1 Lowering the Syringe Item Description Syringe plunger Release button. Press to raise or lower the base. 2. Make sure that the end of the syringe is flush against the base and that the shaft of the syringe rests in the cutout.
  • Page 28 Operating Instructions Hardware Figure 3-2 Automatic Syringe Stop Item Description Automatic syringe stop. After the post hits the automatic syringe stop, the syringe pump stops. Post. Adjust the height to prevent the syringe plunger from hitting the syringe during sample infusion. Post lock screw.

  • Page 29: Reset The Syringe Pump

    Operating Instructions Hardware Figure 3-3 Syringe Pump Screws ® 5. In the Analyst software, on the Navigation bar, double-click Manual Tuning. 6. Click Start Syringe. 7. To stop the syringe pump, click Stop Syringe. Reset the Syringe Pump ® If the Analyst TF software stops communicating with the syringe pump, then reset the syringe pump.
  • Page 30 Operating Instructions Hardware Figure 3-4 Reset Button ® TripleTOF 5600/5600+ System System User Guide 30 / 131 RUO-IDV-05-7040-B...

  • Page 31: Operating Instructions Sample Workflows

    Operating Instructions Sample Workflows Table 4-1 Instrument Setup Step To do this... Find the information in..What does it do? Create a hardware profile. Create a Hardware Profile on page 34 Each hardware profile must include a mass spectrometer and other devices, such as an LC system.
  • Page 32 Operating Instructions Sample Workflows Table 4-2 Sample Acquisition Workflow Step To do this... Find the information in..What does it do? Create projects to store data. Create Projects and Subprojects on Before starting an page 42 experiment, decide where to store the files related to the experiment.
  • Page 33 Table 4-3 Experienced User Workflow Step To do this... Find the information in..Mass calibrate the instrument. Mass Calibration Tutorial located in Start > Programs > SCIEX ® > Analyst TF > Software Guides. Optimize the mass Manual Optimization Tutorial located in Start > Programs >...

  • Page 34: Operating Instructions Hardware Profiles And Projects

    Operating Instructions Hardware Profiles and Projects Hardware Profiles A hardware profile tells the software how the mass spectrometer and the devices are configured and connected to the computer. Multiple hardware profiles can be set up, but only one profile can be active at any time. When a hardware profile is created in the Hardware Configuration Editor, the peripheral devices must be configured so that the software can communicate with them.
  • Page 35 Operating Instructions Hardware Profiles and Projects Figure 5-1 Hardware Configuration Editor Dialog 2. In the Hardware Configuration Editor dialog, click New Profile. ® System User Guide TripleTOF 5600/5600+ System RUO-IDV-05-7040-B 35 / 131...
  • Page 36 Operating Instructions Hardware Profiles and Projects Figure 5-2 Create New Hardware Profile Dialog 3. Type a name in the Profile Name field. 4. Click Add Device. ® TripleTOF 5600/5600+ System System User Guide 36 / 131 RUO-IDV-05-7040-B...
  • Page 37 Operating Instructions Hardware Profiles and Projects Figure 5-3 Available Devices Dialog In the Available Devices dialog, in the Device Type field, Mass Spectrometer is the preset value. 5. In the Devices list, select the appropriate mass spectrometer and then click OK to return to the Create New Hardware Profile dialog.
  • Page 38 Operating Instructions Hardware Profiles and Projects Figure 5-4 Configuration Tab with CDS and Syringe Pump Configured 8. (Optional) To configure the mass spectrometer for the CDS, on the Configuration tab, select Use calibrant delivery system (CDS). 9. (Optional) Select additional features on the Configuration and Communication tabs as required. 10.

  • Page 39: Add Devices To A Hardware Profile

    Operating Instructions Hardware Profiles and Projects 14. Click Activate Profile. The check mark turns green. If a red x is shown, then there is an issue with the hardware profile activation. Tip! A hardware profile need not be deactivated before another is activated. Click a hardware profile and then click Activate Profile.
  • Page 40 Operating Instructions Hardware Profiles and Projects Figure 5-5 Available Devices Dialog 6. Click OK. 7. Select the device from the Devices list and then click OK. 8. Click Setup Device. A dialog containing configuration values for the device opens. 9. (Optional) On the Communication tab, in the Alias field, type a name or other identifier for the device. Note: For devices using serial communication, make sure that the serial port selected matches the serial port to which the device is physically connected.

