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Thermo Scientific LTQ XL Getting Started

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For Research Use Only
Not for use in Diagnostic Procedures
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LTQ XL
Getting Started
97355-97042 Revision A
June 2006

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  • Page 1 ® LTQ XL Getting Started 97355-97042 Revision A June 2006 For Research Use Only Not for use in Diagnostic Procedures...
  • Page 2 © 2004 Thermo Electron Corporation. All rights reserved. ® ® ® Microsoft and Windows are registered trademarks of Microsoft Corporation. Teflon is a registered trademark of ® ® E.I. du Pont de Nemours & Company. Unimetrics is a registered trademark of Unimetrics Company. Tygon is a ®...
  • Page 3 Regulatory Compliance Thermo Electron San Jose performs complete testing and evaluation of its products to ensure full compliance with applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent electromagnetic compatibility (EMC) and safety standards as described below. EMC Directive 89/336/EEC •...
  • Page 4 FCC Compliance Statement THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED, INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.
  • Page 5 WEEE Compliance This product is required to comply with the European Union’s Waste Electrical & Electronic Equipment (WEEE) Directive 2002/96/EC. It is marked with the following symbol: Thermo Electron has contracted with one or more recycling/disposal companies in each EU Member State, and this product should be disposed of or recycled through them. Further information on Thermo Electron’s compliance with these Directives, the recyclers in your country, and information on Thermo Electron products which may assist the detection of substances subject to the RoHS Directive are available at...
  • Page 6 Conformité DEEE Ce produit doit être conforme à la directive européenne (2002/96/EC) des Déchets d'Equipements Electriques et Electroniques (DEEE). Il est marqué par le symbole suivant: Thermo Electron s'est associé avec une ou plusieurs compagnies de recyclage dans chaque état membre de l’union européenne et ce produit devrait être collecté ou recyclé par celles-ci.

  • Page 7: Table Of Contents

    How Should I Set Up the MS Detector for Various LC Flow Rates?..................11 What is Tuning and Calibration of the MS Detector All About?... What Types of Experiments Can I Perform with the LTQ XL MS Detector?................16 General MS or MSn Experiments ..........16 Data-Dependent Experiments..........17...
  • Page 8 Installing the APCI Probe ............111 Chapter 7 Optimizing the MS Detector with Your Analyte in APCI/MS Mode115 Setting Up the Inlet for Tuning Using High-Flow Infusion ..116 Setting Up the MS Detector for APCI/MS Operation ....119 viii LTQ XL Getting Started Thermo Electron Corporation...
  • Page 9 Stock Solution: Reserpine ............144 Reserpine Tuning Solution and Reserpine APCI Sample Solution ................144 Appendix B LTQ XL High Mass Range Calibration .........147 High Mass Range Calibration Solution ........148 Normal Mass Range Calibration ..........149 Enter Normal Mass Range Data into Tune Plus .....150 Tune on m/z 524.3 ..............152...

  • Page 11: Preface

    Preface About This Guide Welcome to the Thermo Electron, LTQ XL™ system. The LTQ XL is a member of the Thermo family of MS detectors. This LTQ XL Getting Started manual provides information on how to set up, calibrate, and tune the LTQ XL MS detector and how to acquire LC/MS ®...

  • Page 12: Contacting Us

    To suggest changes to this guide or to the Help, use either of the following methods: and Online Help • Fill out a reader survey online at www.thermo.com/lcms-techpubs • Send an e-mail message to the Technical Publications Editor at techpubs.finnigan-lcms@thermo.com LTQ XL Getting Started Thermo Electron Corporation...

  • Page 13: Introduction

    Introduction Chapter 1 The LTQ XL™ is a member of the Thermo family of MS detectors. The LTQ XL MS detector is an advanced analytical instrument that includes a syringe pump, a divert/inject valve, an atmospheric pressure ionization (API) source, an MS detector, and the Xcalibur data system. In a typical analysis, a sample can be introduced in any one of the following ways: •...

  • Page 14: Why Use The Ltq Xl Ms Detector

    Why Use the LTQ XL MS Detector? Why Use the LTQ XL The attribute that sets the LTQ XL MS detector apart from other LC MS Detector? detectors is the high level of analytical specificity that it provides. The LTQ XL MS detector can provide multiple levels of analysis.
  • Page 15 MS/MS fragmentation over a fixed mass range of 20 u. This option allows the LTQ XL MS detector to apply collision energy to both the parent ion, as well as to product ions created as a result of non-specific losses of water (18 u) or ammonia (17 u), for example, or to product ions formed from the loss of fragments less than 20 u.

  • Page 16: Which Ms Detector Technique-Esi Or Apci-Is Better For Analyzing My Samples

    With ESI, the range of molecular masses that can be analyzed by the LTQ XL MS detector is greater than 100,000 u, due to multiple charging. ESI is especially useful for the mass analysis of polar compounds, which include: biological polymers (for example, proteins, peptides, glycoproteins, and nucleotides);...

  • Page 17: Using Apci/Ms

    The rate of solvent flowing from the LC into the MS detector in APCI mode is typically high (between 0.2 and 2 mL/min). See Table Thermo Electron Corporation LTQ XL Getting Started...
  • Page 18 This is because the negative ion polarity mode sometimes generates less chemical noise than does the positive mode. Thus, the signal-to-noise ratio might be better in the negative ion mode than in the positive ion mode. LTQ XL Getting Started Thermo Electron Corporation...

  • Page 19: Should I Use Sheath, Auxiliary, And/Or Sweep Gases

    Sheath, Sweep, and/or Auxiliary gas. See Table 2 Table 3 for additional information on using supplemental gas flows. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 20: How Can I Introduce My Samples Into The Ms Detector

    APCI to separate the analytes before they are introduced sequentially into the MS detector. You can refer to subsequent chapters in this manual and to LTQ XL Getting Connected for plumbing diagrams and methods of sample introduction. Table 1.
  • Page 21 Figure 11-8 (APCI) LC Flow With Autosampler injections ESI or APCI analysis Chromatographic into LC column via LC flow of mixtures Separation (one or multiple injections *Provides steady state introduction of sample (direct infusion) Thermo Electron Corporation LTQ XL Getting Started...

