SCIEX 6500 Series System User's Manual
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SCIEX 6500 Series System User's Manual

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6500 and 6500+ Series of Instruments
System User Guide
RUO-IDV-05-2095-A
August 2015

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Summary of Contents for SCIEX 6500 Series

  • Page 1 6500 and 6500+ Series of Instruments System User Guide RUO-IDV-05-2095-A August 2015...
  • 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 Chapter 1 Operational Precautions and Limitations................8 General Safety Information..............................8 Regulatory Compliance..............................8 Australia and New Zealand............................8 Canada..................................9 Europe..................................9 United States................................9 International................................10 Electrical Precautions...............................10 AC Mains Supply................................10 Protective Earth Conductor............................11 Chemical Precautions...............................11 System Safe Fluids..............................12 Ventilation Precautions..............................13 Environmental Precautions..............................14 Electromagnetic Environment............................15 Decommissioning and Disposal..........................15 Qualified Personnel................................16 Equipment Use and Modification.............................16...
  • Page 4 Contents Plumb the Mass Spectrometer ............................47 Adjust the Integrated Syringe Pump Position......................47 Plumb the Diverter Valve in Injector Mode........................50 Plumb the Diverter Valve in Diverter Mode........................52 Chapter 6 Operating Instructions Hardware Profiles and Projects...........54 Hardware Profiles................................54 Create a Hardware Profile............................54 Add Devices to a Hardware Profile..........................58 Troubleshoot Hardware Profile Activation.........................59 Projects and Subprojects..............................60...
  • Page 5 Contents Acquire Data..................................91 Set Sample Locations in the Batch Editor.........................91 Select Vial Positions Using the Locations Tab (Optional)....................92 Set Quantitation Details in the Batch Editor (Optional)....................93 Stop Sample Acquisition..............................94 Import and Submit Batch Files............................94 Build a Batch as a Text File............................94 Import a Batch as a Text File............................95 Batch Editor Right-click Menu............................95 Queue States and Device Status............................96...
  • Page 6 Contents Extract Ion by Selecting Masses..........................125 Generate BPCs................................126 Generate XWCs................................127 Generate DAD Data...............................127 Generate TWCs................................128 Adjust the Threshold..............................128 Chromatogram Panes..............................129 Spectra Panes................................130 Data Processing................................130 Graphs...................................131 Manage Data................................131 Zoom In on the Y-axis..............................133 Zoom In on the X-axis..............................133 Chapter 13 Reporter Software.......................134 Reporter User Interface..............................135 Generate Reports................................137 Chapter 14 Service and Maintenance Information................138...
  • Page 7 Contents Revision History............................173 Index................................174 System User Guide 6500 and 6500+ Series of Instruments RUO-IDV-05-2095-A 7 of 181...

  • Page 8: Chapter 1 Operational Precautions And Limitations

    Operational Precautions and Limitations Note: Before operating the system, carefully read all 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 9: Canada

    Operational Precautions and Limitations • Safety: AS/NZ 61010-1 and IEC 61010-2-061 Canada • Electromagnetic Interference (EMI): CAN/CSAA CISPR11. This ISM device complies with Canadian ICES-001. • Safety: CAN/CSA C22.2 No. 61010-1 and CAN/CSA C22.2 No 61010-2-061 Europe • Electromagnetic Compatibility (EMC): Electromagnetic Compatibility directive 2004/108/EC as implemented in these standards: •...

  • Page 10: International

    WARNING! Electrical Shock Hazard. Do not remove the covers. Removing the covers might cause injury or malfunctioning of the system. The covers need not be removed for routine maintenance, inspection, or adjustment. Contact the SCIEX FSE for repairs that require the covers to be removed.

  • Page 11: Protective Earth Conductor

    This supplementary grounding will reinforce the safety configuration specified by SCIEX. Chemical Precautions WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Determine whether mass spectrometer decontamination is required prior to cleaning or maintenance.

  • Page 12: System Safe Fluids

    CAUTION: Potential System Damage. Do not use any other fluid until confirmation is received from SCIEX that it will not present a hazard. This is not an exhaustive list. • Organic Solvents • MS-grade acetonitrile; up to 100% •...

  • Page 13: Ventilation Precautions

    Operational Precautions and Limitations • Acids and Bases • Formic Acid; less than 1% • Acetic Acid; less than 1% • Trifluoroacetic Acid; (TFA) less than 1% • Heptafluorobutyric Acid; (HFBA) less than 1% • Ammonia/Ammonium Hydroxide; less than 1% •...

  • Page 14: Environmental Precautions

    Hazard. Discontinue use of the ion source if the ion source window is cracked or broken and contact an SCIEX Field Service Employee. Any toxic or injurious materials introduced into the equipment will be present in the ion source and exhaust output.

  • Page 15: Electromagnetic Environment

    Operational Precautions and Limitations Electromagnetic Environment Electromagnetic Compatibility Basic Electromagnetic Environment: Environment existing at locations characterized by being supplied directly at low voltage from the public mains network. Performance Criteria A (Criteria A): Equipment shall operate as intended with no degradation of performance and no loss of function during or after test.

  • Page 16: Qualified Personnel

    Qualified Personnel Only qualified SCIEX personnel shall install 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: Contact Us

    The guides and tutorials for the Analyst software are installed automatically with the software and are available from the Start menu: All Programs > SCIEX > Analyst. A complete list of the available documentation can be found in the Help. To view the Help, press F1.

  • Page 18: Chapter 2 Hazard Symbols

    Hazard Symbols This section lists the hazard symbols and conventions used in the laboratory environment, on the system, and in the documentation. Occupational Health and Safety Symbols This section describes some occupational health and safety symbols found in the documentation and laboratory environment.
  • Page 19 Hazard Symbols Table 2-3 Electrical Hazard Warning Symbols Safety Symbol Definition Electrical Shock Hazard Table 2-4 Pressurized Gas Hazard Warning Symbols Safety Symbol Definition Pressurized Gas Hazard Table 2-5 Mechanical Hazard Symbols Safety Symbol Definition Hot Surface Hazard Puncture Hazard Table 2-6 Radiation Hazard Symbols Safety Symbol Definition...