  • Page 41: Troubleshoot Hardware Profile Activation

    Operating Instructions Hardware Profiles and Projects • If the device uses Ethernet as a communication interface, then type the IP Address assigned to the device by the administrator or use the corresponding Host Name for the address. • If the device uses GPIB Board as a communication interface, then do not change the settings for the GPIB board.

  • Page 42: Projects And Subprojects

    Operating Instructions Hardware Profiles and Projects 8. Activate the hardware profile. 9. If the issue persists, then delete the failing profile and create a new one. 10. If the issue still persists, then contact technical support. Projects and Subprojects Before beginning an experiment, decide where to store the files related to the experiment. Use projects and subprojects for each experiment to better manage data and compare results.
  • Page 43 Operating Instructions Hardware Profiles and Projects Figure 5-6 Create New Project/Subproject Dialog Note: A new subproject cannot be created for a project that was not originally created with a subproject. 2. Type a project name in the Project name field. 3.

  • Page 44: Create Subprojects

    Operating Instructions Hardware Profiles and Projects All new projects are created with this folder configuration. 6. Click OK. Create Subprojects Subprojects can only be created in a project that has an existing subproject structure. 1. On the Project tool bar, from the Project list, select the project. 2.

  • Page 45: Installed Project Folders

    Operating Instructions Hardware Profiles and Projects Figure 5-7 Project List The project list in this figure shows the API Instrument, Default, and Example folders. Installed Project Folders Three project folders are installed with the software: API Instrument, Default, and Example. API Instrument Folder The API Instrument folder is unique and very important to the correct functioning of the mass spectrometer.

  • Page 46: Back Up The Api Instrument Folder

    Operating Instructions Hardware Profiles and Projects Back Up the API Instrument Folder Back up the API Instrument folder regularly and after routine maintenance has been performed. • Copy the API Instrument folder, paste it to a different location, preferably to another computer, and then rename the folder.

  • Page 47: Tune And Calibrate

    • A printer is configured. Required Materials • Tuning solutions that are supplied in the Standards Chemical Kit shipped with the system. If required, a new kit can be ordered from SCIEX. Refer to Recommended Calibration Ions. • Gas-tight syringe (1.0 mL recommended) •...

  • Page 48: About The Verifying Or Adjusting Performance Dialog

    Tune and Calibrate 1. On the Navigation bar, under Tune and Calibrate, double-click Manual Tuning. 2. Run a TOF MS or Product ion scan type and confirm that there is a stable TIC and that the peaks of interest are present in the spectrum.. 3.
  • Page 49 Tune and Calibrate Figure 6-1 Results Summary The Results Summary is automatically saved in the following path: <drive>:\Analyst Data\Projects\API Instrument\Data\Instrument Optimization\yyyy-mm-dd\results.doc, where yyyy-mm-dd is the date on which the report was created. Users can print the Results Summary or open a previously saved Results Summary. ®...

  • Page 50: Operating Instructions Acquisition Methods

    Operating Instructions Acquisition Methods An acquisition method consists of experiments and periods. Use the Acquisition Method Editor to create a sequence of periods and experiments for the instrument and devices. An acquisition method consists of the method for the mass spectrometer and for liquid chromatography (LC) devices.

  • Page 51: Add An Experiment

    Operating Instructions Acquisition Methods 9. On the MS tab, click Edit Parameters. 10. On the Source/Gas tab, specify values in the fields as required. 11. On the Compound tab, specify values in the fields as required and then click OK. 12.

  • Page 52: Copy An Experiment Into A Period

    Operating Instructions Acquisition Methods Note: Users cannot use multiple periods in an IDA experiment. Copy an Experiment into a Period 1. Open a multi-period method. 2. In the Acquisition method pane, press Ctrl, and then drag the experiment to the period. The experiment is copied below the last experiment in the period.

  • Page 53: Scan Techniques

    Operating Instructions Acquisition Methods 6. Type a name for the method and then press Enter. 7. Click Next. 8. On the Ion Source Parameters tab, verify the values, editing them if necessary, and then click Next. 9. On the TOF MS tab, verify the values, editing them if necessary, and then click Finish. Tip! If required, users can further edit the acquisition method using the Acquisition Method Editor.

