SCIEX 5500 Series System User's Manual
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SCIEX 5500 Series System User's Manual

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5500 Series of Instruments
System User Guide
RUO-IDV-05-6768-A
December 2017

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Summary of Contents for SCIEX 5500 Series

  • Page 1 5500 Series of Instruments System User Guide RUO-IDV-05-6768-A December 2017...
  • 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

    Theory of Operation—Analyst Software........................33 Chapter 3 Operating Instructions Sample Workflows...............36 Chapter 4 Operating Instructions Hardware..................45 Start Up the System.................................45 Reset the Mass Spectrometer............................46 Shut Down and Vent the System............................46 System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 3 / 195...
  • Page 4 Copy an Experiment within a Period..........................86 Scan Techniques................................87 Quadrupole-Mode Scan Types...........................87 LIT-Mode Scan Types..............................88 About Spectral Data Acquisition............................89 Chapter 9 Operating Instructions Analyze and Process Quantitative Data.............................90 Quantitative Analysis...............................90 Quantitation Methods..............................90 5500 Series of Instruments System User Guide 4 / 195 RUO-IDV-05-6768-A...
  • Page 5 Adjust the Threshold..............................124 Chromatogram Panes..............................125 Spectra Panes................................126 Graphical Data Processing.............................126 Graphs...................................127 Manage Data................................127 Zoom In on the Y-axis..............................129 Zoom In on the X-axis..............................129 Chapter 11 Reporter Software.......................130 Analyst Reporter User Interface.............................131 System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 5 / 195...
  • Page 6 Confirm the Presence of Compounds........................165 Optimize MS-Specific Parameters..........................167 Determine the Product Ions for Optimization......................168 Optimize Collision Cell Exit Potential for each Product Ion..................170 Manually Optimize the Ion Source and Gas Parameters....................171 5500 Series of Instruments System User Guide 6 / 195 RUO-IDV-05-6768-A...
  • Page 7 Optimize the Ion Source Parameters........................171 Advanced Parameters..............................172 Optimize AF2................................172 About Collision Energy Spread (CES) ........................173 Appendix B 5500 Series System Parameters..................174 Appendix C Calibration Ions and Solutions..................177 Appendix D Toolbar Icons........................180 Appendix E Glossary of Symbols......................189 Appendix F Glossary of Warnings......................194...

  • Page 8: Chapter 1 Operational Precautions And Limitations

    • Electromagnetic Compatibility (EMC): Radio Communications Act 1992 as implemented in these standards: • Electromagnetic Interference—AS/NZS CISPR 11/ EN 55011/ CISPR 11 (Class A). Refer to Electromagnetic Interference on page 5500 Series of Instruments System User Guide 8 / 195 RUO-IDV-05-6768-A...

  • Page 9: Canada

    • Radio Emissions Interference Regulations: 47 CFR 15, as implemented in FCC Part 15 (Class A) • Safety: Occupational Safety and Health Regulations, 29 CFR 1910, as implemented in these standards: • UL 61010-1 • IEC 61010-2-061 System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 9 / 195...

  • Page 10: 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 11: 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! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Determine whether decontamination is required prior to cleaning or maintenance.

  • Page 12: System Safe Fluids

    • 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 13: Ventilation Precautions

    WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Use the ion source only if you have knowledge of and training in the proper use, containment, and evacuation of toxic or injurious materials used with the ion source. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 13 / 195...

  • Page 14: Environmental Precautions

    WARNING! Puncture Hazard, 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 15: Decommissioning And Disposal

    Storage and Handling on page 160. 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 16: Qualified Personnel

    Service office for complimentary equipment pick-up and recycling. Qualified Personnel Only qualified SCIEX personnel shall install, inspect, and service the equipment. After installing the system, the Field Service Employee (FSE) uses the Customer Familiarization Checklist to orient the customer on system operation, cleaning, and basic maintenance.

  • Page 17: Equipment Use And Modification

    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 18: Technical Support

    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 19: Related Documentation

    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 5500 Series of Instruments...

  • Page 20: Chapter 2 Principles Of Operation

    Follow established safe lifting procedures. Refer to the Site Planning Guide for the weights of system components. This system is intended for the qualitative and quantitative analysis of chemical species. The 5500 series of instruments includes the following components: ® • A SCIEX Triple Quad...

  • Page 21: Hardware Overview

    Adjust the Integrated Syringe Pump Position on page 47 Ion source Turbo V Ion Source Operator Guide, available from the ion source documentation DVD, or from the SCIEX Web site, at sciex.com Diverter valve Plumb the Diverter Valve on page...
  • Page 22 The vacuum LED starts flashing. After the correct vacuum level is achieved this LED remains lit. Connections Figure 2-2 shows the location of the mass spectrometer connections, including the locations of the RESET and VENT buttons and the mass spectrometer convenience switch. 5500 Series of Instruments System User Guide 22 / 195 RUO-IDV-05-6768-A...
  • Page 23 Gas tubing from the source exhaust gas supply connects to this port. Source communication Aluminum Contact an FSE. connection RESET button Plastic Refer to Reset the Mass Spectrometer on page System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 23 / 195...

  • Page 24: Theory Of Operation-Hardware

    QJet ion guide increases system sensitivity and improves the signal-to-noise ratio. In the Q0 region, the ions are again focused before passing into the Q1 quadrupole. 5500 Series of Instruments System User Guide 24 / 195...
  • Page 25 Many spectra are rapidly collected in a short period of time and are significantly more intense than spectra collected in a comparable standard quadrupole mode of operation. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 25 / 195...