  • Page 20: Symbols, Indicators, And Labels: Packaging

    Hazard Symbols Symbols, Indicators, and Labels: Packaging Table 2-7 Labels on the Mass Spectrometer Shipping Materials Label/Symbol Definition Tilt Indicator 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.
  • Page 21 IMPORTANT! RECORD ANY VISIBLE CRATE DAMAGE INCLUDING TRIPPED “IMPACT INDICATOR” OR “TILT INDICATOR” ON THE WAYBILL BEFORE ACCEPTING SHIPMENT AND NOTIFY YOUR LOCAL SCIEX CUSTOMER SUPPORT ENGINEER IMMEDIATELY. DO NOT UNCRATE. CONTACT YOUR LOCAL CUSTOMER SUPPORT ENGINEER FOR UNCRATING AND INSTALLATION.

  • Page 22: Symbols, Indicators, And Labels: Mass Spectrometer

    Hazard Symbols Symbols, Indicators, and Labels: Mass Spectrometer Refer to Panel Symbols on page 25 for more information. Table 2-8 Labels on the Mass Spectrometer Label Definition WARNING: No user serviceable parts inside. Refer servicing to qualified personnel. Consult instructions for use. Do not dispose of equipment as unsorted municipal waste (WEEE).

  • Page 23: Documentation Symbols And Conventions

    Hazard Symbols Table 2-8 Labels on the Mass Spectrometer (continued) Label Definition Volt Ampere (power) WARNING: Do not operate without first ensuring bottle cap is secured. This warning appears on the source exhaust waste bottle. Documentation Symbols and Conventions The following symbols and conventions are used throughout the guide. DANGER! Danger signifies an action which leads to severe injury or death.

  • Page 24: Chapter 3 Principles Of Operation

    Chemical Ionization (APCI) probe. Refer to the IonDrive Turbo V Ion Source Operator Guide. ® • A SCIEX-supplied computer and monitor with the Analyst software for instrument optimization, acquisition method development, and data acquisition and processing. For computer specifications and requirements, ®...

  • Page 25: Hardware Overview

    Adjust the Integrated Syringe Pump Position on page Ion source IonDrive Turbo V Ion Source Operator Guide, available from the ion source documentation CD, or from the SCIEX Web site, at sciex.com Diverter valve Plumb the Diverter Valve in Diverter Mode on page...
  • Page 26 Principles of Operation Table 3-1 Panel Symbols Color Name Description Green Power Lit when the system is powered up. Green Vacuum Lit when the correct vacuum has been achieved. Flashing if the vacuum is not at the correct vacuum (during pump down and venting). Green Ready Lit when the system is in the Ready state.
  • Page 27 Principles of Operation Figure 3-2 Back and Side Views Item Description Primary Materials For more information... Roughing pump vacuum Aluminum (hose fitting), Contact an FSE. connection zinc-plated steel (hose clamp) Nitrogen gas supply Plastic Refer to the Site Planning Guide. (Curtain Gas supply, CAD gas)

  • Page 28: Theory Of Operation-Hardware

    Principles of Operation Item Description Primary Materials For more information... Mains supply connection Aluminum/plastic Refer to Start Up the System on page Shut Down the System on page Mass spectrometer Plastic Refer to Start Up the System on page convenience switch Shut Down the System on page (Up = On;...
  • Page 29 Principles of Operation Figure 3-3 Ion Path Item Description Orifice plate QJet ion guide Q0 region Q1 quadrupole Q2 collision cell Q3 quadrupole Detector The Q1 quadrupole is a filtering quadrupole that sorts the ions before they enter the Q2 collision cell. The Q2 collision cell is where the internal energy of an ion is increased through collisions with gas molecules to the point that molecular bonds break creating product ions.

  • Page 30: Analyst Software Overview

    Principles of Operation During the collection phase, ions pass through the Q2 collision cell where the CAD gas focuses the ions into the Q3 region. The Q3 quadrupole is operated with only the main RF voltage applied. Ions are prevented from passing through the Q3 quadrupole rod set and are reflected back by an exit lens to which a DC barrier voltage is applied.
  • Page 31 Principles of Operation Figure 3-4 Example TIC Extracted Ion Chromatogram (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.
  • Page 32 Principles of Operation Figure 3-5 Example XIC Parameters The working parameters are the set of instrument parameters currently being used. • Source and gas parameters: (Ion source-dependent) These parameters can change depending on the ion source used. • Compound parameters: These parameters consist mostly of voltages in the ion path. Optimal values for compound-dependent parameters vary depending on the compound being analyzed.
  • Page 33 Principles of Operation Figure 3-6 Ion Optics Path and Parameters Location Parameter Parameter Scan Type Type IonSpray Source and gas The IS parameter controls the voltage Voltage (IS) applied to the electrode in the ® TurboIonSpray probe that ionizes the sample in the ion source.
  • Page 34 Principles of Operation Location Parameter Parameter Scan Type Type Interface Source and gas The IHT parameter controls the temperature ® Heater of the NanoSpray interface heater and is ® Temperature only available if the NanoSpray ion source (IHT) is installed. The optimal heater temperature depends on the type of sample being analyzed and the solvent used.
  • Page 35 Principles of Operation Location Parameter Parameter Scan Type Type Declustering Compound The DP parameter controls the voltage on Potential the orifice, which controls the ability to (DP) decluster ions between the orifice and the IonDrive QJet ion guide. It is used to minimize the solvent clusters that might remain on the sample ions after they enter the vacuum chamber, and, if required, to...
  • Page 36 Principles of Operation Location Parameter Parameter Scan Type Type CAD Gas Source and gas The CAD parameter controls the pressure of Q3 MI, Q3 MS, MRM, the CAD gas in the collision cell during Q3, Prec, NL, EMS, ER, MS/MS, and LIT scans. For Q3 scans, the EPI, MS/MS/MS, collision gas helps to focus the ions as they EMC, and TDF...
  • Page 37 Principles of Operation Location Parameter Parameter Scan Type Type Collision Compound The CXP parameter is only used in Q3 and Q3, MRM, MS2, Prec, Cell Exit MS/MS scan types. This parameter transmits and NL Potential the ions into the Q3 quadrupole. (CXP) Use the preset value and optimize for the compound.

  • Page 38: Theory Of Operation-Analyst Software

    Principles of Operation Location Parameter Parameter Scan Type Type Dynamic Fill Compound The DFT parameter dynamically calculates EMS, EPI, ER, and Time (DFT) the amount of time that ions are collected MS/MS/MS in the linear ion trap based on the incoming ion signal.
  • Page 39 Principles of Operation The software has two integration algorithms that can be used: MQ4 and SignalFinder1. The MQ4 algorithm selects a low concentration, but not the lowest concentration, standard or quality control sample by default as the representative sample of the analytical run. The SignalFinder algorithm selects a high concentration, but not saturated, standard or quality control sample by default as the representative sample of the analytical run.
  • Page 40 Principles of Operation • Linear (y = mx + b) • Linear through Zero (y = mx) • Quadratic (y = a2 + bx + c) As well, it is possible to add different types of weighting for the regression, including: •...