  • Page 22: What Types Of Buffers Should I Use? What Types Should I Avoid

    Volatile buffer solutions can include the following: • Acetic acid • Ammonium acetate • Ammonium formate • Ammonium hydroxide • Triethylamine (TEA) • Trifluoroacetic acid LTQ XL Getting Started Thermo Electron Corporation...

  • Page 23: How Should I Set Up The Ms Detector For Various Lc Flow Rates

    5 μL/min require more care, especially with the position of the fused silica sample tube within the ESI probe. For the APCI probe, flows below 200 μL/min require more care to maintain a stable spray. Thermo Electron Corporation LTQ XL Getting Started...
  • Page 24 40 to 100 Typical setting: units 0 to 20 units Note: Be sure to choose either Auxiliary gas and/or Sweep gas according to the hints in Should I Use Sheath, Auxiliary, and/or Sweep Gases? LTQ XL Getting Started Thermo Electron Corporation...

  • Page 25: What Is Tuning And Calibration Of The Ms Detector All About

    Introduction What is Tuning and Calibration of the MS Detector All About? What is Tuning and To optimize the performance of data acquisition on the LTQ XL MS Calibration of the MS detector, tune and calibrate in four steps: Detector All About? •...

  • Page 26: What Is Tuning And Calibration Of The Ms Detector All About

    ESI/MS operation are the ion transfer capillary temperature, tube lens voltage, gases, and solution flow rate. For optimum sensitivity, tune with the instrument in the same operational mode as the mode you use for the analytical experiment. LTQ XL Getting Started Thermo Electron Corporation...

  • Page 27: What Is Tuning And Calibration Of The Ms Detector All About

    Semi- Semi- Collision Check Auto Auto Manual Sample Intro auto auto Energy Calibration solution/ Syringe pump Your tune solution/ Syringe pump Your tune solution/ Syringe pump into LC flow by using Tee union Thermo Electron Corporation LTQ XL Getting Started...

  • Page 28: What Types Of Experiments Can I Perform With The Ltq Xl Ms Detector

    The LTQ XL MS detector can then collect data on the ions in the range or on the product ions of the parent ion(s) that you specify.

  • Page 29: Data-Dependent Experiments

    The LTQ XL MS detector can generate reproducible, analyte-specific spectra, even from laboratory to laboratory. Consequently, reference spectra that are generated with the LTQ XL MS detector can be used to confirm structures of compounds generated with other LTQ XL systems.
  • Page 30 Introduction What Types of Experiments Can I Perform with the LTQ XL MS Detector? A data-dependent experiment produces a great deal of data from a single sample analysis. You can run a data-dependent experiment even if you know very little about your sample, and even if you are unfamiliar with the variables of mass spectroscopy.
  • Page 31 Introduction What Types of Experiments Can I Perform with the LTQ XL MS Detector? Figure 2. MS Detector Setup page in Instrument Setup, showing a template for a Data-Dependent Triple Play experiment. (To select a scan event that makes active the Dependent Scan check box, click either the Scan Event 2 or Scan Event 3 button.

  • Page 32: Ion Mapping Experiments

    What Types of Experiments Can I Perform with the LTQ XL MS Detector? even need to specify a parent ion. The LTQ XL MS detector can then collect full scan MS data, pick the most intense parent ion in the spectrum, and fragment the ion to generate product ions.
  • Page 33 Introduction What Types of Experiments Can I Perform with the LTQ XL MS Detector? identify automatically which parent ions were fragmented to yield a specified product ion. The experiment “maps” one or more parent ions by using the information from product ion scans.
  • Page 34 Introduction What Types of Experiments Can I Perform with the LTQ XL MS Detector? Figure 3. Total Ion Map page in Instrument Setup, showing a template that contains parameters for an Ion Mapping experiment In a Total (or full scan) Ion Mapping experiment, you get product ion scans for each parent ion, so you can determine which parent ions lost a particular fragment to yield a particular product ion.

  • Page 35: Ion Tree Experiments

    In an Ion Tree experiment, the LTQ XL MS detector can collect MS data automatically. You can specify a particular parent ion for fragmentation, or you can let the LTQ XL MS detector find the parent ions automatically and fragment them to any level between MS and MS .
  • Page 36 Introduction What Types of Experiments Can I Perform with the LTQ XL MS Detector? Figure 4. Data-Dependent Ion Tree page in Instrument Setup, showing a template for an Ion Tree experiment In an Ion Tree experiment, you can specify either of two options that prioritize how the LTQ XL MS detector gathers information: depth focus and breadth focus.
  • Page 37 What Types of Experiments Can I Perform with the LTQ XL MS Detector? First, with either depth or breadth focus, the LTQ XL MS detector scans for parent ions (MS) over the specified mass range. The most intense ion of the MS spectrum is selected for fragmentation (MS/MS).
  • Page 39 MS Detector This chapter provides information on setting up the hardware for tuning and calibrating your LTQ XL MS detector. You tune and calibrate the MS detector in the ESI mode before you acquire data in either the ESI or APCI mode.

  • Page 40: Placing The Lc/Ms System In Standby

    3. If the MS detector is On, click the On/Standby button to place the MS detector in the Standby mode. When the MS detector is in Standby, the LTQ XL MS detector turns off the ion source sheath gas, auxiliary gas, and high voltage.