  • Page 26: Analyst Software Overview

    The following figures show examples of two types of data views: total ion chromatogram (TIC) and extracted ion chromatogram (XIC). TIC: The plot of the total ion current as a function of time. 5500 Series of Instruments System User Guide 26 / 195...
  • Page 27 XIC: An ion chromatogram created by taking intensity values at a single, discrete mass value or a mass range, from a series of mass spectral scans. It indicates the behavior of a given mass or mass range as a function of time. Figure 2-5 Example XIC System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 27 / 195...
  • Page 28 • Detector parameters: These parameters affect the detector. The following figure shows the location of the parameters on the ion optics path. Figure 2-6 Ion Optics Path and Parameters 5500 Series of Instruments System User Guide 28 / 195 RUO-IDV-05-6768-A...
  • Page 29 The GS2 parameter controls the heater gas ® Gas 2 (GS2) for the TurboIonSpray probe. The GS2 parameter controls the heater gas for the ® TurboIonSpray probe and the nebulizer gas for the APCI probe. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 29 / 195...
  • Page 30 Potential (EP) difference between the voltage on Q0 and ground. The entrance potential guides and focuses the ions through the high-pressure on the Q0 region. Use the preset value. 5500 Series of Instruments System User Guide 30 / 195 RUO-IDV-05-6768-A...
  • Page 31 Q2 collision cell, where they collide with gas molecules and fragment. Use the preset value and optimize for the compound. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 31 / 195...
  • Page 32 Excitation the excitation energy is applied. It is used Time in combination with the excitation energy to fragment the isolated second precursor ion. Use the preset value. 5500 Series of Instruments System User Guide 32 / 195 RUO-IDV-05-6768-A...

  • Page 33: Theory Of Operation-Analyst Software

    The calibration curve relationship between signal response and concentration is used to determine the quantity of a particular analyte in an unknown sample. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 33 / 195...
  • Page 34 The relationship between instrument response and analyte concentration is determined by the line created by these two points. Both the acquisition and quantitation methods should be validated before being accepted for their intended use. 5500 Series of Instruments System User Guide 34 / 195...
  • Page 35 • Quadratic (y = a2 + bx + c) As well, it is possible to add different types of weighting for the regression, including: • 1/x • 1/x • 1/y • 1/y System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 35 / 195...

  • Page 36: Chapter 3 Operating Instructions Sample Workflows

    Verify Instrument Performance on page This is the process of spectrometer. optimizing the resolution and mass spectrometer parameters, and calibrating the mass spectrometer to obtain the best sensitivity and performance from the system. 5500 Series of Instruments System User Guide 36 / 195 RUO-IDV-05-6768-A...
  • Page 37 To submit samples and acquire data, use the Queue Manager. The Queue Manager shows queue, batch, and sample status, and facilitates management of samples and batches in the queue. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 37 / 195...
  • Page 38 Use the Results Table to manually review all of the peaks for each analyte and internal standard within a batch and to view calibration curves, sample statistics, and metric plots. 5500 Series of Instruments System User Guide 38 / 195 RUO-IDV-05-6768-A...
  • Page 39 To submit samples and acquire data, use the Queue Manager. The Queue Manager shows queue, batch, and sample status, and facilitates management of samples and batches in the queue. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 39 / 195...
  • Page 40 ® Analyst software. peaks for each analyte and internal standard within a batch. For quantitative analysis, also review calibration curves, sample statistics, and metric plots. 5500 Series of Instruments System User Guide 40 / 195 RUO-IDV-05-6768-A...
  • Page 41 Create projects to store data. Create Projects and Subprojects on Using projects and page 62 subprojects facilitates data management and makes comparison of results easier. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 41 / 195...
  • Page 42 Equilibrate the system. Equilibrate the System on page 139 Equilibrate the system prior to starting data acquisition. A system that is not equilibrated can result in poor data. 5500 Series of Instruments System User Guide 42 / 195 RUO-IDV-05-6768-A...
  • Page 43 MultiQuant software. Reference Guide: Quantitation quantitative method Method Editor creation tools in the software to analyze the acquired data and build a quantitative method to generate a Results Table. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 43 / 195...
  • Page 44 Generate a report using the Reporter. provided report templates for the generated and reviewed results. For reports specific to qualitative analysis, use the set of report templates labeled with library searching. 5500 Series of Instruments System User Guide 44 / 195 RUO-IDV-05-6768-A...

  • Page 45: Chapter 4 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 46: Reset The Mass Spectrometer

    Contact us for a copy of the Site Planning Guide, if required. For contact information, go to sciex.com/contact-us. • The source exhaust gas, compressed air, and nitrogen gases are connected to the mass spectrometer.

  • Page 47: Adjust The Integrated Syringe Pump Position

    8. (If venting the system) Disconnect the roughing pump mains supply cable from the mains supply outlet. Adjust the Integrated Syringe Pump Position WARNING! Puncture Hazard. Take care when handling the syringe. The tip of the syringe is extremely sharp. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 47 / 195...
  • Page 48 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. 5500 Series of Instruments System User Guide 48 / 195...
  • Page 49 Post lock screw. Tighten the screw after the height of the post is adjusted. 4. Turn the side screws as shown in Figure 4-3 to secure the syringe. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 49 / 195...
  • Page 50 Figure 4-4. The LED beside the button flashes when the syringe pump ® is in use. The syringe pump flow can also be controlled automatically by the Analyst software. 5500 Series of Instruments System User Guide 50 / 195 RUO-IDV-05-6768-A...

  • Page 51: Plumb The Diverter Valve

    Add Devices to a Hardware Profile on page CAUTION: Potential Wrong Result. Do not press the diverter valve button during a run. Doing so might result in incorrect data. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 51 / 195...

  • Page 52: Plumb The Diverter Valve In Injector Mode

    When the valve is in Position A, the sample flows through the external loop. When the valve switches to Position B, the sample is injected. • Plumb the valve for injector mode. Figure 4-5 Diverter Valve Injector Mode Position A Figure 4-6 Diverter Valve Injector Mode Position B 5500 Series of Instruments System User Guide 52 / 195 RUO-IDV-05-6768-A...