  • Page 41: Chapter 4 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 54 Each hardware profile must include a mass spectrometer. Only devices included in the active hardware profile can be used when creating...
  • Page 42 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 60 experiment, decide where to store the files related to the experiment.
  • Page 43 Operating Instructions Sample Workflows Table 4-2 Sample Acquisition Workflow (continued) Step To do this... Find the information in..What does it do? Analyze data in Explore mode. Operating Instructions — Analyze and In Explore mode, many Process Data on page 117 tools are available for —OR—...

  • Page 44: Chapter 5 Operating Instructions Hardware

    WARNING! 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 AC mains supply outlet in an emergency.
  • Page 45 Operating Instructions Hardware Note: Before operating the instrument, read the safety information in Operational Precautions and Limitations on page Prerequisites • The site requirements specified in the Site Planning Guide are met. The Site Planning Guide includes information on the mains supply and connections, ion source exhaust, compressed air, nitrogen, roughing pump, ventilation, exhaust, and site clearance.

  • Page 46: Reset The Mass Spectrometer

    Operating Instructions Hardware Figure 5-1 Roughing Pump On/Off Switch 2. Wait five minutes, and then turn on the mass spectrometer convenience switch. 3. Turn on the computer, if it is not on. ® 4. Start the Analyst software. Reset the Mass Spectrometer 1.

  • Page 47: Plumb The Mass Spectrometer

    Operating Instructions Hardware CAUTION: Potential System Damage. Turn off the sample flow before the system is shut down. 2. Turn off the sample flow to the system. ® 3. In the Analyst software, deactivate the hardware profile, if it is active. 4.
  • Page 48 Operating Instructions Hardware 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. Figure 5-2 Lowering the Syringe Item Description Syringe plunger Release button. Press to raise or lower the base. 3.
  • Page 49 Operating Instructions Hardware Figure 5-3 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.

  • Page 50: Plumb The Diverter Valve In Injector Mode

    Operating Instructions Hardware Figure 5-4 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. Plumb the Diverter Valve in Injector Mode The diverter valve is a two-position, six-port valve.
  • Page 51 Operating Instructions Hardware Table 5-1 Figure Legend (continued) Item Description Mobile phase in To column Figure 5-5 Diverter Valve Injector Mode Position A System User Guide 6500 and 6500+ Series of Instruments RUO-IDV-05-2095-A 51 of 181...

  • Page 52: Plumb The Diverter Valve In Diverter Mode

    Operating Instructions Hardware Figure 5-6 Diverter Valve Injector Mode Position B Plumb the Diverter Valve in Diverter Mode The diverter valve can be plumbed in injector mode or diverter mode. To configure the valve, access the Configuration tab and then make sure that the Use integrated injector/diverter valve check box is selected.
  • Page 53 Operating Instructions Hardware Figure 5-7 Diverter Valve Diverter Mode Position A Figure 5-8 Diverter Valve Diverter Mode Position B System User Guide 6500 and 6500+ Series of Instruments RUO-IDV-05-2095-A 53 of 181...

  • Page 54: Chapter 6 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. Each hardware profile must include a mass spectrometer. Before creating an acquisition method, make sure that all devices used in the method are included in the hardware profile.
  • Page 55 Operating Instructions Hardware Profiles and Projects Figure 6-1 Hardware Configuration Editor Dialog 2. Click New Profile. System User Guide 6500 and 6500+ Series of Instruments RUO-IDV-05-2095-A 55 of 181...
  • Page 56 Operating Instructions Hardware Profiles and Projects Figure 6-2 Create New Hardware Profile Dialog 3. Type a name in the Profile Name field. 4. Click Add Device. In the Available Devices dialog, in the Device Type field, Mass Spectrometer is the preset value. 5.
  • Page 57 Operating Instructions Hardware Profiles and Projects Figure 6-3 Configuration Tab with Syringe Pump Configured 10. On the Configuration tab, in the Dual Mass Mode section, select one of the following options: • Low Mass: To operate in limited mass range, high sensitivity operating mode, select this option. The maximum mass range is 50 Da to 1250 Da for LIT (linear ion trap) scans and 5 to 1000 Da for quadrupole scans.

  • Page 58: Add Devices To A Hardware Profile

    Operating Instructions Hardware Profiles and Projects 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 59: Troubleshoot Hardware Profile Activation

    Operating Instructions Hardware Profiles and Projects 6. Click OK. 7. Select the device from the Devices in current profile list. 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. 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 60: Projects And Subprojects

    Operating Instructions Hardware Profiles and Projects 1. Read the error message generated. Depending on the message, there might be an issue with a device or how the communication is set up. 2. Verify that the device has power and is turned on. 3.

  • Page 61: Create Subprojects

    Operating Instructions Hardware Profiles and Projects 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. Click Tools > Project > Create Subproject. 3.

  • Page 62: Installed Project Folders

    Operating Instructions Hardware Profiles and Projects Figure 6-5 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 63: 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 64: Chapter 7 Operating Instructions 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 65: About The Verifying Or Adjusting Performance Dialog

    Operating Instructions Tune and Calibrate 5. Click Next. 6. Click Approved Tuning. 7. Click Next. 8. Select a Tuning Solution. Depending on the solution selected, different modes are available: a. Click a polarity. b. If available, click Q1 and Q3 in the Quad section. c.
  • Page 66 Operating Instructions Tune and Calibrate Figure 7-1 Results Summary The Results Summary includes the location of data files and instrument settings backups, as well as step-by-step changes and results during optimization. The Results Summary also shows a verification report. This report contains a snapshot of the mass spectrum for each relevant mass for the scan modes being verified.

  • Page 67: Chapter 8 Operating Instructions Automatic Optimization

    Operating Instructions Automatic Optimization This section describes how to: • Automatically optimize for the analyte using the Compound Optimization wizard. • Choose between infusion and flow injection analysis (FIA). • Use an infusion method to optimize compound-dependent parameters. • Use an FIA method to optimize compound- and ion source-dependent parameters. Prerequisites •...