  • Page 41: Removing The Apci Probe

    Note The following procedures assume that you are familiar with your instrument and software. If you need additional guidance, refer to LTQ XL online Help, LTQ XL Getting Connected, Ion Max API Source Hardware Manual, or the LTQ XL Hardware Manual.
  • Page 42 45 degrees counter-clockwise to free the probe from the alignment notch. d. Pull the probe straight out to remove it from the ion source housing. e. Store the APCI probe in its original shipping container. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 43 Unlock the ion source housing door by turning the locks 90 degrees so that the knobs are horizontal. b. Open the ion source housing door. c. Using pliers, grasp the corona needle and pull it straight out of the corona needle contact. See Figure Thermo Electron Corporation LTQ XL Getting Started...
  • Page 44 If you do not want to install the ion sweep cone, go to “Installing the ESI Probe” page Corona Needle Contact Corona Needle (grasp this with pliers to remove it) Figure 7. Corona needle, view from rear LTQ XL Getting Started Thermo Electron Corporation...

  • Page 45: Removing The Ion Max Ion Source Housing

    4. Place the ion source housing in a safe location for temporary storage. The Ion Max ion source housing is now properly removed. Ion Source Housing Locking Levers Ion Source Housing Drain Figure 8. Ion Max ion source housing, detail of components Thermo Electron Corporation LTQ XL Getting Started...

  • Page 46: Installing The Ion Sweep Cone

    2. Note the location of the sweep gas supply port in the API cone seal. The gas inlet on the ion sweep cone is placed in this port. See Figure 9 Figure Sweep Gas Supply Port Figure 9. Sweep gas supply port in the API cone seal LTQ XL Getting Started Thermo Electron Corporation...
  • Page 47 4. If necessary to achieve a proper ion sweep cone installation, you might adjust the set screws around the perimeter of the ion sweep cone. The ion sweep cone is now properly installed on the MS detector. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 48: Installing The Ion Max Ion Source Housing

    See Figure 11 Figure Ion Source Housing Locking Levers Guide Ion Source Pin Holes Housing Drain Figure 11. Rear view of the Ion Max ion source housing LTQ XL Getting Started Thermo Electron Corporation...
  • Page 49 CAUTION Prevent solvent waste from backing up into the ion source and MS detector. Always ensure that liquid in the drain tube is able to drain to a waste container. 3. Reinstall the ion source drain tube as follows: Thermo Electron Corporation LTQ XL Getting Started...
  • Page 50 Attach the free end of the hose to a dedicated drain system. Ideally, the drain system should be vented to a fume exhaust system. The Ion Max ion source housing is now properly installed on the MS detector. LTQ XL Getting Started Thermo Electron Corporation...

  • Page 51: Installing The Esi Probe

    ESI Interlock Plug API Interlock Block Probe Port 8kV Cable Grounding Bar Probe Collar Sheath Gas Fitting Probe Locking Lever (open position) Figure 13. Ion Max ion source housing probe locking lever open Thermo Electron Corporation LTQ XL Getting Started...
  • Page 52 7. Insert the APCI vaporizer heater cable into the API interlock socket. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 53 The ESI probe is now properly installed in the Ion Max ion source housing. Leave the LC/MS system in Standby and go to Chapter 3: “Tuning and Calibrating Automatically in the ESI/MS Mode”. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 55: Chapter 3 Tuning And Calibrating Automatically In The Esi/Ms Mode

    Setting Up the Syringe Pump for Tuning and Calibration • Setting Up the MS Detector in the Xcalibur Data System for Tuning and Calibration • Testing the Operation of the MS Detector in the ESI/MS Mode Thermo Electron Corporation LTQ XL Getting Started...
  • Page 56 Tuning and Calibrating Automatically in the ESI/MS Mode • Tuning the MS Detector Automatically in the ESI/MS Mode • Saving Your ESI/MS Tune Method • Calibrating the MS Detector Automatically • Cleaning the MS Detector after Tuning and Calibrating LTQ XL Getting Started Thermo Electron Corporation...

  • Page 57: Setting Up The Syringe Pump For Tuning And Calibration

    5. While squeezing the blue release button on the syringe pump handle, push the handle forward until it just contacts the syringe plunger. 6. Connect a fused-silica infusion line from the LC union to the (stainless steel) grounding union as follows. See Figure Thermo Electron Corporation LTQ XL Getting Started...
  • Page 58 The syringe pump is now properly set up for infusing solution into the MS detector. Go to the next section, Setting Up the MS Detector in the Xcalibur Data System for Tuning and Calibration. Figure 17. ESI/MS plumbing connections for the fused-silica infusion line LTQ XL Getting Started Thermo Electron Corporation...

  • Page 59: Setting Up The Ms Detector In The Xcalibur Data System For Tuning And Calibration

    MS detector. Note The following procedures assume that you are familiar with your LTQ XL instrument and the Tune Plus window. If you need additional guidance, see LTQ XL online Help, LTQ XL Getting Connected, and/or the LTQ XL Hardware Manual.
  • Page 60 • The MS detector begins scanning. • Nitrogen flows into the ESI probe. • The LTQ XL MS detector applies high voltage to the ESI probe. • The Xcalibur data system shows a real-time display in the Spectrum view.
  • Page 61 Click OK to return to the Tune Plus window. Figure 19. ESI Source dialog box, showing the settings to start a typical low flow experiment 5. Set the scan parameters for tuning and calibration, as follows: Thermo Electron Corporation LTQ XL Getting Started...
  • Page 62 In the Scan Ranges group box, in the Input list box, select From/To to make available the First Mass and Last Mass text boxes in the Scan Ranges table. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 63 (The picture on the button should be the same as that shown here). The MS detector is now properly set up in the Xcalibur data system for tuning and calibration in the ESI/MS mode. Thermo Electron Corporation LTQ XL Getting Started...
  • Page 64 Type 5 in the Flow Rate spin box to specify a rate of 5 μL/min. Note This procedure assumes that you are using the 500-μL Unimetrics syringe that is provided with your LTQ XL system. If you are using another type of syringe, select the option button corresponding to your syringe.
  • Page 65 Note Based on the LC flow rate of your experiment, you can specify the value of each of the following tuning parameters on the LTQ XL MS detector: sheath, Auxiliary, and Sweep gas pressures, ESI needle (or “spray”) voltage, ion transfer capillary temperature, and probe position.
  • Page 66 Congratulations! You have demonstrated that your MS detector is operating properly in the ESI mode. You are now ready to tune and calibrate the MS detector. Leave your LTQ XL MS detector as it is, and go to the next section, Tuning the MS Detector Automatically in the ESI/MS Mode.
  • Page 67 Testing the Operation of the MS Detector in the ESI/MS Mode NL=normalization level IT=ionization time Figure 22. Spectrum view of the Tune Plus window, showing ionization time (IT) and normalization level (NL) of the calibration solution Thermo Electron Corporation LTQ XL Getting Started...