  • Page 53: Plumb The Diverter Valve In Diverter Mode

    When the valve is in Position A, the flow goes to waste. When the valve switches to Position B, the flow goes to the mass spectrometer. • Plumb the valve for diverter mode. Figure 4-7 Diverter Valve Diverter Mode Position A System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 53 / 195...
  • Page 54 Operating Instructions Hardware Figure 4-8 Diverter Valve Diverter Mode Position B Item Description To mass spectrometer From column Waste out 5500 Series of Instruments System User Guide 54 / 195 RUO-IDV-05-6768-A...

  • Page 55: Chapter 5 Operating Instructions Hardware Profiles And Projects

    Create a Hardware Profile The user can create multiple hardware profiles, but only one profile can be active at any time. 1. On the Navigation bar, under Configure, double-click Hardware Configuration. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 55 / 195...
  • Page 56 Operating Instructions Hardware Profiles and Projects Figure 5-1 Hardware Configuration Editor Dialog 2. In the Hardware Configuration Editor dialog, click New Profile. 5500 Series of Instruments System User Guide 56 / 195 RUO-IDV-05-6768-A...
  • Page 57 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. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 57 / 195...
  • Page 58 13. Click the hardware profile to be activated in the Hardware Configuration Editor. 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. 5500 Series of Instruments System User Guide 58 / 195...

  • Page 59: Add Devices To A Hardware Profile

    Note: Remember to add a mass spectrometer. For more information, refer to Create a Hardware Profile on page 5. In the Available Devices dialog, in the Device Type list, select the device and then click OK. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 59 / 195...
  • Page 60 Alias. • If the device uses a Serial Port as a communication interface, then in the COM Port Number list, select the COM port to which the device is connected. 5500 Series of Instruments System User Guide 60 / 195...

  • Page 61: Troubleshoot Hardware Profile Activation

    4. Verify that the communication settings for the device (for example, dip switch settings) are set correctly and match the settings on the Communication tab. 5. Turn off the device. 6. Wait 10 seconds. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 61 / 195...

  • Page 62: Projects And Subprojects

    Figure 5-5 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. 5500 Series of Instruments System User Guide 62 / 195...

  • Page 63: Create Subprojects

    7. Click OK. 8. Do one of the following: • To copy all folders and files from the Subproject Source into the Subproject Destination, select the Copy Contents check box. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 63 / 195...

  • Page 64: Switch Between Projects And Subprojects

    The Example folder contains sample methods and data files. Users can practice working with the Explore or Quantitate modes using the example data files. The example files are sorted into subfolders by mass spectrometer type and application area. 5500 Series of Instruments System User Guide 64 / 195...

  • Page 65: Back Up The Api Instrument Folder

    API Instrument folder, do the following: 1. Rename the current API Instrument folder. 2. Copy the backup folder into the Projects folder. 3. Change the name of the backup folder to API Instrument. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 65 / 195...

  • Page 66: Chapter 6 Tune And Calibrate

    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. • 5 mL, 1 mL, and 250 µL serial gas-tight syringes. • Red PEEK sample tubing.

  • Page 67: About The Verifying Or Adjusting Performance Dialog

    Results Summary The Results Summary is a record of any instrument settings changes that were made by the Instrument Optimization wizard. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 67 / 195...
  • Page 68 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. 5500 Series of Instruments System User Guide 68 / 195...

  • Page 69: Chapter 7 Automatic Optimization

    • (For FIA analysis) Mobile phase: 1:1 acetonitrile:water + 2 mM ammonium acetate + 0.1% formic acid. Note: Users can choose a different mobile phase based on the experimental properties of the compound. • LC pump and autosampler. • (For FIA Analysis) Autosampler vials. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 69 / 195...

  • Page 70: About Automatic Optimization

    Use infusion optimization to optimize compound-dependent parameters only at much lower flow rates than those used during LC-MS/MS analysis. 5500 Series of Instruments System User Guide 70 / 195...

  • Page 71: Automatically Optimize For An Analyte Using Infusion

    4. On the Navigation bar, under Tune and Calibrate, double-click Manual Tuning. 5. In the method list field, click Syringe Pump Method. 6. On the Syringe Pump Method Properties tab, type the appropriate parameter values. Refer to Table 7-4. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 71 / 195...
  • Page 72 In the first case, the peak might not be a real compound. In the second case, the concentration might be too high for the software to optimize properly. 5500 Series of Instruments System User Guide...

  • Page 73: Perform Automatic Ms And Ms/Ms Optimization Using Infusion With A Known Precursor Ion And An Unknown Product Ion

    2. On the Navigation bar, under Tune and Calibrate, double-click Compound Optimization. 3. On the Instrument Settings page, in the Inlet section, click Infusion. 4. Click MS/MS Analysis in the Mass Spectrometer section. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 73 / 195...
  • Page 74 7. Click Criteria next to the Auto Select option. 8. In the Product Ion Auto Selection Criteria dialog, type the appropriate parameters. Refer to Table 7-6. 5500 Series of Instruments System User Guide 74 / 195 RUO-IDV-05-6768-A...
  • Page 75 10. Click Next. 11. In the Target Components dialog, type the appropriate parameter values. Refer to Table 7-7. Note: The compound name must be unique for each compound or transition. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 75 / 195...

  • Page 76: Review The Optimization Results

    1. After completing the optimization, print the text file containing the optimized parameters for each compound. 2. Click File > Open and then select the Reserpine_QOpt_FinalMRM.POS.dam file. 5500 Series of Instruments System User Guide 76 / 195...