  • Page 68: Types Of Sample Introduction

    Operating Instructions Automatic Optimization Types of Sample Introduction Infusion Infusion is the continuous flow of the sample at low flow rates into the ion source using a syringe pump. During the infusion optimization process, the software can select precursor and product ions and optimize for declustering potential, collision energy, and collision cell exit potential.
  • Page 69 Operating Instructions Automatic Optimization 2. Activate the hardware profile. 3. Infuse the compound in solution at a rate of 5 µL/min to 10 µL/min. 4. On the Navigation bar, under Tune and Calibrate, double-click Manual Tuning. 5. On the Syringe Pump Method Properties tab, type the parameter values shown in Table 8-2.
  • Page 70 Operating Instructions Automatic Optimization Table 8-3 MS Tab (continued) Parameter Value Duration (min) * These fields are instrument-dependent. 9. Click Start. 10. Wait until an even TIC is shown on the left and peaks are shown on the right and then click Stop. 11.

  • Page 71: Perform Automatic Ms And Ms/Ms Optimization Using Infusion With A

    Operating Instructions Automatic Optimization Perform Automatic MS and MS/MS Optimization Using Infusion with a Known Precursor Ion and an Unknown Product Ion Automatic optimization for MS/MS analysis optimizes certain compound-dependent parameters for one or more MRM transitions. The software finds the ion of interest and then optimizes the compound-dependent parameters to get the maximum sensitivity for the compound.
  • Page 72 Operating Instructions Automatic Optimization Table 8-5 Product Ion Auto Selection Criteria Dialog Parameters Parameter Value Description From the Most Intense The number of fragment peaks to be optimized. The algorithm will (peaks) generate a product ion scan spectrum while ramping the CE in MCA mode.

  • Page 73: Check The Optimization Results

    Operating Instructions Automatic Optimization Table 8-6 Target Compounds Dialog Parameters Target Field Value* Compound Reserpine Compound Name Reserpine MW (Da) 609.3 No. Charges Minoxidil Compound Name Minoxidil MW (Da) 210.2 No. Charges Tolbutamide Compound Name Tolbutamide MW (Da) 271.1 No. Charges Rescinnamine (IS) Compound Name Rescinnamine...

  • Page 74: Automatically Optimize For An Analyte Using Fia

    Operating Instructions Automatic Optimization 3. Compare the values in the text file to those in the .dam file. 4. Check the contents of the following folders: • Data: Look through all the runs executed during optimization. Compare a .wiff file with the optimized value in the method or printed parameters.
  • Page 75 Operating Instructions Automatic Optimization Figure 8-3 Acquisition Method with LC Sync Selected 3. Make sure that the ion source and gas parameters are set to reasonable levels to prevent the contamination of the mass spectrometer. 4. Set the horizontal micrometer to 5. 5.
  • Page 76 Operating Instructions Automatic Optimization Table 8-7 Instrument Settings Parameters (continued) Parameter Value Injection Volume 10 µL Mass Spectrometer MS/MS Analysis 9. Click Next. 10. Make sure that the Int. Std. check box is cleared. Selecting the check box indicates which MRM corresponds to the internal standards. Internal standards are not optimized during the optimization process.
  • Page 77 Operating Instructions Automatic Optimization 13. On the FIA Source Parameters page, type numbers that are lower or higher than the original value as long as they are still within specifications. Be sure not to go too low with any of the settings to keep the system clean.
  • Page 78 Operating Instructions Automatic Optimization Figure 8-5 Replicate Injection for each Parameter Field 15. Click Next. 16. On the FIA Compound Parameters page, type the parameters shown in Table 8-9. Note: The values in Table 8-9 are suggested values. For more information, refer to the Help. Table 8-9 FIA Compound Parameters Page Parameter Select the...
  • Page 79 Operating Instructions Automatic Optimization Table 8-9 FIA Compound Parameters Page (continued) Parameter Select the Values for Optimization Optimize Check Box? Collision Energy 20;30;40;50;70;80;100 Collision Cell Exit 2;4;6;8;10;12 Potential The total number of injections and dependent sample volume update automatically. In contrast to ion source parameters, which require one injection per value per replicate, compound-dependent parameters only require one injection per parameter.
  • Page 80 Operating Instructions Automatic Optimization Figure 8-6 Mass Spec. Duration Field 18. Click Finish to begin the optimization process. The software optimizes the specified ion source- and compound-dependent parameters to get the maximum sensitivity for the MRM transition of the compound. As the software proceeds through the optimization, it creates a Compound Optimization report.

  • Page 81: Chapter 9 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. We recommend that only users who are proficient in method development create or modify acquisition and quantitation methods.

  • Page 82: Configure The Syringe Pump

    Operating Instructions Acquisition Methods Configure the Syringe Pump 1. Click the Syringe Pump icon in the Acquisition method pane. The Syringe Pump Method Properties tab opens in the Acquisition Method editor pane. 2. Type the syringe diameter in the Syringe Diameter (mm) field. 3.

  • Page 83: Copy An Experiment Within A Period

    Operating Instructions Acquisition Methods Copy an Experiment within 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. A copy of the experiment is added below the last experiment created.

  • Page 84: Lit-Mode Scan Types

    Operating Instructions Acquisition Methods MRM (MRM): An MS/MS scan in which a user-selected ion is passed through the Q1 quadrupole and then fragmented in the Q2 collision cell. The Q3 quadrupole then selects the fragment ion that enters the detector. This scan mode is used primarily for quantitation.

  • Page 85: About Spectral Data Acquisition

    Operating Instructions Acquisition Methods product ions are scanned out of the trap at one of three scan speeds. As with any in-trap Collision Induced Disassociation (CID) technique, there is a low mass cut-off for the second MS/MS step due to the condition that ®...

  • Page 86: Chapter 10 Operating Instructions Batches

    Operating Instructions Batches CAUTION: Potential System Damage. If the HPLC system connected to the mass spectrometer is not controlled by the software, then do not leave the mass spectrometer unattended while in operation. The HPLC system can flood the ion source when the mass spectrometer goes into Standby mode.

  • Page 87: Add Sets And Samples To A Batch

    Operating Instructions Batches Add Sets and Samples to 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. Figure 10-1 Batch Editor Dialog 2.
  • Page 88 Operating Instructions Batches Figure 10-2 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 89 Operating Instructions Batches 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. 14.

  • Page 90: Submit A Sample Or Set Of Samples

    Operating Instructions Batches Table 10-1 Batch Editor Tips (continued) To do this..do this To apply a previously created quantitation select the method from the Quantitation list. method To select more than one well or vial at a hold down the Shift key and then click the first and last well or time vial in the range.