  • Page 54: Time-Of-Flight Single Mass Spectrometry

    Operating Instructions Acquisition Methods Time-of-Flight Single Mass Spectrometry In a time-of-flight single mass spectrometry (TOF MS) scan, the system generates mass spectrometric information by pulsing ions into a flight tube and recording their precise arrival time at the detector. Ions with a greater mass-to-charge ratio take longer to travel the flight tube.

  • Page 55: Parameters

    Operating Instructions Acquisition Methods Table 7-1 Spectral Data Mode Description Profile The preset value is 0.1 Da. Profile data is the data generated by the mass spectrometer and corresponds to the intensity recorded at a series of evenly spaced discrete mass values.For example, for the mass range 100 Da to 200 Da and step size 0.1, the instrument scans from 100 Da to 200 Da in 0.1 Da increments (for example, 100.0, 100.1, 100.2, 100.3…...
  • Page 56 Operating Instructions Acquisition Methods Figure 7-2 Ion Optics Path and Parameters Location Parameter Parameter Scan Type Type IonSpray Source and gas The ISVF parameter affects the stability of Voltage the spray and hence the signal sensitivity. Floating This is the voltage applied to the needle that (ISVF) sprays the sample.
  • Page 57 Operating Instructions Acquisition Methods Location Parameter Parameter Scan Type Type Ion Source Source and gas The GS1 parameter controls the nebulizer ® Gas 1 (GS1) gas for both the TurboIonSpray and APCI probes. The GS1 parameter controls the ® nebulizer gas for the TurboIonSpray probe.
  • Page 58 Operating Instructions Acquisition Methods Location Parameter Parameter Scan Type Type CAD Gas Source and gas The CAD parameter controls the pressure of CAD gas in the collision cell. The collision gas helps to focus the ions as they pass through the collision cell; the preset for the CAD parameter is in fixed mode.
  • Page 59 Operating Instructions Acquisition Methods Location Parameter Parameter Scan Type Type Ion Release Compound The amount of time in milliseconds before MS/MS only, Delay (IRD) the ion pulse. The default (11 msec) is Enhanced calculated based on the TOF masses and can be adjusted by the operator.

  • Page 60: Operating Instructions Batches

    Operating Instructions Batches CAUTION: Potential System Damage. If the HPLC system connected to the mass spectrometer are not controlled by the software, then do not leave the mass spectrometer unattended while in operation. The liquid stream from the HPLC system can flood the ion source when the mass spectrometer goes into Standby mode.
  • Page 61 Operating Instructions Batches Figure 8-1 Queue Options Dialog 3. In the Max. Num. Waiting Samples field, set the maximum number of samples to a value that is greater than the number of samples that will be submitted to the queue 4.

  • Page 62: Add Sets And Samples To A Batch

    Operating Instructions Batches 9. Select the Continue Whole Batch if Missing Sync found check box to continue acquiring the whole batch when a missing sync signal is encountered. If this check box is not selected, then the current sample fails and the queue does not proceed to the next sample when this signal is encountered. Add Sets and Samples to a Batch A set can consist of a single sample or multiple samples.
  • Page 63 Operating Instructions Batches Figure 8-3 Add Sample Dialog 5. In the Sample name section, in the Prefix field, type a name for the samples in this set. 6. To add incremental numbering to the end of the sample name, select the Sample number check box. 7.
  • Page 64 Operating Instructions Batches 12. In the New samples section, in the Number field, type the number of new samples to add. 13. Click OK. The sample table fills with the sample names and data file names. Tip! Fill Down and Auto Increment options are available in the right-click menu after a single column heading or several rows in a column are selected.

  • Page 65: Submit A Sample Or Set Of Samples

    Operating Instructions Batches Submit a Sample or Set of Samples Note: Run the sample again in the event of an abnormal termination during sample acquisition. If the abnormal termination is caused by a power failure, then the temperature of the autosampler tray is not maintained and sample integrity might be compromised.

  • Page 66: Change Sample Order

    Operating Instructions Batches parameters, and the masses used for calibration. It informs the users whether the calibration succeeded. The report also summarizes the parameters used for calibration. Change Sample Order The order of the samples can be edited before the samples are submitted to the Queue. •...

  • Page 67: Set Sample Locations In The Batch Editor

    Operating Instructions Batches Set Sample Locations in the Batch Editor If an autosampler is used in the acquisition method, then the vial positions of the samples must be defined in the acquisition batch. Define the location in the Sample tab or in the Locations tab. For more information about creating batches, refer to Add Sets and Samples to a Batch on page 1.