  • Page 77: Automatically Optimize For An Analyte Using Fia

    3. Make sure that the ion source and gas parameters are set to reasonable levels to prevent the contamination of the mass spectrometer while optimizing. For more information, refer to the ion source Operator Guide. 4. Set the horizontal micrometer to 5. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 77 / 195...
  • Page 78 Rack Code Autosampler specific Rack Position Autosampler specific Injection Volume 10 µL Mass Spectrometer MS/MS Analysis 9. Click Next. 10. Make sure that the Int. Std. check box is cleared. 5500 Series of Instruments System User Guide 78 / 195 RUO-IDV-05-6768-A...
  • Page 79 Be sure not to go too low with any of the settings to keep the system clean. Refer to Table 7-10 for parameters that can be used as a starting point. Tip! Type the values before selecting the check box. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 79 / 195...
  • Page 80 The total number of injections and the total sample volume are calculated based on the specifications here. Note the total sample volume needed. Sample volume might be high depending on how many variables for each parameter are being optimized, as each variable is a separate method. 5500 Series of Instruments System User Guide 80 / 195...
  • Page 81 For more information, refer to the Help. Table 7-11 Example FIA Compound Parameters Page Parameter Select the Values for Optimization Optimize Check Box? Declustering Potential 60;80;100;120;200 Entrance Potential — System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 81 / 195...
  • Page 82 18. Repeat step 19 until all of the parameters for all of the compounds are provided. 19. Type 1.5 in the Mass Spec. Duration field. Note: This value should be at least the required length of time for each injection. 5500 Series of Instruments System User Guide 82 / 195...
  • Page 83 Note: Typically, the ion source and gas parameters must be narrowed using one more FIA cycle. 22. Open the final optimized FIA method called *_FIA_sample_1. Note: The software generates several acquisition methods. 23. Save this method using a simpler name. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 83 / 195...

  • Page 84: Chapter 8 Operating Instructions Acquisition Methods

    12. Click a device icon and then select the parameters for the device. 13. Add any additional periods and experiments. Refer to Add an Experiment on page 85 Add a Period on page 14. Click File > Save. 5500 Series of Instruments System User Guide 84 / 195 RUO-IDV-05-6768-A...

  • Page 85: Configure The Integrated Syringe Pump

    5. Select the units of flow from the Unit list. Add an Experiment 1. In the Acquisition method pane, on the period where the experiment is to be added, right-click and then click Add experiment. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 85 / 195...

  • Page 86: Add A Period

    Use this procedure to add the same or similar experiments to a period if most or all of the parameters are the same. • Right-click the experiment and then click Copy this experiment. 5500 Series of Instruments System User Guide 86 / 195...

  • Page 87: Scan Techniques

    Product Ion (MS2): An MS/MS full scan where the Q1 quadrupole is fixed to transmit a specific precursor ion and the Q3 quadrupole scans a defined mass range. Used to identify all of the products of a particular precursor ion. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 87 / 195...

  • Page 88: Lit-Mode Scan Types

    28 percent of the mass of the precursor ion during MS3 experiments. This phenomenon is often referred to as the one-third cut-off rule. 5500 Series of Instruments System User Guide 88 / 195...

  • Page 89: About Spectral Data Acquisition

    The disadvantage is that peak shape information is lost and if data has been collected as a centroid then it cannot be altered. We recommend the use of profile mode and centroiding of the data post-acquisition. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 89 / 195...

  • Page 90: Chapter 9 Operating Instructions Analyze And Process Quantitative Data

    With the Quantitation Wizard, a Results Table is generated at the same time as the quantitation method. Alternatively, an existing quantitation method can be used to quantitate different sets of data. 5500 Series of Instruments System User Guide 90 / 195...

  • Page 91: About Results Tables

    • Select the project that contains the data to be quantified. • Switch Between Projects and Subprojects on page 64 1. Make sure that the Example folder is selected. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 91 / 195...
  • Page 92 12. Save the quantitation method. The new method can be used when a batch is created in the Batch Editor or when the Quantitation Wizard is used to generate a Results Table. 5500 Series of Instruments System User Guide 92 / 195...

  • Page 93: Create A Results Table Using The Quantitation Wizard

    Note: It is the responsibility of the user to evaluate and validate the query to be used for specific applications. 8. Click Next. The Create Quantitation Set - Select Method page opens. 9. Click Choose Existing Method. 10. Select PK Data_Mix.qmf from the Method list. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 93 / 195...

  • Page 94: Create A Standard Query (Optional)

    2. Select samples in the Create Quantitation Set - Select Samples page. 3. Click Next. 4. In the Select Settings & Query page, in the Default Query section, select Create New Standard Query. 5. Type a query name. 5500 Series of Instruments System User Guide 94 / 195 RUO-IDV-05-6768-A...
  • Page 95 Operating Instructions Analyze and Process Quantitative Data Figure 9-1 Create Quantitation Set Select Settings & Query Page 6. Click Next. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 95 / 195...
  • Page 96 If the concentrations were not specified during acquisition, then they are not shown here. Type the concentrations in the Concentration column. 9. Click Next. 5500 Series of Instruments System User Guide 96 / 195...

  • Page 97: Results Table Right-Click Menu

    Right-click in the Results Table to access the options shown in Table 9-1. Table 9-1 Results Table Right-click Menu Menu Function Full Shows all the columns. Summary Shows specific columns. Analyte Shows a specific analyte. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 97 / 195...

  • Page 98: Peak Review And Manual Integration Of Peaks

    To help the software find a peak, define the exact start and end points of the peak and background manually. These changes will apply only to that individual peak unless the global method is updated. 5500 Series of Instruments System User Guide...
  • Page 99 5. In the Peak Review Options dialog, in the Appearance section, change Num. rows to 1 and Num. columns to 2. 6. In the Automatic Zooming section, click Zoom Y axis to: 100% of largest peak to show the entire peak. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 99 / 195...
  • Page 100 In this example, the peak can be integrated closer to the baseline by selecting the Specify Parameters option. Tip! To move to a specific peak in the Peak Review pane, select the corresponding row in the Results Table. 5500 Series of Instruments System User Guide 100 / 195...
  • Page 101 Operating Instructions Analyze and Process Quantitative Data Figure 9-6 Peak Review Pane System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 101 / 195...
  • Page 102 Note: The Update Method function only updates the algorithm values for that specific analyte (or internal standard) and not all analytes. 15. To update the algorithm for all peaks, right-click in the pane and then click Update Method. 5500 Series of Instruments System User Guide 102 / 195...