  • Page 91: Change Sample Order

    Operating Instructions Batches Change Sample Order The order of the samples can be edited before the samples are submitted to the Queue. • On the Submit tab, double-click any of the numbers at the far left of the table (a very faint square box is visible), and then drag them to the new location.

  • Page 92: Select Vial Positions Using The Locations Tab (Optional)

    Operating Instructions Batches Note: Depending on the autosampler being used, it might not be necessary to type details in additional columns. 1. In the Sample tab, from the Set list, select the set. 2. For each sample in the set, do the following if applicable: •...

  • Page 93: Set Quantitation Details In The Batch Editor (Optional)

    Operating Instructions Batches Figure 10-4 Locations Tab 6. 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. If the button shows a red vertical line, then the Batch Editor marks the samples by column.

  • Page 94: Stop Sample Acquisition

    Operating Instructions Batches 4. If applicable, type the peak concentration in the Analyte column. 5. If applicable, type the Internal Standard. 6. Repeat this procedure for each set in the batch. 7. Save the file. Note: The order of samples can be edited before the samples are submitted to the queue. To change the order of a sample, on the Submit tab, double-click any of the numbers at the far left of the table (a very faint square box is shown), and then drag them to the new location.

  • Page 95: Import A Batch As A Text File

    Operating Instructions Batches 1. In the Batch Editor, create a single-set, single-sample batch. 2. Click File > Export. The Save As dialog opens. 3. Type a name for the text file in the File name field and then click Save. 4.

  • Page 96: Queue States And Device Status

    Operating Instructions Batches Menu Function Save As Batch Saves the batch with a different name. Save As a Template Saves the batch as a template. Used with the Express View feature. Hide/Show Column Hides or shows a column. Save Column Settings Saves the batch column settings.

  • Page 97: View Instrument And Device Status Icons

    Operating Instructions Batches Table 10-2 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 98: 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 99 Operating Instructions Batches 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. Sort Sorts on the preselected column.

  • Page 100: Chapter 11 Operating Instructions

    Operating Instructions Analyze and Process Quantitative Data Use the sample files found in the Example folder to learn how to select samples for quantitation, how to select preset queries and create table-specific queries, and how to analyze the acquired data. For more information about the following topics, refer to the Advanced User Guide: •...

  • Page 101: About Results Tables

    Operating Instructions Analyze and Process Quantitative Data also be used to change existing quantitation methods. This is the most flexible way of creating a quantitation method. Quick Quant Quick Quant is part of the Batch Editor. Use Quick Quant to add compound concentrations prior to data acquisition.
  • Page 102 Operating Instructions Analyze and Process Quantitative Data Note: If the Compound ID field was populated for the samples and internal standards in the acquisition method, then in the Internal Standards table, when a value is selected in the Q1/Q3 field, the Name field is automatically populated.

  • Page 103: Create A Results Table Using The Quantitation Wizard

    Operating Instructions Analyze and Process Quantitative Data Create a Results Table Using the Quantitation Wizard Prerequisites • Switch Between Projects and Subprojects on page 61 • Show Basic Quantitative Data on page 121 1. On the Navigation bar, under Quantitate, double-click Quantitation Wizard. The Create Quantitation Set - Select Samples page opens.

  • Page 104: Create A Standard Query

    Operating Instructions Analyze and Process Quantitative Data Note: We recommend that users do not change datafile (.wiff) names if a Results Table includes samples from that file. Tip! Well-formatted reports can be created from a Results Table using the Reporter software. We recommend that the user validate the results if a Reporter template that contains a query is used.
  • Page 105 Operating Instructions Analyze and Process Quantitative Data 6. Click Next. Figure 11-2 Create Quantitation Set Create Default Query Page 7. In the Maximum Allowed Accuracy Variation for QCs (%) table in the Max. Variation column, type the maximum allowable percent of variation for each QC, for example 5 is ± 5%, in the same row as the corresponding concentration.

  • Page 106: Results Table Right-Click Menu

    Operating Instructions Analyze and Process Quantitative Data Figure 11-3 Create Quantitation Set Select Method Page 10. Select or create a method. 11. Click Finish. The query is applied as a standard query. The query results are shown as a Pass or Fail entry in the Standard Query Status column of the Results Table.

  • Page 107: Peak Review And Manual Integration Of Peaks

    Operating Instructions Analyze and Process Quantitative Data Table 11-1 Results Table Right-click Menu (continued) Menu Function Sample Type Shows samples of a specific type or all samples. Add Formula Adds a formula column. Column We recommend that the user validate the results if a formula column is used. Table Settings Edits or selects a table setting.
  • Page 108 Operating Instructions Analyze and Process Quantitative Data Note: We recommend that manually integrated results be validated. Tip! To review an individual peak, right-click on a point on the curve and then click Show Peak. The software opens the Peak Review window with the selected peak. 1.
  • Page 109 Operating Instructions Analyze and Process Quantitative Data Item Definition Number of rows Number of columns Zoom Y-axis to 100% of largest peak to show the entire peak 7. Click OK. 8. To move through the peaks, click the right-pointing arrow. Refer to Figure 11-5.
  • Page 110 Operating Instructions Analyze and Process Quantitative Data Item Definition Arrows: Click to move through the peaks. Show or Hide Parameters: Click to show the integration parameters. Integration parameters: Click to change the parameters. 10. Click Show or Hide Parameters twice. 11.

  • Page 111: Manually Integrate Peaks

    Operating Instructions Analyze and Process Quantitative Data Manually Integrate Peaks Manually integrating peaks should be done last, to limit person-to-person variability. Manually integrate peaks only if all the peaks have not been found after the algorithm parameters have been adjusted and updated. Note: Peaks that are manually integrated, or where the algorithm was changed for only that peak, are identified in the Record Modified column of the Results Table, as are peaks that have algorithm parameter changes for a sample that are not applied to the entire analyte group.

  • Page 112: Peak Review Right-Click Menu

    Operating Instructions Analyze and Process Quantitative Data The software shades the area bounded by the base and sides of the peak. Peak parameters are gray as they are no longer applicable because the peak was drawn manually. 4. Do one of the following: •...

  • Page 113: View Calibration Curves

    Operating Instructions Analyze and Process Quantitative Data The calibration curve is generated by plotting the concentration of the standard versus its area or height. If an internal standard is used, then the ratio of the standard concentration or internal standard versus the ratio of the standard peak height or area to the internal standard peak height or area is plotted.