  • Page 68: Stop Sample Acquisition

    Operating Instructions Batches Figure 8-5 Locations Tab Note: Depending on the autosampler being used, it might not be necessary to type details in additional columns. 7. To select whether samples are marked by row or column, click the Row/Column selection selector button. If the button shows a red horizontal line, then the Batch Editor marks the samples by row.

  • Page 69: Batch Editor Right-Click Menu

    Operating Instructions Batches 4. To continue processing the batch, click Acquire > Start Sample. Batch Editor Right-click Menu Right-click in the Batch Editor table to access the options. Figure 8-6 Batch Right-Click Menu Menu Function Open Opens a batch file. Import From Imports a file.

  • Page 70: Queue States And Device Status

    Operating Instructions Batches Menu Function Delete Samples Deletes the selected row. Select Autosampler Selects an autosampler. Queue States and Device Status The Queue Manager shows queue, batch, and sample status. Detailed information about a particular sample in the queue can also be viewed. Tip! Click to view the queue.

  • Page 71: View Instrument And Device Status Icons

    Operating Instructions Batches Table 8-1 Queue States Icons State Definition Not Ready The hardware profile is deactivated and the queue is not accepting any sample submissions. Stand By The hardware profile has been activated, but all devices are idle. Pumps are not running and gases are turned off. Warming Up The mass spectrometer and devices are equilibrating, columns are being conditioned, the autosampler needle is being washed,...

  • Page 72: Queue Right-Click Menu

    Operating Instructions Batches determine whether the LC pump pressure is appropriate or view the detailed status of the mass spectrometer to confirm the temperature of the ion source. Note: For each status, the background color can be red. A red background indicates that the device encountered an error while in that state.
  • Page 73 Operating Instructions Batches Figure 8-9 Queue Manager Right-Click Menu Menu Function Sample Details Opens the Sample Details dialog. Reacquire Acquires a sample again. Insert Pause Inserts a pause, in seconds, between two samples. Delete Deletes either the batch or the selected samples. Move Batch Moves the batch within the queue.

  • Page 74: Operating Instructions Analyze And Explore Data

    Operating Instructions Analyze and Explore Data Use the sample files installed in the Example folder to learn how to view and analyze data using the most common analysis and processing tools. For more information about the following topics, refer to the Advanced User Guide: •...

  • Page 75: Navigate Between Samples In A Data File

    Operating Instructions Analyze and Explore Data Navigate Between Samples in a Data File Note: If samples were saved in separate data files, then open each file individually. Table C-5 on page 119 shows the navigation icons used in this procedure. •...

  • Page 76: Show Data In Tables

    Operating Instructions Analyze and Explore Data Table 9-1 Right-click Menu for Show File Information Pane (continued) Menu Function Save To File Saves data as an rtf file. Font Changes the font. Save Acquisition Method Saves the acquisition method as a dam file. Save Acquisition Method to Opens the Specify Compound Information dialog.
  • Page 77 Operating Instructions Analyze and Explore Data Figure 9-1 Peak List Tab Table 9-2 Right-click Menu for Spectral Peak List Tab Menu Function Column Options Opens the Select Columns for Peak List dialog. Save As Text Saves the data as a .txt file. Delete Pane Deletes the selected pane.

  • Page 78: Show Adc Data

    Operating Instructions Analyze and Explore Data Table 9-3 Right-click Menu for Chromatographic Peak List Tab Menu Function Show Peaks in Graph Show the peaks in two colors in the graph. IntelliQuan Parameters Opens the Intelliquan dialog. Save As Text Saves the data as a txt file. Delete Pane Deletes the selected pane.

  • Page 79: Show Basic Quantitative Data

    Operating Instructions Analyze and Explore Data Show Basic Quantitative Data 1. Open a data file. 2. Click Explore > Show > Show List Data. Figure 9-3 List Data 3. In the Peak List tab, right-click and then select Show Peaks in Graph. Peaks are shown in two colors.

  • Page 80: Show Tics From A Spectrum

    Operating Instructions Analyze and Explore Data The software plots intensity, in counts per second (cps), on the Y-axis against time on the X-axis. Peaks above a set threshold are labeled automatically. In the case of LC-MS, the chromatogram is often shown as a function of time.

  • Page 81: Show A Spectrum From A Tic

    Operating Instructions Analyze and Explore Data Tip! Right-click inside a pane containing a spectrum and then click Show TIC. Show a Spectrum from a TIC 1. In a pane containing a TIC, select a range. 2. Click Explore > Show > Show Spectrum. The spectrum opens in a new pane.