  • Page 68: Tuning The Ms Detector Automatically In The Esi/Ms Mode

    See Figure 3. In the What to Optimize On group box, select the Mass option button to make active the Mass spin box. Figure 23. Tune dialog box, showing the Automatic tuning page LTQ XL Getting Started Thermo Electron Corporation...
  • Page 69 Tuning and Calibrating Automatically in the ESI/MS Mode Tuning the MS Detector Automatically in the ESI/MS Mode 4. In the Mass spin box, enter 195.1 to specify that the LTQ XL MS detector optimize your Tune Method on the peak at m/z 195.1.
  • Page 70 Tuning and Calibrating Automatically in the ESI/MS Mode Tuning the MS Detector Automatically in the ESI/MS Mode Figure 24. Tune Plus window, showing the results of a typical automatic tune procedure LTQ XL Getting Started Thermo Electron Corporation...
  • Page 71 Figure 25. ESI Source dialog box, showing typical parameters after automatic tuning Figure 26. Ion Optics dialog box, showing examples of voltages of lenses and Intermultipoles, which are optimized by the LTQ XL automatic tuning procedure Thermo Electron Corporation LTQ XL Getting Started...

  • Page 72: Saving Your Esi/Ms Tune Method

    1. Choose File > Save As to display the Save As dialog box. See Figure Figure 27. Save As dialog box, showing files in the folder C:\Xcalibur\methods 2. Select the C:\Xcalibur\methods folder. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 73 4. Click Save to save the Tune Method, and return to the Tune Plus window. Note that the Tune Method is named ESImyTune.LTQTune. Once you have tuned the MS detector, you are now ready to calibrate. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 74: Calibrating The Ms Detector Automatically

    Figure 28. Calibrate dialog box, showing the Automatic calibration page 3. Start the automatic calibration procedure, as follows: a. Click Start. A message box displays the following message: Please ensure that the 500 microliter syringe is full. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 75 Instrument Messages dialog box is displayed, which indicates whether or not the calibration procedure for an item is successful. • If a calibration item is successful, the LTQ XL MS detector saves the new calibration parameter automatically to the hard disk.
  • Page 76 Tuning and Calibrating Automatically in the ESI/MS Mode Calibrating the MS Detector Automatically Figure 29. Tune Plus window with Calibrate dialog box, showing the results of a successful semi-automatic calibration procedure LTQ XL Getting Started Thermo Electron Corporation...

  • Page 77: Cleaning The Ms Detector After Tuning And Calibrating

    Clean the MS detector after calibrating 1. Click On/Standby to put the MS detector in Standby mode. When the MS detector is in Standby, the LTQ XL MS detector turns off the sheath gas, Auxiliary gas, Sweep gas, ESI high voltage, and syringe pump. The...
  • Page 78 Flush the sample transfer line, sample tube, and ESI probe with the solution by slowly depressing the syringe plunger. Visually confirm that the solution is exiting the tip of the ESI probe on the inside of LTQ XL Getting Started Thermo Electron Corporation...
  • Page 79 If you plan to run analytical samples in high-flow ESI mode (using flow rates between 50 and 1000 μL/min), the procedures in Chapter 4: “Tuning with Your Analyte in LC/ESI/MS Mode” explain how to optimize the tune for this situation. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 81: Tuning With Your Analyte In Lc/Esi/Ms Mode

    LC/ESI/MS mode using your analyte. You optimize the sensitivity of the MS detector to your analyte through an automatic procedure. The customized Tune Methods contained in your LTQ XL data system are optimized for a wide range of applications, and they can be used without further tuning of your MS detector.

  • Page 82: Chapter 4 Tuning With Your Analyte In Lc/Esi/Ms Mode

    2. Before you optimize the tune for your analyte of interest, ensure that the LTQ XL MS detector has been calibrated within the previous three months. If the system needs to be calibrated, refer to the procedures in Chapter 3: “Tuning and Calibrating Automatically in...

  • Page 83: Setting Up To Introduce Sample By Syringe Pump Into Solvent Flow From An Lc

    Connect the PEEK tubing with a (brown) fingertight fitting and a (brown) ferrule to the grounding union. c. Connect the other end of the PEEK tubing with a (brown) fingertight fitting and a (brown) ferrule to the LC Tee union. Thermo Electron Corporation LTQ XL Getting Started...
  • Page 84 (black) LC Tee union, as follows. a. Connect a length of PEEK tubing with a (stainless steel) nut and a (stainless steel) ferrule to port 3 of the divert/inject valve. Figure LTQ XL Getting Started Thermo Electron Corporation...
  • Page 85 Insert the other end of the PEEK tubing in a suitable waste container. The MS detector is now properly set up to introduce your analyte by syringe pump into solvent flow from an LC. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 86: Setting Up To Tune The Ms Detector With Your Analyte

    2. In Tune Plus, click the On/Standby button to take the MS detector out of Standby mode and turn it On. The MS detector begins scanning, the LTQ XL MS detector applies high voltage to the ESI probe, and the LTQ XL MS detector shows a real-time display in the Spectrum view.
  • Page 87 Verify that the settings in your Define Scan dialog box are the same as those shown in Figure l. Click OK to apply the MS detector scan parameters and to close the Define Scan dialog box. Thermo Electron Corporation LTQ XL Getting Started...
  • Page 88 6. Click Positive/Negative to toggle the ion polarity mode to positive. (The picture on the button should be the same as that shown here). You have completed setting up to tune your MS detector with your analyte in ESI/MS mode. LTQ XL Getting Started Thermo Electron Corporation...

