Agilent Technologies 1100 series Quick Start Manual
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Agilent Technologies 1100 series Quick Start Manual

Agilent Technologies 1100 series Quick Start Manual

Lc/msd trap system
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See also: Service Manual , Reference Manual
Agilent 1100 Series LC/MSD Trap
System Quick Start Guide
A guide to help you get started with the
LC/MSD Trap system
What is the Agilent 1100 Series LC/MSD Trap System?
Where to find additional system information
What is new in version 5.2 software?
Instructional overview
Step 1—Start the software
Step 1a—Become familiar with the software
Step 2—Prepare the instrument
Step 3—Set up and run an acquisition method
Step 4—Review data and identify compounds
Optional steps
34
Deconvolute and search protein spectra
Quantify compounds
Shut down or place the instrument in Standby
Agilent methods, data files and report layouts
Use this document to find help to install and troubleshoot
system hardware, to install the system software and to acquire
and analyze data with the LC/MSD Trap.
Agilent Technologies
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Summary of Contents for Agilent Technologies 1100 series

  • Page 1 System Quick Start Guide A guide to help you get started with the LC/MSD Trap system What is the Agilent 1100 Series LC/MSD Trap System? Where to find additional system information What is new in version 5.2 software? Instructional overview Step 1—Start the software...

  • Page 2: What Is The Agilent 1100 Series Lc/Msd Trap System

    What is the Agilent 1100 Series LC/MSD Trap System? The LC/MSD Trap system consists of the Agilent 1100 Series LC, an atmospheric pressure ion source and the MSD Trap mass spectrometer, which can be one of several models: Classic, VL, SL, or XCT.

  • Page 3: Where To Find Additional System Information

    Presents instructions to back up and recover the PC, including OS and application software, if there is a problem. Included with new system bundles; also available on the CD as a PDF file. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 4: What Is New In Version 5.2 Software

    New for individual programs with or without compliance software LC/CE/Sequence control with ChemStation A.10.02 • Capacity to store methods in any location (recommended to use subdirectories in the default method root) Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 5: Data Analysis

    • Improved Find Compounds - AutoMS(n) algorithm (limits algorithm to find the x most intense compounds) • Improved monoisotopic peak determination of precursor • Library Search: Inclusion of the measured mass range with the spectrum properties. QuantAnalysis • Improved weighted calibration Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 6: Instructional Overview

    Instructional overview Install the Trap System hardware Use the instructions in the Agilent 1100 Series LC/MSD Trap System Installation Guide to install the hardware. Install the Trap System software Use the instructions in the Agilent 1100 Series LC/MSD Trap System Installation Guide to install all the software components.

  • Page 7: Step 1-Start The Software

    The instructions below include the following assumptions: • The hardware and software are properly installed. • The instrument is configured. Use instructions in the Agilent 1100 Series LC/MSD Trap System Installation Guide to configure the instrument for the first time.
  • Page 8 MSD Trap Control. ChemStation MSD Trap Control • Click the ChemStation button in MSD Trap Control. DataAnalysis • Select Tools > ChemStation, or • Click the ChemStation button in DataAnalysis. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 9: Start The Trap Software For An Offline Installation

    The ReportDesigner program lets you create your own report layouts or modify the existing ones. • Select Start > Programs > LCMSD Trap > ReportDesigner, 1 Open DataAnalysis. 2 Select Print..., or Print Preview..., > ReportDesigner..Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 10: Chemstation Window

    LC part of LC-only or LC/MS methods, set up information for single runs or sequences and acquire data. See the Agilent ChemStation document set and ChemStation Online Help to familiarize yourself with this software. Figure 1 ChemStation window Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 11: Msd Trap Control Window