  • Page 82: About Generating Xics

    Operating Instructions Analyze and Explore Data About Generating XICs XICs can be generated only from single-period, single-experiment chromatograms or spectra. To obtain an XIC from multi-period or multi-experiment data, split the data into separate panes by clicking the triangle under the X-axis.

  • Page 83: Generate An Xic Using The Maximum Peak

    Operating Instructions Analyze and Explore Data An XIC of the selection opens in a pane below the spectrum pane. The experiment information at the top of the pane contains the mass range and the maximum intensity in counts per second. Generate an XIC Using the Maximum Peak 1.

  • Page 84: Generate Bpcs

    Operating Instructions Analyze and Explore Data Figure 9-5 Extract Ions Dialog 3. Type the values for each XIC to be created. If a stop value is not typed, then the range is defined by the start value. • In the Start field, type the start value (lower value) for the mass range. •...
  • Page 85 Operating Instructions Analyze and Explore Data 3. Click Explore > Show > Show Base Peak Chromatogram. The selections are shown in the Start Time and End Time fields. Figure 9-6 Base Peak Chromatogram Options 4. In the Mass Tolerance field, type the value to indicate the mass range used to find a peak. The software finds the peak using a value twice the typed range (±...

  • Page 86: Generate Xwcs

    Operating Instructions Analyze and Explore Data Generate XWCs An XWC is a wavelength chromatogram created by taking intensity values at a single wavelength, or by the sum of the absorbance for a range of several wavelengths. Up to three ranges can be extracted from a DAD spectrum to generate the XWC.

  • Page 87: Generate Twcs

    Operating Instructions Analyze and Explore Data Tip! If the pane with the TWC is closed, then click a point anywhere in the TWC to open it again. Click Explore > Show > Show DAD TWC. Generate TWCs A TWC is a less commonly used chromatogram. It shows the total absorbance (mAU) as a function of time. The TWC provides a way of viewing an entire data set in a single pane.

  • Page 88: Chromatogram Panes

    Operating Instructions Analyze and Explore Data Chromatogram Panes Table 9-6 Right-click Menu for Chromatogram Panes Menu Function List Data Lists the data points and integrates the peaks found in chromatograms. Show Spectrum Generates a new pane containing the spectrum. Show Contour Plot Shows a color-coded plot of a data set, where the color represents the intensity of the data at that point.

  • Page 89: Spectra Panes

    Operating Instructions Analyze and Explore Data Spectra Panes Table 9-7 Right-click Menu for Spectra Panes Menu Function List Data Lists the data points and integrates chromatograms. Show TIC Generates a new pane containing the TIC. Extract Ions (Use Range) Extracts a specific ion or set of ions from a selected pane and then generates a new pane containing a chromatogram for the specific ions.

  • Page 90: Graphs

    Operating Instructions Analyze and Explore Data Graphs The same data can be examined in different ways. Data can also be kept for comparison purposes before performing processing operations such as smoothing or subtraction. A window contains one or more panes arranged in such a way that all the panes are fully visible and that they do not overlap.
  • Page 91 Operating Instructions Analyze and Explore Data Table 9-8 Graph Options (continued) To do this... use this menu option..or click this icon Move a pane • Select the graph. Click Window > Move Pane. • Select the pane or window and then drag it to the new position.

  • Page 92: Zoom In On The Y-Axis

    Operating Instructions Analyze and Explore Data Table 9-8 Graph Options (continued) To do this... use this menu option..or click this icon Maximize a pane Select the graph. Click Window > Maximize Pane. Tile panes Select the graph. Click Window > Tile all Panes. Zoom In on the Y-axis 1.

  • Page 93: Service And Maintenance Information

    Tip! Perform maintenance tasks regularly to make sure that the mass spectrometer is performing optimally. For information on maintaining the ion source, refer to the ion source Operator Guide. Contact a Qualified Maintenance Person (QMP) to order consumable parts. Contact a SCIEX Field Service Employee (FSE) for maintenance service and support.
  • Page 94 Service and Maintenance Information Table 10-1 Maintenance Tasks (continued) Component Frequency Task For more information... Mass Spectrometer Curtain plate Daily Clean Refer to Clean the Curtain Plate on page Orifice plate (front) Daily Clean Refer to Clean the Front of the Orifice Plate on page 101.