  • Page 89: Optimizing The Ms Detector Tune Automatically With Your Analyte

    4. In the Mass spin box, enter 609.2 (or the appropriate mass of your analyte of interest) to specify that the LTQ XL MS detector is to use the peak at m/z 609.2 (or the appropriate mass of your analyte of interest) to optimize your tune.
  • Page 90 Click OK to close the message box, and return to the Tune Plus window. 7. In the File/Display toolbar, click the Graph View button to display the Graph view. Figure 33. Tune dialog box, showing the Automatic tuning page LTQ XL Getting Started Thermo Electron Corporation...
  • Page 91 Figure 34. Divert/Inject Valve dialog box 8. Observe the Tune Plus window and the Tune dialog box. While automatic tuning is in progress, the LTQ XL MS detector displays various tests in the Spectrum and Graph views in the Tune Plus window and displays various messages in the Status group box in the Tune dialog box.
  • Page 92 Tuning with Your Analyte in LC/ESI/MS Mode Optimizing the MS Detector Tune Automatically with Your Analyte Figure 35. Tune Plus window with the Tune dialog box, showing the Automatic tuning page LTQ XL Getting Started Thermo Electron Corporation...

  • Page 93: Saving The Esi/Ms Tune Method

    3. Click the File Name text box, and enter reserpine (or the name of your analyte of interest). 4. Click Save to save the Tune Method, and return to the Tune Plus window. Note that the Tune Method is named reserpine.LTQTune. Thermo Electron Corporation LTQ XL Getting Started...
  • Page 94 The Tune Method is now properly saved and you are ready to acquire data on your analyte of interest.

  • Page 95: Acquiring Esi Sample Data Using The Tune Plus Window

    Note The following procedures assume that you are familiar with your LTQ XL instrument and the Tune Plus window. If you need information, refer to the LTQ XL online Help, LTQ XL Getting Connected, and/or the LTQ XL Hardware Manual.

  • Page 96: Setting Up To Acquire Ms/Ms Data In The Full Scan Type

    The relative collision energy for a particular analysis depends on the type of sample you are analyzing. The information in this topic applies to operation of the LTQ XL MS detector in either the ESI or the APCI mode.
  • Page 97 Type 5 in the Flow Rate spin box to specify a rate of 5 μL/min. Note This procedure assumes that you are using the 500-μL Unimetrics syringe that is provided with your LTQ XL system. If you are using another type of syringe, select the option button corresponding to your syringe.
  • Page 98 500 (or your syringe size) from the list to set the proper syringe volume. Note that, if you are using a Unimetrics syringe, the LTQ XL MS detector automatically sets the syringe ID to its proper value of 3.260 mm.
  • Page 99 (or your analyte of interest). If necessary, increase the value for the Normalized Collision Energy in increments of 5% to cause the clear display of product ion mass spectrum. (After each change in value, click Apply to implement the change.) See Figure Thermo Electron Corporation LTQ XL Getting Started...
  • Page 100 12. Click the Product Ion Mass option button to make active the spin box. Type 397.2 to specify the product ion at m/z 397.2 for reserpine. The LTQ XL MS detector can optimize collision energy automatically by using this product ion of reserpine.

  • Page 101: Optimizing The Collision Energy Automatically For An Ms/Ms Experiment

    Start to start the optimization procedure. A message box displays the following message: Ensure that the 500 microliter syringe is full. Ensure the syringe contains at least 450 μL of the 125 fg/μL reserpine solution. Thermo Electron Corporation LTQ XL Getting Started...
  • Page 102 Click Close to close the Syringe Pump dialog box. 7. Click Cancel to close the Tune dialog box. After you optimize the relative collision energy, the LTQ XL MS detector is ready to acquire MS/MS data on your analyte of interest.
  • Page 103 Setting Up to Acquire MS/MS Data in the Full Scan Type Figure 41. Tune Plus window, showing MS/MS product ions of reserpine in the Spectrum view Figure 42. Accept Optimized Value dialog box Thermo Electron Corporation LTQ XL Getting Started...

  • Page 104: Setting Up To Introduce Sample By Loop Injection Into Solvent Flow From An Lc

    3. Connect a 5 μL sample loop with (stainless steel) nuts and (stainless steel) ferrules to ports 1 and 4 of the divert/inject valve. (See Figure Figure 43. ESI/MS plumbing connections for the divert/inject valve and grounding union LTQ XL Getting Started Thermo Electron Corporation...
  • Page 105 Connect a length of PEEK tubing with a (stainless steel) nut and (stainless steel) ferrule to port 6 of the divert/inject valve. b. Insert the other end of the PEEK tubing into a suitable waste container. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 106: Acquiring Ms Data In The Sim Scan