    Top Menu Toolbar Line spectra displayed here Profile spectra displayed here Display Panes Chromatograms displayed here Status Modes Tabs General Trap Parameters Acquisition Method Editor Figure 2 Initial MSD Trap Control window Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 12 ChemStation, then the file name and directory locations are prescribed in ChemStation’s Sample Info. Stop the acquisition Acquisition > Stop Run (F8) Pause the acquisition Acquisition > Pause (Ctrl + F8) Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 13 Tile the spectrum windows View > Tile Spectrum Windows Show the LC program View > LC Program (Shift+F11) Show DataAnalysis Program View > DataAnalysis (F11) About MSD Trap Control Help > About... Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 14 To adjust the frame border move the cursor to the edge and click and drag the border until your screen appears as in Figure Figure 3 Comparison of a Line spectrum and Profile spectrum Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 15 See “Exercise 3.Change and run method to optimize peak height” on page 45 of the Familiarization Guide to learn how to set up segments. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 16 This results in a slight degradation of mass assignment and resolution. Suggested values for the ICC Target are provided with the default methods (e.g., DEF_LCMS.M). Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 17 This action improves the spectral quality at the expense of chromatographic fidelity. Peaks appear skewed (rapid rise followed by a longer tailing edge). Disable this feature for quantitative work. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 18: Status Modes

    Trap trap. The Divert Valve is switched To Waste. before you are able to switch the ion sources.] Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 19: Dataanalysis Window

    7 to learn how to open this window. “Step 4—Review data and identify compounds” on page 28 and “Deconvolute and search protein spectra” on page 34 for more information on how to to use this window. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 20: Quantanalysis Window

    Figure 6 QuantAnalysis window “Step 1—Start the software” on page 7 to learn how to open this window. “Quantify compounds” on page 35 for more information on how to use this window. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 21: Step 2-Prepare The Instrument

    Do a scan Prepare the Start calibration LC to run the here! sample Do an Prepare the isolation calibration instrument Optimize Optimize Do a fragmentation sensitivity fragmentation (MS/MS) (MS) calibration Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 22: Step 3-Set Up And Run An Acquisition Method

    Start Enter LC Enter MS parameters parameters Here! Set up and run an Enter sample acquisition information method Acquire data Set up displays Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 23: Set Up An Acquisition Method

    If infusing into LC flows, set LC rate to be used during the analysis. pump rate in ChemStation. Figure 7 Tubing from the Syringe Pump (1) to the Nebulizer (2) Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 24 Dry Temp 325 – 350 °C 5 Switch to Operate state. • On the Main window, select the • All of the electrical elements for Operate button. generating and directing ions are turned on. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 25 • You cannot change the name of the b Replace the name of the default default method. You must save all method with the name of your new changes under a new method name. method. c Click OK. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 26: Acquire Ms/Ms Spectral Data Only

    • The previously selected mass is set window to open a context menu, as the isolation mass. and select Isolate/Fragment. • Check that the ion is isolated and all other ions in the Line Spectrum window disappear. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 27: Acquire Chromatographic And Spectral Data

    Sample Info tab. 2 Stop the acquisition. Stop the method manually: • Click the Stop button, or • From the top menu, select RunControl > Stop Run. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 28: Step 4-Review Data And Identify Compounds

    Review data for automatic compounds and identify processing and based on compounds reporting spectra Create and (Optional) Generate use library to Create your reports from identify own report default layouts compounds layouts Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 29: Start The Dataanalysis Software

    Select the trace with the mouse cursor. c Make the desired changes. d Click Change to confirm the changes to the trace. e Click OK. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 30: Find Compound Ms Spectra

    Line and profile spectra. MS chromatogram. f Select Find > Compounds – Chromatogram. View three spectra in the same a Right-click the Compound Mass window. Spectra window. b Select List windows > 3 windows. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 31: Find Compound Ms/Ms Spectra And Generate A Results Report

    Report. b For this example, select Cmpd Mass Spec Report –AutoMS(n) (P) from the list of Layouts. c Click OK. d When prompted to save your processed results, always click Yes. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 32: Create And Use A Library To Identify Unknowns

    Select Identify > Parameters... c Click the Libraries tab. d Click the New (Insert) button in the Libraries tab. e Click the Browse button (...). f Select the database, and click Open. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 33 Print the results from the Compound a In DataAnalysis, select File > List window to a Library Search Report. Print..b Select Library Search Report – AutoMS(n) from the pull-down list. c Click OK. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 34: Optional Steps