  • Page 114: Overlay Calibration Curves

    Operating Instructions Analyze and Process Quantitative Data c. Select 1 / x in the Weighting list. d. Click OK. The calibration curve opens. The user can review individual peaks on the curve or exclude points from the curve to produce a better curve. 5.

  • Page 115: Sample Statistics

    Operating Instructions Analyze and Process Quantitative Data Table 11-3 Calibration Curve Right-click Menu Menu Function Exclude (Include) Right-click the point and then click Exclude to exclude the point from the curve. Right-click the point and then click Include to include the point. Exclude All Analytes (Include Right-click a point and then click Exclude All Analytes to exclude all the All Analytes)

  • Page 116: Compare Results Between Batches

    Operating Instructions Analyze and Process Quantitative Data 5. Select Standard in the Sample Type field. The results are shown. 6. Look at the %CV and Accuracy columns. The %CV shows the coefficient of variance between the measurements of a single parameter, for example the area.

  • Page 117: Chapter 12 Operating Instructions Analyze And Process Data

    Operating Instructions Analyze and Process 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 118: Show Experimental Conditions

    Operating Instructions Analyze and Process Data If samples were saved in separate data files, then open each file individually. • Open a data file and then do one of the following: • Click the icon with the arrow pointing to the right to skip to the next sample in the data file. •...

  • Page 119: Show Data In Tables

    Operating Instructions Analyze and Process Data Table 12-1 Right-click Menu for Show File Information Pane (continued) Menu Function Save Acquisition Method to Opens the Specify Compound Information dialog. Select the IDs and molecular CompoundDB weights to be saved in the compound database. Delete Pane Deletes the selected pane.
  • Page 120 Operating Instructions Analyze and Process Data Figure 12-1 Peak List Tab Table 12-2 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 121: Show Adc Data

    Operating Instructions Analyze and Process Data Table 12-3 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 122: Chromatograms

    Operating Instructions Analyze and Process Data Peaks are shown in two colors. 4. To change the peak finding algorithm settings, right-click and then select either Analyst Classic Parameters or Intelliquan Parameters, whichever is active. 5. (Optional) To remove the colored peaks, right-click in the Peak List tab and then clear Show Peaks in Graph.

  • Page 123: Show Tics From A Spectrum

    Operating Instructions Analyze and Process Data Show TICs from a Spectrum To see an example data file, make sure that the Example project is selected. • Click Explore > Show > Show TIC. The TIC opens in a new pane. Tip! Right-click inside a pane containing a spectrum and then click Show TIC.

  • Page 124: Generate An Xic Using A Selected Range

    Operating Instructions Analyze and Process Data Table 12-5 Summary of XIC Generation Methods (continued) Method Use with Use with Extraction Chromatogram Spectrum Base peak masses Can be used only with Base Peak Chromatograms (BPCs). Use the Use Base Peak Masses command to extract ions results in an XIC with a different colored trace for each mass.

  • Page 125: Extract Ion By Selecting Masses

    Operating Instructions Analyze and Process Data 2. In a BPC, select the peak from which to extract ions. The selection is indicated in blue. 3. Click Explore > Extract Ions > Use Base Peak Masses. An XIC of the specified selection opens below the spectrum pane. The experiment information at the top of the pane shows the mass range and the maximum intensity in counts per second.

  • Page 126: Generate Bpcs

    Operating Instructions Analyze and Process Data An XIC of the selection opens below the chromatogram pane. The experiment information at the top of the pane includes the masses and the maximum intensity in counts per second. Generate BPCs BPCs can be generated only from single-period, single-experiment data. 1.

  • Page 127: Generate Xwcs

    Operating Instructions Analyze and Process Data • 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.

  • Page 128: Generate Twcs

    Operating Instructions Analyze and Process Data The DAD spectrum opens in a pane below the TWC. The Y-axis shows the absorbance and the X-axis shows the wavelength. Tip! If the pane with the TWC is closed, then click a point anywhere in the TWC to open it again. Click Explore >...

  • Page 129: Chromatogram Panes

    Operating Instructions Analyze and Process Data Chromatogram Panes Table 12-6 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 130: Spectra Panes

    Operating Instructions Analyze and Process Data Spectra Panes Table 12-7 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 131: Graphs

    Operating Instructions Analyze and Process Data The user can zoom in on part of a graph to view a particular peak or an area in greater detail in both spectra and chromatograms. The user can also zoom in repeatedly to view smaller peaks. ®...
  • Page 132 Operating Instructions Analyze and Process Data Table 12-8 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 133: Zoom In On The Y-Axis

    Operating Instructions Analyze and Process Data Table 12-8 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 134: Chapter 13 Reporter Software

    Reporter Software ® The Reporter software extends the reporting functionality available in the Analyst software. The Reporter software can be used to create custom reports with Microsoft Word and Excel (2010 or 2013). The Reporter software has the following features: •...

  • Page 135: Reporter User Interface

    These dictionary files are contained in the folder: C:\Program Files\AB SCIEX\AnalystReporter\Resources\Languages on Windows 7 32- bit operating systems or C:\Program Files (x86)\AB SCIEX\AnalystReporter\Resources\Languages on Windows 7 64-bit operating systems.
  • Page 136 Reporter Software Item Option Description Settings > Select Library Browse to a spectral library. This library will be used for matching and scoring MS/MS data from Results Tables that contain data from information dependent acquisition (IDA) triggered MS/MS scan types. Settings >...

  • Page 137: Generate Reports

    Reporter Software Generate Reports The Reporter software extracts numerical data from the Results Table and sample and graphical information from the .wiff file. Select a template in the Available Template field. 1. Open a Results Table. 2. Under Companion Software, double-click Reporter. 3.

  • Page 138: Chapter 14 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 139 Service and Maintenance Information Table 14-1 Maintenance Tasks (continued) Component Frequency Task For more information... Orifice plate (front) Daily Clean Refer to Clean the Front of the Orifice Plate on page 145. Mass spectrometer Every 6 months Replace Contact the local QMP or FSE. air filter Roughing pump oil Annually...

  • Page 140: Clean The Surfaces

    Service and Maintenance Information • Clean the mass spectrometer surfaces after a spill or when they become dirty. • Empty the drain bottle before it becomes full. Clean the Surfaces Clean the external surfaces of the mass spectrometer after a spill or when they become dirty. CAUTION: Potential System Damage.