    Acquire a file of reserpine data using the selected ion monitoring (SIM) the SIM Scan scan from the Tune Plus window Note The LTQ XL MS detector automatically saves the data you acquire on your hard disk. 1. On the Control/Scan Mode toolbar, click On/Standby to take the MS detector out of Standby mode and turn it On.
  • Page 107 8. Click Start in the Acquire Data dialog box to begin acquiring data. The Acquisition Status group box displays the following message. State: Acquiring Time (min): 9. Click Divert/Inject Valve to open the Divert/Inject Valve dialog box. Figure Thermo Electron Corporation LTQ XL Getting Started...
  • Page 108 Spectrum view. See Figure 48. Wait about 1 min before you inject again (step 13.b, below). 13. Perform the following repetitive sequence to obtain a total of four consecutive loop injections of reserpine. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 109 14. Click Close in the Divert/Inject Valve dialog box to return to the Tune Plus window. 15. Click Stop in the Acquire Data dialog box to end the data acquisition. Click Cancel to close the Acquire Data dialog box. Thermo Electron Corporation LTQ XL Getting Started...
  • Page 110 Review the mass spectrum and chromatogram in the Xcalibur Qual Browser window. See Figure For more information about reviewing the data you acquired using the LTQ XL MS detector with the Xcalibur data system, refer to the Xcalibur Getting Productive: Qualitative Analysis manual. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 111 Figure 49. Qual Browser window, showing loop injections of reserpine in the Chromatogram view (left) and showing m/z 609 in the Spectrum view. Note that the injections occur at intervals of approximately 1 min Thermo Electron Corporation LTQ XL Getting Started...
  • Page 112 Acquiring ESI Sample Data Using the Tune Plus Window Acquiring MS Data in the SIM Scan LTQ XL Getting Started Thermo Electron Corporation...
  • Page 113 • Removing the Ion Max Ion Source Housing • Removing the Ion Sweep Cone (optional) • Installing the Corona Needle • Installing the Ion Max Ion Source Housing • Installing the APCI Probe Thermo Electron Corporation LTQ XL Getting Started...

  • Page 114: Removing The Esi Probe

    CAUTION Handle the 8 kV cable with care. a. Unlock the cable by rotating the locking ring counter-clockwise. b. Unplug the 8 kV cable from the ESI needle high voltage receptacle. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 115 API interlock block. Once the probe is all the way back and aligned with the slot, turn the probe 45 degrees Thermo Electron Corporation LTQ XL Getting Started...
  • Page 116 9. Pull the probe straight out to remove it from the ion source housing. 10. Store the ESI probe in its original shipping container. The ESI probe is properly removed from the Ion Max ion source housing. LTQ XL Getting Started Thermo Electron Corporation...

  • Page 117: Removing The Ion Max Ion Source Housing

    Removing the Ion Sweep Cone. Otherwise, go to the topic “Installing the Corona Needle” page 107. Ion Source Housing Locking Lever(s) Ion Source Housing Drain Figure 51. Ion Max ion source housing, detail of components Thermo Electron Corporation LTQ XL Getting Started...

  • Page 118: Removing The Ion Sweep Cone

    The ion sweep cone is now properly removed. If you need to install the corona needle, go to the next section, Installing the Corona Needle. Otherwise, go to the section, “Installing the Ion Max Ion Source Housing” page 108. LTQ XL Getting Started Thermo Electron Corporation...

  • Page 119: Installing The Corona Needle

    2. Make sure the tip of the needle is aligned with the path of travel between the APCI probe and the ion source interface on the instrument. The corona needle is now properly installed. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 120: Installing The Ion Max Ion Source Housing

    See Figure 53 Figure Ion Source Housing Locking Levers Guide Ion Source Pin Holes Housing Drain Figure 53. Rear view of the Ion Max ion source housing LTQ XL Getting Started Thermo Electron Corporation...
  • Page 121 Route the drain tube from the API source to a waste container. Vent the waste container to a dedicated fume exhaust system 3. Reinstall the ion source drain tube as follows: Thermo Electron Corporation LTQ XL Getting Started...
  • Page 122 Attach the free end of the hose to a waste container. Ideally, the waste container should be vented to a fume exhaust system. The Ion Max ion source housing is now properly installed on the MS detector. LTQ XL Getting Started Thermo Electron Corporation...

  • Page 123: Installing The Apci Probe

    6. Seat the probe all the way down into the alignment notch. Thermo Electron Corporation LTQ XL Getting Started...
  • Page 124 11. Connect the auxiliary gas fitting (green) to the auxiliary gas inlet (A) on the probe. (Figure 55) 12. Connect the sample transfer line to the APCI probe inlet. The APCI probe is now properly installed in the Ion Max ion source housing. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 125 Leave the LC/MS system in Standby and go to Chapter 7: “Optimizing the MS Detector with Your Analyte in APCI/MS Mode”. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 127: Mode115

    Note The following procedures assume that you are familiar with your LTQ XL instrument and the Tune Plus window. For more information, refer to the LTQ XL online Help, LTQ XL Getting Connected, or the LTQ XL Hardware Manual. Ensure that you have completed the procedures in the topics Tuning and Calibrating Automatically in the ESI/MS Mode and Setting Up to Acquire Data in the APCI/MS Mode.

  • Page 128: Setting Up The Inlet For Tuning Using High-Flow Infusion

    (brown) ferrule to the free end of the LC union. b. Connect the other end of the infusion line with a (red) fingertight fitting and a (brown) ferrule to the side arm of the LC Tee union. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 129 (brown) ferrule to a free end of the (black) LC Tee union. c. Connect the other end of the PEEK tubing with a (red) fingertight fitting and a (brown) ferrule to the LC inlet located on the APCI probe. Thermo Electron Corporation LTQ XL Getting Started...
  • Page 130 Insert the other end of the PEEK tubing in a suitable waste container. The LC plumbing connections are now properly made for APCI/MS sample introduction from the syringe pump into solvent flow from an LC. LTQ XL Getting Started Thermo Electron Corporation...