    • Online Help for the tasks listed for the roadmap below and descriptions of the fields found on the windows and dialog boxes needed for these tasks. Start Deconvolute Extract spectra spectra for Here! deconvolution Deconvolute and search Export spectra protein spectra Search MASCOT database Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 35: Quantify Compounds

    Start Create a Import and quantitation modify a Here! method sequence Quantify an Quantify unknown compounds sample Print the quantitation report Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 36: Shut Down Or Place The Instrument In Standby

    3 Select Ask which mode to activate, and click Apply. 4 Exit the MSD Trap Control software. 5 When the message appears to ask for Standby or Shutdown, select Standby, and click OK. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 37: Power Off The Instrument

    • Power failure to the PC or to the Trap (Upon power restoration, the instrument remains shut down.) • Gas flow error Shutdown mode indicator becomes red. Active run or sequence is stopped. Divert valve is set To Waste. • Vacuum fault Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 38: Agilent Methods, Data Files And Report Layouts

    Demonstrates all properties of UV chromatograms Add_UV.d Add_Var.M Demonstrates all properties of acquisition parameter traces Add_VAR.d Add_Mult.M Creates an array of chromatograms Add_Mult.d Add_Range.M Demonstrates the 'AddRangeSelection' and RangeAvg.d 'AverageMassSpectrum' methods Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 39 Opens another data file Add_BPC.d Base.d RngeSelDiss.M Runs the Find Compounds Dissect function for a specified time S_MS.d range RngeSelAutoMSn.M Runs the Find Compounds AutoMSn function for a specified S_AMS2N1.d time range Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 40 Compound Mass Spectra entry with the averaged spectrum. BaseLineSubtract Add_Range Performs a baseline subtraction on spectra of a Compound Mass Spectra object. The parameters for this algorithm will be taken from method. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 41 Also export spectra to MGF, ASCII, XML, or CSV ExpSpec; Form; Metabolite_ID; Smooth formats and Compound MS to MGF, XML, and CSV formats. ExportMassList ExpMList Exports Compound MS mass lists to ASCII or CSV formats. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 42 Chromatogram. Data Mining of MS and UV data files. Finds peaks within the chromatograms traces and integrates them. Places results in Compound List Open Open_File Opens *.d file from user-specified directory. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 43 Help > VBScript on the Web > Install Microsoft ActiveX Control Pad… This enables the use of a special toolbox for use in the Object View of the VBScript window (see figure below). Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 44: Comma Separated Value (Csv) Methods For Msd Trap Control

    SL_XCT Options Options and Advanced dialogs VL OneSegmentMRM(2)_2Ions Defines a Method with only one Segment, MRM operations and two iterations of two precursor ions Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 45: Report Layouts For Dataanalysis And Quantanalysis

    (overlaid), compound mass spectra and corresponding mass lists Cmpd Mass Spec Report - AutoMSn Analysis Info, most important acquisition parameters (P).layout (including AutoMS(n)), chromatogram display (overlaid) and compound mass spectra Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 46 Modified Cmpd Chrom Report 3R1C - MS (P).layout to represent S/N results for installation checkout Single Mass Spec Decon Report Analysis info, important acquisition parameters, (P).layout display of Mass Spectrum window and deconvolution results for spectrum Agilent 1100 Series LC/MSD Trap System Quick Start Guide...
  • Page 47 † For all Display reports, the windows available to open include Chromatogram, Mass Spectrum View, Compound Mass Spectra and Mass Spectrum windows. Agilent 1100 Series LC/MSD Trap System Quick Start Guide...

  • Page 48: In This Book

    • Shut down or place the instrument in standby This book also contains a listing of new 5.2 software features and shipped methods and report layouts.  Agilent Technologies, Inc. 2004 Printed in USA First Edition, April 2004 *G2440-90089 * G2440-90089 Agilent Technologies...

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