  • Page 103: Manually Integrate Peaks

    1. In the Peak Review pane, click Manual Integration Mode. Figure 9-9 Peak Review Pane: Manual Integration 2. Zoom in on the lower 10% of the peak. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 103 / 195...

  • Page 104: Peak Review Right-Click Menu

    Tip! If a peak was correct as originally selected, right-click the peak and then click Revert to Method. Peak Review Right-Click Menu Right-click in the Peak Review window or pane to access the options shown in Table 9-2. 5500 Series of Instruments System User Guide 104 / 195 RUO-IDV-05-6768-A...

  • Page 105: Calibration Curves

    Plot a calibration curve to see the curve used for regression. The Calculated Concentration field in the Results Table reflects any changes resulting from the fit of the curve to the points of the standard. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 105 / 195...
  • Page 106 4. To change the regression options for the calibration curve, do the following: a. Click Regression. Figure 9-12 Regression Options Dialog b. Select Linear in the Fit list. c. Select 1 / x in the Weighting list. d. Click OK. 5500 Series of Instruments System User Guide 106 / 195 RUO-IDV-05-6768-A...

  • Page 107: Overlay Calibration Curves

    The software plots the curves for all selected tables on the same graph. Calibration Curve Right-Click Menu Right-click in the Calibration window or pane table to access the options shown in Table 9-3. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 107 / 195...

  • Page 108: Sample Statistics

    QCs. 1. Open a Results Table. 2. Click Tools > Statistics. 3. Select Concentration from the Statistics Metric list. 4. Select an analyte in the Analyte Name field. 5500 Series of Instruments System User Guide 108 / 195 RUO-IDV-05-6768-A...

  • Page 109: Compare Results Between Batches

    The software sorts the results. At the end of each batch or group, one or two additional rows are shown: All (statistics for all Results Tables in that group) and Average (statistics on the statistics for that batch or group). System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 109 / 195...

  • Page 110: Chapter 10 Operating Instructions Analyze And Explore Data

    The data acquired from the sample is shown. If data is still being acquired, then the mass spectrum, DAD/UV trace, and TIC continue to update automatically. Navigate Between Samples in a Data File Note: If samples were saved in separate data files, then open each file individually. 5500 Series of Instruments System User Guide 110 / 195 RUO-IDV-05-6768-A...

  • Page 111: View Experimental Conditions

    Selects all the data in the pane. Save To File Saves data as an rtf file. Font Changes the font. Save Acquisition Method Saves the acquisition method as a dam file. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 111 / 195...

  • Page 112: Show Data In Tables

    Deletes the selected pane. Show Data in Tables 1. Open a data file. 2. Click Explore > Show > Show List Data. The data is shown in a pane below the graph. 5500 Series of Instruments System User Guide 112 / 195 RUO-IDV-05-6768-A...
  • Page 113 Operating Instructions Analyze and Explore Data Figure 10-1 Peak List Tab System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 113 / 195...

  • Page 114: Show Adc Data

    3. In the Data Files field, double-click Devices and then click Adc16chan.wiff. 4. In the Samples list, select a sample, and then click OK. 5. Click Explore > Show > Show ADC Data. 5500 Series of Instruments System User Guide 114 / 195...

  • Page 115: Show Basic Quantitative Data

    The ADC data is shown in a new pane beneath the active pane. Show Basic Quantitative Data 1. Open a data file. 2. Click Explore > Show > Show List Data. Figure 10-3 List Data System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 115 / 195...

  • Page 116: Chromatograms

    It consists of the summed absorbances of all ions in a scan plotted against time in a chromatographic pane. 5500 Series of Instruments System User Guide 116 / 195...

  • Page 117: Show Tics From A Spectrum

    2. Click Explore > Show > Show Spectrum. The spectrum opens in a new pane. Tip! Double-click in the TIC pane at a particular time to show the spectrum. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 117 / 195...

  • Page 118: About Generating Xics

    Several methods are available for extracting ions to generate an XIC, depending on whether chromatographic or spectral data is used. Table 10-5 contains a summary of methods that can be used with chromatograms and spectra. 5500 Series of Instruments System User Guide 118 / 195 RUO-IDV-05-6768-A...

  • Page 119: Generate An Xic Using A Selected Range

    Generate an XIC Using the Maximum Peak 1. Open a data file containing spectra. 2. Select a range in a spectrum. The selection is indicated in blue. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 119 / 195...

  • Page 120: Generate An Xic Using Base Peak Masses

    Extract Ion by Selecting Masses 1. Open a spectrum or chromatogram. 2. Click Explore > Extract Ions > Use Dialog. 5500 Series of Instruments System User Guide 120 / 195 RUO-IDV-05-6768-A...

  • Page 121: Generate Bpcs

    Generate BPCs BPCs can be generated only from single-period, single-experiment data. 1. Open a data file. 2. Select an area within a TIC. The selection is indicated in blue. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 121 / 195...
  • Page 122 • In the Start Time field, type the time that determines the start of the experiment. • In the End Time field, type the time that determines the end of the experiment. 9. Click OK. The BPC is generated in a new pane. 5500 Series of Instruments System User Guide 122 / 195 RUO-IDV-05-6768-A...