  • Page 95: Clean The Surfaces

    Service and Maintenance Information For “As needed” tasks, follow these guidelines: • Clean the mass spectrometer surfaces after a spill or when they become dirty. • Empty the drain bottle before it becomes full. ® • Clean the orifice plate, QJet ion guide, and Q0 region if system sensitivity degrades.

  • Page 96: Symptoms Of Contamination

    If any of these issues are observed, then clean the mass spectrometer front-end. Required Materials Note: U.S. customers can call 877-740-2129 for ordering information and inquiries. International customers can visit sciex.com/contact-us. • Powder-free gloves (nitrile or neoprene recommended) • Safety glasses •...

  • Page 97: Cleaning Best Practices

    Service and Maintenance Information • Lint-free wipes. Refer to Tools and Supplies Available from the Manufacturer on page • (Optional) Polyester (poly) swabs Tools and Supplies Available from the Manufacturer Description Part Number Small poly swab (thermally bonded). Also available in the Cleaning kit. 1017396 Lint-free wipe (11 cm x 21 cm, 4.3 inches x 8.3 inches).

  • Page 98: Prepare The Mass Spectrometer

    Service and Maintenance Information • Do not use cleaning supplies other than those specified in this procedure. • If possible, prepare cleaning solutions just before cleaning. • Prepare and store all of the organic solutions and organic-containing solutions in very clean glassware only. Never use plastic bottles.

  • Page 99: Clean The Curtain Plate

    Service and Maintenance Information CAUTION: Potential System Damage. Do not drop anything into the source drain when the ion source is removed. Figure 10-2 Source Drain on the Vacuum Interface 1. Deactivate the hardware profile. 2. Remove the ion source. Refer to the ion source Operator Guide. When the ion source is not in use, store it to protect it from damage and to maintain operating integrity.
  • Page 100 Service and Maintenance Information Figure 10-3 Curtain Plate Removal The curtain plate is held in place by three retaining ball catches mounted on the orifice plate. Tip! If the curtain plate does not immediately separate from the orifice plate, then turn the curtain plate slightly (less than 90 degrees) to release the ball spring latches.

  • Page 101: Clean The Front Of The Orifice Plate

    Service and Maintenance Information Clean the Front of the Orifice Plate CAUTION: Potential System Damage. When cleaning the surface of the orifice plate, do not remove the interface heater. Frequent removal of the interface heater can result in damage to the interface heater. Surface cleaning of the interface heater is adequate for routine cleaning.
  • Page 102 Service and Maintenance Information WARNING! Ionizing Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Take care to vent exhaust gases to a dedicated laboratory fume hood or exhaust system and make sure that the ventilation tubing is secured with clamps. Make sure that the laboratory has appropriate air exchange for the work performed.

  • Page 103: Inspect The Roughing Pump Oil Level

    • Inspect the sight glass on the roughing pump to verify that the oil is above the minimum level. If the oil is below the minimum level, then contact the qualified maintenance person (QMP) or SCIEX field service employee (FSE).

  • Page 104: Replace The Mass Spectrometer Cooling Fans Filter

    Service and Maintenance Information Figure 10-5 Sight Glass Replace the Mass Spectrometer Cooling Fans Filter The mass spectrometer cooling fans are on the left side of the mass spectrometer. Prerequisite Procedures • Shut down the system by following the procedure in the System User Guide. WARNING! Environmental Hazard.
  • Page 105 Service and Maintenance Information 1. Remove the four thumbscrews on the cooling fan cover. Figure 10-6 Cooling Fan Filters 2. Remove the filter and then replace it with a new one. Figure 10-7 Cooling Fans Filter Item Description Cooling fans cover Filter 3.

  • Page 106: Storage And Handling

    Follow local regulations when disposing of components. If the mass spectrometer must be stored for a long time or prepared for shipping, then contact a SCIEX FSE for decommissioning information. To disconnect power from the mass spectrometer, remove the mains supply connector from the AC mains supply.

