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Transcript of Agilent G1974A PDF-MALDI Source for LC/MSD .Agilent Technologies Agilent G1974A PDF-MALDI Source

  • Agilent Technologies

    Agilent G1974A PDF-MALDI Source for LC/MSD Trap and TOF Systems

    Installation Guide

  • Notices Agilent Technologies, Inc. 2004

    No part of this manual may be reproduced in any form or by any means (including electronic storage and retrieval or transla-tion into a foreign language) without prior agreement and written consent from Agi-lent Technologies, Inc. as governed by United States and international copyright laws.

    Manual Part Number

    G1974-90004

    Edition

    First Edition, November 2004

    Printed in USA

    Agilent Technologies, Inc.5301 Stevens Creek Blvd. Santa Clara, CA 95052

    Warranty

    The material contained in this docu-ment is provided as is, and is sub-ject to being changed, without notice, in future editions. Further, to the max-imum extent permitted by applicable law, Agilent disclaims all warranties, either express or implied, with regard to this manual and any information contained herein, including but not limited to the implied warranties of merchantability and fitness for a par-ticular purpose. Agilent shall not be liable for errors or for incidental or consequential damages in connection with the furnishing, use, or perfor-mance of this document or of any information contained herein. Should Agilent and the user have a separate written agreement with warranty terms covering the material in this document that conflict with these terms, the warranty terms in the sep-arate agreement shall control.

    Technology Licenses

    The hardware and/or software described in this document are furnished under a license and may be used or copied only in accordance with the terms of such license.

    Restricted Rights Legend

    If software is for use in the performance of a U.S. Government prime contract or sub-contract, Software is delivered and licensed as Commercial computer soft-ware as defined in DFAR 252.227-7014 (June 1995), or as a commercial item as defined in FAR 2.101(a) or as Restricted

    computer software as defined in FAR 52.227-19 (June 1987) or any equivalent agency regulation or contract clause. Use, duplication or disclosure of Software is subject to Agilent Technologies standard commercial license terms, and non-DOD Departments and Agencies of the U.S. Gov-ernment will receive no greater than Restricted Rights as defined in FAR 52.227-19(c)(1-2) (June 1987). U.S. Govern-ment users will receive no greater than Limited Rights as defined in FAR 52.227-14 (June 1987) or DFAR 252.227-7015 (b)(2) (November 1995), as applicable in any technical data.

    Safety Notices

    CAUTION

    A CAUTION notice denotes a haz-ard. It calls attention to an operat-ing procedure, practice, or the like that, if not correctly performed or adhered to, could result in damage to the product or loss of important data. Do not proceed beyond a CAUTION notice until the indicated conditions are fully understood and met.

    WARNING

    A WARNING notice denotes a hazard. It calls attention to an operating procedure, practice, or the like that, if not correctly per-formed or adhered to, could result in personal injury or death. Do not proceed beyond a WARNING notice until the indicated condi-tions are fully understood and met.

  • G1974A PDF-MALDI Installation Guide iii

    Contents

    1 Installation for LC/MSD SL, XCT Trap, and XCT Plus Trap Systems

    Installation 2

    Step 1. Prepare to install the Source 2Step 2. Connect the APPI Internal cable 10Step 3. Install the Video Capture Board software 11Step 4. Install the Video Capture Board hardware 18Step 5. Install the Source 19Step 6. Attach cables to the Control Unit and the Source 25Step 7. Install the Target software 31Step 8. Load the PDF-MALDI USB Drivers 35

    Configuration and verification 38

    Step 1. Program the default methods 38Step 2. Use the Alignment Tool 41Step 3. Verify the hardware installation 45Step 4. Check the Target Plate alignment 46Step 5. Center the matrix spot 48Step 6. Calibrate the Video Capture sample-positioning system 50Step 7. Verify the installation 55

    2 Installation for LC/MSD TOF Systems

    Installation 62

    Step 1. Prepare to install the Source 62Step 2. Install the Video Capture Board software 68Step 3. Install the Video Capture Board hardware 74Step 4. Install the Source 76Step 5. Attach cables to the Control Unit and the Source 81Step 6. Install the Target software 87

    Configuration and verification 93

    Step 1. Program the default method 93Step 2. Use the Alignment Tool 94Step 3. Verify the hardware installation 45

  • iv G1974A PDF-MALDI Installation Guide

    Step 4. Check the Target Plate alignment 99Step 5. Center the matrix spot 100Step 6. Calibrate the Video Capture sample-positioning system 103Step 7. Verify the installation 108

    3 Reference

    PDF-MALDI Method Settings for LC/MSD Trap SL, XCT, or XCT Plus 114Default setting for an MS method 114Processing script for auto_PMF_MgfExport.MS 115Default settings for an MS/MS method 116Processing script for auto_MIS_MgfExport 118Default PDF-MALDI method settings for LC/MSD TOF 119