  • Page 141: Required Materials

    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 • Laboratory coat •...

  • Page 142: Best Practices

    Service and Maintenance Information Best Practices WARNING! Toxic Chemical Hazard. Refer to chemical product Safety Data Sheets and follow all safety guidelines when handling, storing, and disposing of chemicals. For health and safety precautions, refer to Chemical Precautions on page WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard.

  • Page 143: Prepare The Mass Spectrometer

    Service and Maintenance Information • Larger parts of the vacuum interface, such as the curtain plate, might require several cleanings, using multiple wipes. • Only dampen the wipe or swab slightly when applying water or cleaning solution. Water, more often than organic solvents, might cause the wipe to deteriorate, leaving residue on the mass spectrometer.

  • Page 144: Clean The Curtain Plate

    Service and Maintenance Information Clean the Curtain Plate CAUTION: Potential System Damage. Do not rest the curtain plate or orifice plate on the aperture tip. Make sure that the conical side of the curtain plate faces up. 1. Pull the curtain plate off the vacuum interface and then place it, conical side up, on a clean, stable surface. Figure 14-3 Curtain Plate Removal It is held in place by three retaining ball catches mounted on the orifice plate.

  • Page 145: 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 146 Service and Maintenance Information WARNING! 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 vent tubing is secured with clamps. Inspect the source exhaust drain bottle regularly, and empty it before it becomes full. Also inspect the bottle and its fitting for leaks, and tighten connections or replace components, if required.
  • Page 147 Service and Maintenance Information Figure 14-4 Source Exhaust Drain Bottle Item Description Connection to vent Source exhaust drain tubing: 2.5 cm (1.0 inch) inside diameter (i.d.) Roughing pump exhaust hose: 3.2 cm (1.25 inch) i.d. Source exhaust drain bottle. The drain bottle may be located at the side of the mass spectrometer in the drain bottle holder.

  • Page 148: 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 149: Chapter 15 Mass Spectrometer Troubleshooting

    There is a leak. Inspect and repair leaks. The wrong orifice plate is installed. Install the correct orifice plate. For sales, technical assistance or service, contact an FSE or visit the SCIEX Web site at sciex.com for contact information. System User Guide...

  • Page 150: Appendix A Operating Instructions Manual Optimization

    Operating Instructions Manual Optimization The user must control the autosampler and injection valve manually, as these devices cannot be controlled through the system while it is in Tune and Calibrate mode. Prerequisites • The mass spectrometer is tuned and calibrated. •...

  • Page 151: About Manual Compound Optimization

    Operating Instructions Manual Optimization About 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 Calibrate mode.

  • Page 152: Confirm The Presence Of Compounds

    Operating Instructions Manual Optimization Confirm the Presence of Compounds 1. Create a project. 2. Activate the hardware profile. 3. Infuse the compound in solution at a rate of 5 µL/min to 10 µL/min. 4. On the Navigation bar, under Tune and Calibrate, double-click Manual Tuning. 5.

  • Page 153: Optimize Ms-Specific Parameters

    Operating Instructions Manual Optimization Table A-3 MS Tab Parameter Value Scan type Q1 MS (Q1) Start (Da) Stop (Da) Scan rate (Da/s) (if available) Duration (min) 10. Click Start. 11. Wait until an even TIC is shown on the left and peaks are shown on the right and then click Stop. 12.
  • Page 154 Operating Instructions Manual Optimization 1. Return to the Tune Method Editor and change the method to the Q1 Multiple Ions (Q1 MI) scan type. 2. In the mass table, type the parameter values as shown in Table A-4. Table A-4 Mass Table Parameters Q1 Multiple Ions (Q1 MI) Compound Q1 Mass Time...

  • Page 155: Determine The Product Ions For Optimization

    Operating Instructions Manual Optimization Table A-5 MS-Specific Parameters Parameter Comment Set the DP to the value that provides the highest intensity. 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.

  • Page 156: Optimize Collision Cell Exit Potential For Each Product Ion

    Operating Instructions Manual Optimization 12. Right-click the bottom-right XIC pane and then click Open File. 13. Pick the product ions with the greatest intensity. Note the product ion m/z to the first decimal point, such as 195.1. 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.

  • Page 157: Manually Optimize The Ion Source And Gas Parameters

    Operating Instructions Manual Optimization Manually Optimize the Ion Source and Gas Parameters The ion source and gas settings must be set correctly to prevent contamination of the mass spectrometer and that the compounds of interest have been optimally put into the gas phase as ions. The ion source and gas settings must be adjusted when the LC conditions change significantly.
  • Page 158 Operating Instructions Manual Optimization 1. On the Navigation bar, under Tune and Calibrate, double-click Manual Tuning. 2. Click File > Open. 3. In the Files list, click the acquisition method used to optimize the compound parameter and then click OK. The method opens in the Tune Method Editor.

  • Page 159: Appendix B 6500 And 6500+ Series System Parameters

    6500 and 6500+ 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 6500 and 6500 Series System Parameters Parameter ID Access ID Positive Ion Mode Negative Ion Mode MS/MS...
  • Page 160 6500 and 6500+ Series System Parameters Table B-1 6500 and 6500 Series System Parameters (continued) Parameter ID Access ID Positive Ion Mode Negative Ion Mode MS/MS MS/MS –10 –10 –10 (EP = –Q0) 2 to 15 2 to 15 2 to 15 –15 to –2 –15 to –2 –15 to –2...
  • Page 161 Turbo V ion source with the APCI probe (a) QTRAP 6500 or 6500 system Low Mass (LM) (b) QTRAP 6500 or 6500 system High Mass (HM) (c) SCIEX Triple Quad 6500 or 6500 system LM (d) SCIEX Triple Quad 6500 or 6500 system HM...
  • Page 162 6500 and 6500+ Series System Parameters Table B-2 6500 and 6500 Series System Parameters for LIT Scan Types Only (continued) Parameter ID Access ID Positive Ion Mode Negative Ion Mode –10 (Q0 - ROS) 5 to 180 –5 to –180 ** MS/MS/MS only ®...