  • Page 107: Mass Spectrometer Troubleshooting

    Troubleshooting This section contains information for troubleshooting basic system issues. Certain activities can only be carried out by a SCIEX -trained Qualified Maintenance Person (QMP) in the laboratory. For advanced troubleshooting, contact a SCIEX Field Service Employee (FSE). Table 11-1 System Issues...
  • Page 108 Mass Spectrometer Troubleshooting Table 11-1 System Issues (continued) Symptom Possible Cause Corrective Action Sensitivity is reduced. 1. The ion source parameters are 1. Optimize the ion source not optimized. parameters. Refer to ® theAnalyst TF software Help 2. The mass spectrometer is not system.
  • Page 109 Refer to the ion source Operator Guide. For sales, technical assistance, or service, contact an FSE or visit the SCIEX Web site at sciex.com for contact information.

  • Page 110: A Recommended Calibration Ions

    Recommended Calibration Ions ® The following tables list the standards recommended by SCIEX for calibrating the TripleTOF 5600 system. For information about tuning solutions, refer to Tune and Calibrate on page Table A-1 Q1 PPG Positive Calibration Ions Masses 59.04914 233.17472...
  • Page 111 Recommended Calibration Ions Table A-4 APCI Positive Calibration Solution and ESI Positive Calibration Solution: MSMS (Clomipramine) MSMS (Clomipramine) Masses 58.0651 86.0964 220.1121 227.0496 235.1356 242.0731 270.1044 315.16225 Table A-5 APCI Negative Calibration Solution and ESI Negative Calibration Solution: TOF MS TOF MS Masses 7-aminoheptanoic acid...
  • Page 112 Recommended Calibration Ions Table A-6 APCI Negative Calibration Solution and ESI Negative Calibration Solution: MSMS (Sulfinpyrazone) (continued) MSMS (Sulfinpyrazone) Masses 277.0983 403.11219 Table A-7 APCI Negative Calibration Solution and ESI Negative Calibration Solution: MSMS (Sulfinpyrazone Fragment) MSMS (Sulfinpyrazone Fragment) Masses 77.03967 116.0506 130.0662...

  • Page 113: B Exact Masses And Chemical Formulas

    Exact Masses and Chemical Formulas Table B-1 contains the exact monoisotopic masses and charged species (positive and negative) observed with the PPG (polypropylene glycol) calibration solutions. The masses and ions were calculated using the formula M = H[OC OH, while the positive ion MSMS fragments used the formula, [OC ).
  • Page 114 Exact Masses and Chemical Formulas Table B-1 PPG Exact Masses (continued) – Exact Mass (M) (M + NH MSMS (M + NH (M + COOH) Fragments 946.68032 964.71414 929.67704 491.37398 991.67851 1004.72218 1022.75600 987.71890 520.39491 1049.72037 1062.76404 1080.79786 1045.76076 549.41584 1107.76223 1120.80590 1138.83972...
  • Page 115 Exact Masses and Chemical Formulas Table B-3 Taurocholic Acid Exact Masses (continued) Description Mass Fragment C 124.00739 Fragment SO 79.95736 TOF Calibration Solution Table B-4 TOF Calibration Solution Exact Masses Description Mass Molecular Ion Cs 132.90488 Molecular Ion Peptide ALILTLVS 829.53933 ®...