  • Page 123: Generate Xwcs

    3. Click Explore > Show > Show DAD Spectrum. The DAD spectrum opens in a pane below the TWC. The Y-axis shows the absorbance and the X-axis shows the wavelength. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 123 / 195...

  • Page 124: Generate Twcs

    The graph updates to show the new threshold. Peak labeling and the peak list are also updated. Tip! To view the current threshold value, move the pointer over the threshold handle. 5500 Series of Instruments System User Guide 124 / 195...

  • Page 125: Chromatogram Panes

    Locks or unlocks the subtract ranges. If the subtract ranges are not locked, then each subtract range can be moved independently. The subtract ranges are preset to locked. Delete Pane Deletes the selected pane. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 125 / 195...

  • Page 126: Spectra Panes

    Searches the library using the criteria typed in Search Constraints dialog. Graphical Data Processing Graphical data can be processed many ways. This section provides information and procedures for using some of the most commonly used tools. 5500 Series of Instruments System User Guide 126 / 195 RUO-IDV-05-6768-A...

  • Page 127: Graphs

    XIC to the BPC from which it was extracted. Zooming in the BPC also zooms the XIC, so that both chromatograms are shown with the same magnification. • Use the following menu options or icons to manage data in graphs. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 127 / 195...
  • Page 128 Select the graph. Click Window > Delete Pane. Lock a pane Select the graph. Click Window > Lock Panes. Hide a pane Select the graph. Click Window > Hide Pane. 5500 Series of Instruments System User Guide 128 / 195 RUO-IDV-05-6768-A...

  • Page 129: Zoom In On The Y-Axis

    1. Move the pointer under the X-axis to either side of the area to be expanded and then drag away from the starting point in a horizontal direction while holding the left mouse button. 2. Release the mouse button to draw the graph to the new scale. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 129 / 195...

  • Page 130: Chapter 11 Reporter Software

    • By a batch script to automate report generation within a batch. Users can generate reports on a sample-by-sample basis, either during or after batch acquisition. ® • By applications that do not use the Analyst software. 5500 Series of Instruments System User Guide 130 / 195 RUO-IDV-05-6768-A...

  • Page 131: Analyst Reporter User Interface

    Reporter Software Analyst Reporter User Interface Figure 11-1 Analyst Reporter System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 131 / 195...
  • Page 132 Shows a list of available report templates. Selecting a template will show a description of the template. To change the folder from which available templates are read, select Settings > Select Template Folder > Browse. 5500 Series of Instruments System User Guide 132 / 195 RUO-IDV-05-6768-A...

  • Page 133: Generate Reports

    For more information about batch scripts, refer to the Scripts User Guide. 1. Open a Results Table. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 133 / 195...
  • Page 134 Results Table. Some reports can take seconds to generate, others can take longer. A large data set with many MRM transitions or a large number of graphics might result in reports of several hundred pages that take hours to generate. 5500 Series of Instruments System User Guide 134 / 195...

  • Page 135: Chapter 12 Operating Instructions Batches

    Standby mode. For information about the other fields in the Queue Options dialog, refer to the Help. 1. On the Navigation bar, click Configure. 2. Click Tools > Settings > Queue Options. Figure 12-1 Queue Options Dialog System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 135 / 195...

  • Page 136: Create And Submit A Batch

    A set can consist of a single sample or multiple samples. Note: For more information about adding quantitation information to a batch, refer to the Advanced User Guide. 1. On the Navigation bar, under Acquire, double-click Build Acquisition Batch. 5500 Series of Instruments System User Guide 136 / 195 RUO-IDV-05-6768-A...
  • Page 137 2. In the Sample tab, in the Set list, type a name. 3. Click Add Set. 4. Click Add Samples to add samples to the new set. Figure 12-3 Add Sample Dialog System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 137 / 195...
  • Page 138 15. To change the injection volumes from the volumes listed in the method, in the Inj. Volume (µL) column, type the injection volume for each sample. 16. To set sample locations, do one of the following: 5500 Series of Instruments System User Guide 138 / 195...

  • Page 139: Equilibrate The System

    3. Type the equilibration time in the Time (min) field, in minutes. 4. Select OK. The system starts the equilibration. After the equilibration is completed, the system will change to Ready status. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 139 / 195...

  • Page 140: Submit A Sample Or Set Of Samples

    Standby mode, then sample acquisition will start automatically. 1. Make sure that the column oven temperature is reached. 5500 Series of Instruments System User Guide 140 / 195...

  • Page 141: Set Sample Locations In The Batch Editor

    • In the Plate Position column, select the position of the plate on the rack. • In the Vial Position column, type the position of the vial in the plate or tray. 3. Save the file. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 141 / 195...

  • Page 142: Select Vial Positions Using The Locations Tab (Optional)

    If the button shows a red horizontal line, then the Batch Editor marks the samples by row. If the button shows a red vertical line, then the Batch Editor marks the samples by column. 5500 Series of Instruments System User Guide...

  • Page 143: Set Quantitation Details In The Batch Editor (Optional)

    The queue stops after the current scan in the selected sample is complete. The sample status in the Queue Manager (Local) window changes to Terminated, and all other samples following in the queue are Waiting. 4. To continue processing the batch, click Acquire > Start Sample. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 143 / 195...

  • Page 144: Import Batch Files

    1. In the Batch Editor, in the Sample tab, right-click, and then click Import From > File. The Open dialog opens. 2. Click the required text file and then click Open. 5500 Series of Instruments System User Guide 144 / 195...

  • Page 145: Batch Editor Right-Click Menu

    Imports a file. Save As Batch Saves the batch with a different name. Save As a Template Saves the batch as a template. Hide/Show Column Hides or shows a column. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 145 / 195...

  • Page 146: Queue States And Device Status

    The first icon indicates the queue state. The second icon indicates whether the queue is in Tune mode (for tuning) or Normal mode (for running samples). Table 12-1 describes the icons and queue states. 5500 Series of Instruments System User Guide 146 / 195 RUO-IDV-05-6768-A...