    Troubleshooting 120To change the position of the fiber optic cable 112To refocus the laser spot 120To disassemble and uninstall the Source 121

  • Agilent Technologies

    1Installation for LC/MSD Trap Systems

    Installation 2

    Step 1. Prepare to install the Source 2

    Step 2. Connect the APPI Internal cable 10

    Step 3. Install the Video Capture Board software 11

    Step 4. Install the Video Capture Board hardware 18

    Step 5. Install the Source 19

    Step 6. Attach cables to the Control Unit and the Source 25

    Step 7. Install the Target software 31

    Step 8. Load the PDF-MALDI USB Drivers 35

    Configuration and verification 38

    Step 1. Program the default methods 38

    Step 2. Use the Alignment Tool 41

    Step 3. Verify the hardware installation 45

    Step 4. Check the Target Plate alignment 46

    Step 5. Center the matrix spot 48

    Step 6. Calibrate the Video Capture sample-positioning system 50

    Step 7. Verify the installation 55

    This chapter contains instructions for the initial installation, configuration, and verification of the PDF-MALDI Ion Source on the LC/MSD SL Trap, XCT Trap, and XCT Plus Trap systems. For subsequent installations, you can skip steps in the procedure as noted.

  • 2 G1974A PDF-MALDI Installation Guide

    1 Installation for LC/MSD Trap Systems

    Installation

    This step describes how to install the PDF-MALDI Ion Source on LC/MSD SL Trap, XCT Trap, and XCT Plus Trap systems. It also describes how to install the Target 5.0 software on LC/MSD SL, LC/MSD XCT, and LC/MSD XCT Plus system control computers.

    Step 1. Prepare to install the Source

    You do this only the first time the Source is installed. If this is a subsequent installation, skip to Step 5. Install the Source on page 19.

    1 Check the calibration of the LC/MSD Ion Trap. All the tuning mass ions must have the correct mass assignments and acceptable peak widths. You should also check the electron multiplier voltage (EMV).

    For LC/MSD SL Trap systems - If the accumulation time is greater than 0.2 ms with an ICC setting of 50,000, clean the capillary, skimmer 1, and octopole 1. After cleaning the ion optics components, the detector voltage should be recalibrated. Rerun the scan calibration to confirm that the mass assignments and peak widths are correct.

    For LC/MSD XCT Trap systems - If the accumulation time is greater than 0.2 ms with a smart ICC setting of 125,000, clean the capillary, skimmer 1, and octopole 1. After cleaning the ion optics components, the detector voltage should be recalibrated. Rerun the scan calibration to confirm that the mass assignments and peak widths are correct.

    For LC/MSD XCT Plus Trap systems - If the accumulation time is greater than 0.2 ms with a smart ICC setting of 500,000, clean the capillary, skimmer 1, and octopole 1. After cleaning the ion optics components, the detector voltage should be recalibrated. Rerun the scan calibration to confirm that the mass assignments and peak widths are correct.

    For All LC/MSD Trap systems - The vacuum and helium conditions are correct. The high vacuum pressure reading should be less than 2.0 x 10-5 mtorr or 2.5 x 10-5 mbar (depending on the pressure units you use). The helium differential pressure reading should be 0.6 x 10-5 mbar less than the high vacuum reading. If the helium pressure is not set correctly, you will experience a loss of sensitivity.

  • Installation for LC/MSD Trap Systems 1

    G1974A PDF-MALDI Installation Guide 3

    After you clean the system, check the mass calibration again for proper mass assignments, accumulation times, and EMV settings.

    2 Check that you have received all components:

    Control Unit - Figure 1.

    PDF-MALDI Ion Source shown from various angles. - See Figures 2 and 3.

    Capillary Extension - Figure 4.

    Heating Sleeve - Figure 4.

    Centering Bushing - Figure 4.

    Wave Disk Spring - Figure 4.

    APPI internal cable - Figure 5.

    USB cable to connect Control Unit to computer - Figure 6.

    cable to connect Control Unit to Source - Figure 7.

    Laser Synchronization cable -Figure 8.

    video cable for CDD camera - Figure 9.

    video capture board components - Figures 10, 11, and 12.

    UV-grade fiber optic cable with SMA-connectors - Figure 13.

    Laser Alignment Tool - Figure 14

    Figure 1 Control Unit

  • 4 G1974A PDF-MALDI Installation Guide

    1 Installation for LC/MSD Trap Systems

    Figure 2 PDF-MALDI Ion Source

    Figure 3 PDF-MALDI Ion Source open to show the 96-spot target plate

    Cable AMale connector

    Laser ON Indicator

    Target PlateHV c