  • Page 116: C Toolbar Icons

    Toolbar Icons For additional toolbar icons, refer to the Advanced User Guide. Table C-1 Tool Bar Icons Icon Name Description New Subproject Creates a subproject. Subprojects can only be created later in the process if the project was originally created with subprojects. Copy Subproject Copies a Subproject folder.
  • Page 117 Toolbar Icons Table C-3 Acquire Mode Icons Icon Name Description View Queue Shows the sample queue. Instrument Queue Shows a remote instrument station. Status for Remote Shows the status of a remote instrument. Instrument Start Sample Starts the sample in the queue. Stop Sample Stops the sample in the queue.
  • Page 118 Toolbar Icons Table C-3 Acquire Mode Icons (continued) Icon Name Description Reserve Reserves the mass spectrometer for tuning and calibrating. Instrument for Tuning Method Wizard Starts the Method Wizard. Purge Modifier Starts the modifier purge from the modifier pump. Table C-4 Tune and Calibrate Mode Icons Icon Name Description...
  • Page 119 Toolbar Icons Table C-5 Explore Quick Reference: Chromatograms and Spectrum Icon Name Description Open Data File Opens files. Show Next Sample Goes to the next sample. Show Previous Goes to the previous sample. Sample Go To Sample Opens the Select Sample dialog. List Data Views the data in tables.
  • Page 120 Toolbar Icons Table C-5 Explore Quick Reference: Chromatograms and Spectrum (continued) Icon Name Description Force Peak Labels Labels all of the peaks. Expand Selection Sets the expansion factor for a portion of a graph to be viewed in greater detail. Clear ranges Returns the expanded selection to normal view.
  • Page 121 Toolbar Icons Table C-6 Explore Toolbar Quick Reference: Overlaying Graphs (continued) Icon Name Description Cycle Overlays Click to cycle between overlaid graphs. Sum Overlays Click to add the graphs together. Table C-7 Explore Toolbar Quick Reference: Fragment Interpretation Tool Icon Name Description Show Fragment...
  • Page 122 Toolbar Icons Table C-8 Navigation Icons on the Explore Toolbar (continued) Icon Name Function Threshold Click to adjust the threshold. Noise Filter Click to use the Noise Filter Options dialog to define the minimum width of a peak. Signals below this minimum width are regarded as noise. Show ADC Click to view ADC data.
  • Page 123 Toolbar Icons Table C-8 Navigation Icons on the Explore Toolbar (continued) Icon Name Function Show DAD Click to generate a DAD spectrum. Spectrum Extract Click to extract up to three wavelength ranges from a DAD spectrum to view Wavelength the XWC. Table C-9 Integration Tab and Quantitation Wizard Icons Icon Name...
  • Page 124 Toolbar Icons Table C-10 Results Table Icons (continued) Icon Name Description Show all Samples Shows all the samples in the Results Table. Delete Formula Column Deletes formula columns. Report Generator Opens the Reporter software. Table C-11 Icon Quick Reference: Quantitate Mode Icon Name Description...

  • Page 125: D Glossary Of Symbols

    Authorized representative in the European community Biohazard CE Marking of Conformity cCSAus mark. Indicates electrical safety certification for Canada and USA. Catalogue number Caution Note: In SCIEX documentation, this symbol identifies a personal injury hazard. ® System User Guide TripleTOF 5600/5600+ System RUO-IDV-05-7040-B...
  • Page 126 Glossary of Symbols Symbol Description China RoHS Caution Label. The electronic information product contains certain toxic or hazardous substances. The center number is the Environmentally Friendly Use Period (EFUP) date, and indicates the number of calendar years the product can be in operation. Upon the expiration of the EFUP, the product must be immediately recycled.
  • Page 127 Glossary of Symbols Symbol Description Fuse Hertz High Voltage. Electrical Shock Hazard If the main cover must be removed, contact a SCIEX representative to prevent electric shock. Hot Surface Hazard In Vitro Diagnostic Device Ionizing Radiation Hazard Keep dry. Do not expose to rain.
  • Page 128 Glossary of Symbols Symbol Description Pinch Hazard Pressurized Gas Hazard Protective Earth (ground) Puncture Hazard Puncture Hazard Reactive Chemical Hazard Serial number Toxic Chemical Hazard Transport and store the system within 66 kPa to 103 kPa. Transport and store the system within 75 kPa to 101 kPa. Transport and store the system within 10% to 90% relative humidity.
  • Page 129 Glossary of Symbols Symbol Description Transport and store the system within –30 °C to +60 °C. USB 2.0 connection USB 3.0 connection Ultraviolet Radiation Hazard Volt Ampere (power) Volts (voltage) WEEE. Do not dispose of equipment as unsorted municipal waste. Environmental Hazard Watts yyyy-mm-dd Date of manufacture...

  • Page 130: E Glossary Of Warnings

    TRIPPED “IMPACT INDICATOR” OR “TILT INDICATOR” TRIPPED “IMPACT INDICATOR” OR “TILT INDICATOR” ON THE WAYBILL BEFORE ACCEPTING SHIPMENT AND ON THE WAYBILL BEFORE ACCEPTING SHIPMENT AND NOTIFY YOUR LOCAL AB SCIEX CUSTOMER SUPPORT NOTIFY YOUR LOCAL AB SCIEX CUSTOMER SUPPORT ENGINEER IMMEDIATELY. ENGINEER IMMEDIATELY.
  • Page 131 Glossary of Warnings Label Translation (if applicable) TiltWatch PLUS Tilt Indicator ShockWatch Note: Indicates whether the container was tipped or mishandled. Write on the Bill of Lading and inspect for damage. Any claims for tipping require a notation. WARNING: DO NOT OPERATE WITHOUT FIRST WARNING: DO NOT OPERATE WITHOUT FIRST ENSURING BOTTLE CAP IS SECURED.

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