  • Page 131: Setting Up The Ms Detector For Apci/Ms Operation

    Scroll down until you see the folder C:\Xcalibur\methods. Then, select the file APCIhighflow.LTQTune. c. Click OK to open the file. LTQ XL MS detector downloads the Tune Method parameters to the MS detector. 3. Verify that the LTQ XL MS detector opened the Tune Method, as follows: a.
  • Page 132 In the Scan Time group box, in the Microscans spin box, type 1 to set the total number of microscans to 1. f. In the Max. Inject Time spin box, type 200.000 to specify a 200 ms maximum injection time. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 133 Click OK to apply the MS detector scan parameters and to close the Define Scan dialog box. 5. On the Control/Scan Mode toolbar, click Centroid/Profile to toggle the data type to centroid. (The picture on the button should be the same as that shown here). Thermo Electron Corporation LTQ XL Getting Started...
  • Page 134 6. Click the Positive/Negative button to toggle the ion polarity mode to positive. (The picture on the button should be the same as that shown here). You have now completed setting up your MS detector for APCI/MS operation. LTQ XL Getting Started Thermo Electron Corporation...

  • Page 135: Optimizing The Tune Of The Ms Detector Automatically In Apci/Ms Mode

    Please ensure that the 500 microliter syringe is full. Ensure the syringe pump contains at least 450 μL of the 125 fg/μL reserpine tuning solution. b. Click OK to close the message box, and return to the Tune Plus window. Thermo Electron Corporation LTQ XL Getting Started...
  • Page 136 Figure 60. Tune dialog box, showing the Automatic tuning page 7. Observe the Tune Plus window and the Tune dialog box. While automatic tuning is in progress, the LTQ XL MS detector displays various tests in the Spectrum and Graph views in the Tune Plus window and displays various messages in the Status group box in the Tune dialog box.
  • Page 137 Optimizing the MS Detector with Your Analyte in APCI/MS Mode Optimizing the Tune of the MS Detector Automatically in APCI/MS Mode Figure 61. Tune Plus window with the Tune dialog box, showing the Automatic tuning page Thermo Electron Corporation LTQ XL Getting Started...

  • Page 138: Saving The Apci/Ms Tune Method

    Select the C:\Xcalibur\methods folder. 2. Click the File Name text box, and then enter APCImyTune to name the Tune Method APCImyTune.LTQTune. Figure 62. Save As dialog box, showing files in the folder C:\Xcalibur\methods LTQ XL Getting Started Thermo Electron Corporation...
  • Page 139 3. Click Save to save the Tune Method and close the Save As dialog box. Note that the Tune Method is named APCImyTune.LTQTune. Before you acquire data, go to the next section, Cleaning the MS Detector after Tuning in APCI Mode. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 140: Cleaning The Ms Detector After Tuning In Apci Mode

    APCI Mode 1. Click On/Standby to put the MS detector in Standby mode. When the MS detector is in Standby, the LTQ XL MS detector turns off the vaporizer heater, corona discharge voltage, and syringe pump. The MS detector stops scanning, and the LTQ XL MS detector freezes the Standby displays for the Spectrum and Graph views.
  • Page 141 7. Reinstall the Ion Max ion source housing as described in “Installing the Ion Max Ion Source Housing” page If you plan to run analytical samples in APCI mode, go to Chapter 8: “Acquiring APCI Sample Data Using the Tune Plus Window”. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 143: Acquiring Apci Sample Data Using The Tune Plus Window

    Note The following procedures assume that you are familiar with your LTQ XL instrument and the Tune Plus window. If you need information, refer to the LTQ XL online Help, LTQ XL Getting Connected and/or LTQ XL Hardware Manual.

  • Page 144: Setting Up To Introduce Sample By Loop Injection Into Solvent Flow From An Lc

    To Waste Load Position Inject Position Figure 63. Divert/Inject valve, showing the correct setup for analysis by loop injection and showing the flow of liquid through the valve in the Load and Inject positions LTQ XL Getting Started Thermo Electron Corporation...
  • Page 145 Insert the other end of the PEEK tubing into a suitable waste container. The MS detector is now set up to introduce sample by loop injection into solvent flow from an LC. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 146: Acquiring Apci Data In The Sim Scan Mode

    1. If you have not already done so, in Tune Plus, click On/Standby to take the MS detector out of Standby mode and turn it On. The MS detector begins scanning, and the LTQ XL MS detector applies high voltage to Standby the corona needle and shows a real-time display in the Spectrum view.
  • Page 147 See Figure 67. The Acquisition Status group box displays the following message. State: Acquiring Time (min): Figure 66. Acquire Data dialog box, showing the acquisition status of the raw data file Thermo Electron Corporation LTQ XL Getting Started...
  • Page 148 Figure 67. Tune Plus window, showing the SIM spectrum of reserpine during analysis by loop injection 9. Inject the reserpine solution into the APCI source from the Instrument Setup toolbar, as follows: a. Click Divert/Inject Valve to display the Divert/Inject Valve dialog box. See Figure LTQ XL Getting Started Thermo Electron Corporation...
  • Page 149 Xcalibur Qual Browser window. See Figure For more information about reviewing the data you acquire using the LTQ XL MS detector with the Xcalibur data system, refer to the Xcalibur Getting Productive: Qualitative Analysis manual. Thermo Electron Corporation LTQ XL Getting Started...
  • Page 150 “Setting Up to Acquire MS/MS Data in the Full Scan Type” page 84 for information about setting up the LTQ XL MS detector Figure 69. Qual Browser window, showing loop injections of reserpine in the Chromatogram view (left) and m/z 609 in the...

  • Page 151: Appendix A Sample Formulations

    Read the MSDS for each chemical you use. Dispose of all laboratory reagents in the appropriate way (see the MSDS). Potentially hazardous chemicals used in procedures throughout this manual include: • Acetic acid • Acetonitrile • Methanol • Reserpine • Formic Acid Thermo Electron Corporation LTQ XL Getting Started...

  • Page 152: Caffeine, Mrfa, And Ultramark 1621 Stock Solutions

    Sigma, write or call: Sigma Chemical Company P. O. Box 14508 St. Louis, Missouri, USA 63178-9916 (800) 325-3010 (in the USA) (905) 829-9500 (in Canada) (314) 771-3750 (outside the USA or Canada) www.sigmaaldrich.com LTQ XL Getting Started Thermo Electron Corporation...