  • Page 147: View Instrument And Device Status Icons

    Icons representing the mass spectrometer and each device in the active hardware configuration are shown on the status bar in the bottom right corner of the window. The user can view the detailed status of an LC pump to System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 147 / 195...

  • Page 148: Queue Right-Click Menu

    The device is not running, but is ready to run. Error The device has encountered an error that should be investigated. Queue Right-click Menu Right-click in the Queue table to access the options. 5500 Series of Instruments System User Guide 148 / 195 RUO-IDV-05-6768-A...
  • Page 149 Delete Deletes either the batch or the selected samples. Move Batch Moves the batch within the queue. Sort Sorts on the preselected column. Column Settings Changes the column settings. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 149 / 195...

  • Page 150: Chapter 13 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 151 Refer to the ion source Operator needle Guide. Turbo heater As needed Replace Contact the local QMP or FSE. Sample tubing As needed Replace Refer to the ion source Operator Guide. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 151 / 195...

  • Page 152: Clean The Surfaces

    Clean the mass spectrometer front-end using the routine cleaning method, to: • Minimize unscheduled system downtime. • Maintain optimum sensitivity. • Avoid more extensive cleaning that requires a service visit. 5500 Series of Instruments System User Guide 152 / 195 RUO-IDV-05-6768-A...

  • Page 153: Symptoms Of Contamination

    • 1:1 acetonitrile:water with 0.1% acetic acid solution (freshly prepared) • Clean 1 L or 500 mL glass beaker to prepare cleaning solutions • 1 L beaker to catch used solvent • Organic waste container System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 153 / 195...

  • Page 154: Cleaning Best Practices

    • Always wear clean, powder-free gloves (nitrile or neoprene recommended) for the cleaning procedures. • After cleaning the mass spectrometer components, and before reassembling them, put on a new, clean pair of gloves. 5500 Series of Instruments System User Guide 154 / 195...

  • Page 155: Prepare The Mass Spectrometer

    WARNING! Hot Surface Hazard. Let the ion source cool for at least 30 minutes before starting any maintenance procedures. Surfaces of the ion source and the vacuum interface components become hot during operation. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 155 / 195...

  • Page 156: Clean The Curtain Plate

    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. 5500 Series of Instruments System User Guide 156 / 195...

  • Page 157: Clean The Front Of The Orifice Plate

    1. Install the curtain plate on the mass spectrometer. 2. Install the ion source on the mass spectrometer. Refer to the ion source Operator Guide. 3. Activate the hardware profile. Refer to the System User Guide. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 157 / 195...

  • Page 158: 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 159 Connection to the mass spectrometer: 1.6 cm (0.625 inch) i.d. Note: Source exhaust hose connections at the drain bottle, mass spectrometer, and the lab vent are secured with hose clamps. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 159 / 195...

  • Page 160: 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 161: Chapter 14 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 14-1 System Issues...
  • Page 162 9. If the O-rings are on the ion source, then install them on the vacuum interface. If they are missing, then contact an FSE. 10. Troubleshoot the LC system. 5500 Series of Instruments System User Guide 162 / 195 RUO-IDV-05-6768-A...
  • Page 163 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 164: Appendix A Operating Instructions Manual Compound Optimization

    Manual compound optimization is used to optimize compound- and ion source-dependent parameters for an analyte. When the user manually optimizes for an analyte, an MS acquisition method is created in Tune and 5500 Series of Instruments System User Guide 164 / 195...

  • Page 165: About Scan Types

    Determine the Product Ions for Optimization on page 168 Optimize Collision Cell Exit Potential for each Product Ion on page 170 Confirm the Presence of Compounds 1. Create a project. 2. Activate the hardware profile. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 165 / 195...
  • Page 166 11. Select the MCA check box. 12. Type 10 In the Cycles field. 13. Click Start. 14. When ten scans are complete, the masses of the four compounds are shown as ions. 5500 Series of Instruments System User Guide 166 / 195 RUO-IDV-05-6768-A...

  • Page 167: Optimize Ms-Specific Parameters

    Time Reserpine 609.4 Minoxidil 210.2 Tolbutamide 271.3 Rescinnamine 635.4 Start with reserpine for a simple case. Repeat the manual optimization process for the remaining compounds. 3. Click Edit Ramp. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 167 / 195...

  • Page 168: Determine The Product Ions For Optimization

    Rarely optimize this parameter because it has a smaller effect. Determine the Product Ions for Optimization The collision energy (CE) controls the amount of energy that the precursor ions receive as they are accelerated into the collision cell. 5500 Series of Instruments System User Guide 168 / 195 RUO-IDV-05-6768-A...
  • Page 169 We recommend that two or three product ions be optimized for each compound. The additional transitions can be used for confirmation, or to avoid the need to re-optimize a compound in case an interference is found. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 169 / 195...

  • Page 170: Optimize Collision Cell Exit Potential For Each Product Ion

    13. Repeat if other product ions were monitored. 14. Add the optimized values to the appropriate row. 15. Save the method. 16. Repeat this procedure for any other compounds that were previously optimized. 5500 Series of Instruments System User Guide 170 / 195 RUO-IDV-05-6768-A...

  • Page 171: Manually Optimize The Ion Source And Gas Parameters

    Use the following procedure to optimize the Curtain Gas flow parameter. The main function of the Curtain Gas flow parameter is to prevent the contamination of the ion optics. The Curtain Gas flow parameter should always System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 171 / 195...

  • Page 172: Advanced Parameters

    The AF2 parameter controls the fragmentation of the second precursor ion in an MS3 scan. The amount of excitation energy used depends on the compound and the desired amount of fragmentation. 5500 Series of Instruments System User Guide 172 / 195...