  • Page 163: Appendix C Calibration Ions And Solutions

    Table C-2 Suggested Tuning Solutions for 6500 and 6500 Series Systems System Q1 and Q3 Positivie Negative Positive and Negative –7 –5 SCIEX SCIEX Triple Quad PPG, 2 × 10 M (500:1) NEG PPG, 3 × 10 (10:1) 6500 or 6500 LC-MS/MS system (Low Mass and High Mass) –5...
  • Page 164 Calibration Ions and Solutions Table C-3 Q1 and Q3 Scans for 6500 or 6500 Series Systems (continued) Polarity Masses Positive 59.05 175.133 500.38 616.464 906.673 1254.925 1545.134 1952.427 Negative 44.998 411.259 585.385 933.636 1223.845 1572.097 1863.306 1979.389 Table C-4 LIT Scans for the QTRAP 6500 or 6500 LC-MS/MS System Polarity Masses...

  • Page 165: Appendix D Toolbar Icons

    Toolbar Icons For additional toolbar icons, refer to the Advanced User Guide. Table D-1 Tool Bar Icons Icon Name Description Creates a subproject. Subprojects can only be created later in the process Subproject if the project was originally created with subprojects. Copy Copies a Subproject folder.
  • Page 166 Toolbar Icons Table D-3 Acquire Mode Icons Icon Name Description View Queue Shows the sample queue. Instrument Shows a remote instrument station. Queue Status for Shows the status of a remote instrument. Remote Instrument Start Sample Starts the sample in the queue. Stop Sample Stops the sample in the queue.
  • Page 167 Toolbar Icons Table D-3 Acquire Mode Icons (continued) Icon Name Description Ready Puts the instrument in Ready mode. Reserve Reserves the mass spectrometer for tuning and calibrating. Instrument for Tuning IDA Method Starts the IDA Method Wizard. Wizard Purge Starts the modifier purge from the modifier pump. Modifier Table D-4 Tune and Calibrate Mode Icons Icon...
  • Page 168 Toolbar Icons Table D-4 Tune and Calibrate Mode Icons (continued) Icon Name Description Reserve Reserves the instrument for tuning and calibrating. Instrument for Tuning IDA Method Starts the IDA Method Wizard. Wizard Table D-5 Explore Quick Reference: Chromatograms and Spectrum Icon Name Description...
  • Page 169 Toolbar Icons Table D-5 Explore Quick Reference: Chromatograms and Spectrum (continued) Icon Name Description Threshold Adjusts the threshold. Noise Filter Shows the Noise Filter Options dialog, which can be used define the minimum width of a peak. Signals below this minimum width are regarded as noise.
  • Page 170 Toolbar Icons Table D-5 Explore Quick Reference: Chromatograms and Spectrum (continued) Icon Name Description Show Contour Shows selected data as either a spectrum graph or an XIC. Additionally, for Plot data acquired by a DAD, a contour plot can show selected data as either a DAD spectrum or an XWC.
  • Page 171 Toolbar Icons Table D-7 Results Table Icons Icon Name Description Sort Sorts the selected column by ascending values. Ascending by Selection Sort Sorts the selected column by descending values. Descending by selection Lock Or Locks or unlocks the selected column. A locked column cannot be moved. Unlock Column Metric Plot By...
  • Page 172 Toolbar Icons Table D-8 Icon Quick Reference: Quantitate Mode (continued) Icon Name Description Calibration - Window Opens the calibration curve in a window. Show First Peak Shows the first peak in the pane or window. Show Last Peak Shows the last peak in the pane or window. Show Audit Trail Shows the audit trail for the Results Table.

  • Page 173: Revision History

    Revision History Revision Reason for Change Date First release of document. August 2015 System User Guide 6500 and 6500+ Series of Instruments RUO-IDV-05-2095-A 173 of 181...

  • Page 174: Index

    Index described 67 equipment and solutions 67 prerequisites 67 acids, list of 13 Acquire mode, icons 166 Acquiring state, described 97 acquisition method editor, icons 165 base peak chromatograms, generating 126 acquisition methods bases, list of 13 changing from the Batch Editor 89 Batch Editor compound IDs and quantitation methods 102 acquisition methods, changing 89...
  • Page 175 Index viewing 113 diverter valve 57 CEM parameter, defined 38 syringe pump 56, 82 centroid, spectral data acquisition 85 confirming, presence of compounds 68, 152 changing connections acquisition methods in the Batch Editor 89 mass spectrometer 26 sample order 91 contamination, troubleshooting tips 149 chemical precautions, protective equipment 12 contour plots, showing 129...
  • Page 176 Index panes, tiling 133 copying into a period 82 processing graphical data 130 copying within a period 83 quantitative data, showing 121 extracted ion chromatograms rescaling graphs 131 extracting ions by selecting masses 125 show data in tables 119 generating 123 show experimental conditions 118 generating using selected ranges 124 skip to a non-sequential sample 118...
  • Page 177 Index defined 34 GS2 parameter defined 34 LEDs, described 25 library search with constraints 130 hardware profiles searching 130 activating 57 linking panes 132 adding devices 58 LIT mode, described 30 creating 54 locking panes 132 described 54 failed activation 59 hazard symbols 18 maintenance hiding, panes 132...
  • Page 178 Index MS/MS/MS Fragmentation Time parameter, defined 37 peak hopping, spectral data acquisition 85 MS/MS/MS scan types, defined 83 peak review Multi-Charge Separation Barrier parameter, defined 37 calibration curves, overlaying 114 described 107 manually integrating peaks 111 options dialog, opening 112 Nebulizer Current parameter, defined 33 right-click menu 112 Not Ready state, described 97...
  • Page 179 Index QJet ion guide and IQ0 lens rescaling graphs 131 frequency of maintenance 139 resting the system 46 Quantitate mode, icons 171 Results Summary, described 65 quantitation methods Results Tables applying 90 Add Custom Column option 107 creating 101 Add Formula Column option 107 defining details in the Batch Editor 93 calibration curves, generating 113 described 100...
  • Page 180 Index vials 90 samples 90 sensitivity loss, troubleshooting 149 sets 90 sensitivity, and maintenance 139 subprojects setting copying 61 peak review options 108 creating 61 threshold options 128 surfaces Show File Information pane, right-click menu 118 mass spectrometer, cleaning 140 Show or Hide Parameters icon 102 switch, roughing pump, location of 45 showing...
  • Page 181 Index generating BPCs 126 y-axis 133 generating from a spectrum 123 total wavelength chromatograms, generating data 128 troubleshooting hardware profiles 59 system 149 Tune and Calibrate mode , icons 167 TWC total wavelength chromatograms vacuum pressure, troubleshooting tips 149 vacuum, routine cleaning 140 ventilation requirements 13 verifying instrument performance 64...

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