  • Page 153: Stock Solution: Caffeine

    Stock Solution: Caffeine A 1 mg/mL stock solution of caffeine in 100% methanol is provided with your LTQ XL system. This is also the concentration of the Sigma replacement mentioned in the Note above (Sigma #C6035). Thermo Electron Corporation...

  • Page 154: Stock Solution: Mrfa

    Special care in taking the sample may be needed as the Ultramark 1621 has a high viscosity. Dissolve the 10 μL of Ultramark 1621 in 10 mL of acetonitrile. 3. Mix the solution thoroughly. 4. Label the vial Ultramark 1621 stock solution. LTQ XL Getting Started Thermo Electron Corporation...

  • Page 155: Esi Calibration Solution: Caffeine, Mrfa, Ultramark 1621

    50:50 methanol:water. 7. Mix the calibration solution thoroughly. 8. Transfer the solution to a clean, dry vial. 9. Label the vial ESI Calibration Solution and store it in a refrigerator until it is needed. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 156: Stock Solution: Reserpine

    6. Mix this solution (1 ng/μL=1.64pmol/μL) thoroughly. 7. Transfer 10 μL of the 1 ng/μL solution into a clean polypropylene tube. 8. Add 990 μL of 1% acetic acid in 50:50 methanol:water to the tube. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 157 16. Label the tube Reserpine APCI Sample Solution (250 fg/ L) . It is best to use this solution immediately after it is made. Keep it in a light-resistant container in a refrigerator if it must be stored. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 159: Appendix Bltq Xl High Mass Range Calibration

    Appendix B Calibration A high mass range calibration is necessary if you want to use your LTQ XL to analyze masses in the 2000 u-4000 u range. This appendix provides instructions for the high mass range calibration of the LTQ XL. The...

  • Page 160: High Mass Range Calibration Solution

    MSDS. Read the material safety data sheets for each chemical you use. LTQ XL Getting Started Thermo Electron Corporation...

  • Page 161: Normal Mass Range Calibration

    2. The expected high mass (1822.00 peak of the Ultramark 1621 component) 3. Observed low mass (observed mass of the caffeine component) 4. Observed high mass (observed mass of the 1822 peak of the Ultramark 1621 component). Thermo Electron Corporation LTQ XL Getting Started...

  • Page 162: Enter Normal Mass Range Data Into Tune Plus

    Manual Coarse Calibration group box. 5. In the Calibrate Current Scan Type group box, choose User in the Mass list box. In the Expected Low Mass box type 195.10 and type 1822.00 LTQ XL Getting Started Thermo Electron Corporation...
  • Page 163 6. In the Estimate Other Calibration Modes Using Current Full Scan box, click Execute. 7. Click Save at the bottom right of the Manual Coarse Calibration window. 8. Click OK at the bottom of the Diagnostics dialog box. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 164: Tune On M/Z 524.3

    4. In the Mass spin box, type 524.3 to specify that the LXQ MS detector uses the peak at m/z 524.3 to optimize your tune. Figure 71. Tune window showing the MS detector Tune on m/z 524.3u 5. Click Start. A message box displays the following message: LTQ XL Getting Started Thermo Electron Corporation...
  • Page 165 LXQ MS detector displays various tests in the Spectrum and Graph views in the Tune Plus window and displays various messages in the Status group box in the Tune dialog box. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 166: High Mass Range Calibration Procedure

    Figure 73. Click Execute, click Save, and close the window. 4. In the Tune Plus window, choose Control>Calibrate to open the Calibrate dialog box (Figure 74). Figure 72. PPG2700 mass spectrum LTQ XL Getting Started Thermo Electron Corporation...
  • Page 167 High Mass Range Calibration Procedure Figure 73. Tune Plus Diagnostics dialog box, two point high mass calibration Thermo Electron Corporation LTQ XL Getting Started...
  • Page 168 Figure 74). 6. In the What To Do box, select the Calibrate button. Type a calibration mass list name in the Name list box inside the Calibration Mass List group box. LTQ XL Getting Started Thermo Electron Corporation...
  • Page 169 • If you want the LTQ XL to remain in the On mode after the calibration, clear the check box. 11. Start the calibration procedure.
  • Page 170 At the conclusion of the procedure, you must clean the syringe and API source (change the tubing and syringe, clean the API source with acetone to remove the polypropylene glycol). LTQ XL Getting Started Thermo Electron Corporation...

  • Page 171: Notes

    3. In order to calibrate with High Mass Range Zoom Scan, it may be necessary to reduce the Zoom Scan target from 3000 u to 1000u. Thermo Electron Corporation LTQ XL Getting Started...

  • Page 173: Index

    50, 75, 94, 120, Calibrate dialog box Depth Focus, discussion description dialog boxes displaying Accept Optimized Value figure APCI Source messages in Status box Tune calibration discussion ions LTQ XL setup Thermo Electron Corporation LTQ XL getting Started 161...
  • Page 174 Tune Method, LC/ESI/MS operation introducing sample placing in Standby introducing samples into Finnigan LTQ, discussion setting up for APCI/MS operation Ion Max ion source setting up for ESI/MS operation discussion installing removing Ion Optics dialog box LTQ XL getting Started Thermo Electron Corporation...
  • Page 175 Tune Plus preparing calibration solution from calibrating LTQ XL automatically reordering (note) cleaning Finnigan LTQ after tuning and calibrating spectral ion from cleaning LTQ XL after tuning and calibrating MRFA Stock solution installing MS/MS APCI probe acquiring, data corona discharge needle...
  • Page 176 LTQ XL for LC/ESI/MS operation setup for LTQ XL (note) syringe pump, setup for voltages Ultramark 1621 cleaning spray shield of contamination from (in caution note) preparing calibration solution from preparing stock solution of LTQ XL getting Started Thermo Electron Corporation...

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