  • Page 173: About Collision Energy Spread (Ces)

    (CES) field allows users to specify the difference in collision energies that will be applied in the experiment. For example, if CE value of 30 and a CES value of 15 are used, then collision energies of 15, 30, and 45 are used. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 173 / 195...

  • Page 174: Appendix B 5500 Series System Parameters

    5500 Series System Parameters The first number under each scan type is the preset value. The range of numbers is the accessible range for each parameter. Table B-1 5500 Series System Parameters Parameter Access ID Positive Ion Mode Negative Ion Mode...
  • Page 175 5500 Series System Parameters Table B-1 5500 Series System Parameters (continued) Parameter Access ID Positive Ion Mode Negative Ion Mode MS/MS MS/MS –1 –1 (IE1 = Q0 – 0 to 3 0 to 3 –3 to –0 –3 to –0 RO1) Q0+ (–10)
  • Page 176 5500 Series System Parameters Table B-1 5500 Series System Parameters (continued) Parameter Access ID Positive Ion Mode Negative Ion Mode MS/MS MS/MS 0 to 90 0 to 90 0 to 90 0 to 90 0 to 90 0 to 90...

  • Page 177: Appendix C Calibration Ions And Solutions

    Every 2 weeks, as Both 3 months to 6 Automated only required months Table C-2 Suggested Tuning Solutions for the 5500 Series of Instruments System Q1 and Q3 Positive Negative Positive and Negative SCIEX Triple Quad 5500 POS PPG, 2e-7 M...
  • Page 178 Calibration Ions and Solutions Table C-3 Q1 and Q3 PPG Ion Scans Polarity Masses Positive 59.05 175.13 616.46 906.67 1080.80 1196.88 Negative 45.00 585.39 933.64 1223.85 1572.10 5500 Series of Instruments System User Guide 178 / 195 RUO-IDV-05-6768-A...
  • Page 179 Calibration Ions and Solutions ® Table C-4 LIT Scans for the QTRAP 5500 LC-MS/MS System (Agilent) Polarity Masses Positive 118.09 322.05 622.03 922.01 Negative 112.99 431.98 601.98 System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 179 / 195...

  • Page 180: Appendix D Toolbar Icons

    Click to open the DAD Method Editor. Refer to Generate DAD Data on page 123. Click to open the ADC Properties tab. Refer to Show ADC Data on page 114. 5500 Series of Instruments System User Guide 180 / 195 RUO-IDV-05-6768-A...
  • Page 181 Selects the method to be used to equilibrate the devices. This method should be the same as the method used with the first sample in the queue. Standby Puts the instrument in Standby mode. Ready Puts the instrument in Ready mode. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 181 / 195...
  • Page 182 Status for Remote Views the status of a remote instrument. Instrument Reserve Reserves the instrument for tuning and calibrating. Instrument for Tuning IDA Method Starts the IDA Method Wizard. Wizard 5500 Series of Instruments System User Guide 182 / 195 RUO-IDV-05-6768-A...
  • Page 183 Offset Graph Compensates for slight differences in the time during which the ADC data and the mass spectrometer data were recorded. This is useful when overlaying graphs for comparison. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 183 / 195...
  • Page 184 Extracts up to three wavelength ranges from a DAD spectrum to view the XWC. Wavelength Table D-6 Explore Toolbar Quick Reference: Overlaying Graphs Icon Name Description Home Graph Click to return the graph to the original scale. Overlay Click to overlay graphs. 5500 Series of Instruments System User Guide 184 / 195 RUO-IDV-05-6768-A...
  • Page 185 Click to generate a spectrum from a TIC. Copy Graph to Click to copy the active graph to a new window. new Window Baseline Subtract Click to open the Baseline Subtract dialog. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 185 / 195...
  • Page 186 DAD, a contour plot can display selected data as either a DAD spectrum or an XWC. Show DAD TWC Click to generate a TWC of the DAD. 5500 Series of Instruments System User Guide 186 / 195 RUO-IDV-05-6768-A...
  • Page 187 Lock Or Unlock Column Locks or unlocks the selected column. A locked column cannot be moved. Metric Plot By Selection Creates a metric plot from the selected column. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 187 / 195...
  • Page 188 Shows the audit trail for the Results Table. Clear Audit Trail Clears the audit trail for the Results Table. This functionality is not available. Statistics Opens the Statistics window. Report Generator Opens the Reporter software. 5500 Series of Instruments System User Guide 188 / 195 RUO-IDV-05-6768-A...

  • Page 189: Appendix E Glossary Of Symbols

    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 5500 Series of Instruments RUO-IDV-05-6768-A 189 / 195...
  • Page 190 TUV Rheinland of North America. Data Matrix symbol that can be scanned by a barcode reader to obtain a unique device identifier (UDI). Ethernet connection Explosion Hazard Fire Hazard Fragile Fuse Hertz 5500 Series of Instruments System User Guide 190 / 195 RUO-IDV-05-6768-A...
  • Page 191 Glossary of Symbols Symbol Description 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 192 Transport and store the system within –30 °C to +45 °C. 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) 5500 Series of Instruments System User Guide 192 / 195 RUO-IDV-05-6768-A...
  • Page 193 Glossary of Symbols Symbol Description Volts (voltage) WEEE. Do not dispose of equipment as unsorted municipal waste. Watts yyyy-mm-dd Date of manufacture System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 193 / 195...

  • Page 194: Appendix F 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 195 WARNING: NO USER SERVICEABLE PARTS INSIDE. WARNING: NO USER SERVICEABLE PARTS INSIDE. REFER SERVICING TO QUALIFIED PERSONNEL. REFER SERVICING TO QUALIFIED PERSONNEL. Note: Consult instructions for use. System User Guide 5500 Series of Instruments RUO-IDV-05-6768-A 195 / 195...

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