Agilent Technologies G1701EA Familiarization Manual
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Agilent Technologies G1701EA Familiarization Manual

Agilent Technologies G1701EA Familiarization Manual

Msd productivity chemstation
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  • Page 1 Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Agilent Technologies...
  • Page 2 Further, to the max- agreement and written consent from imum extent permitted by applicable Agilent Technologies, Inc. as governed by C AU TI ON law, Agilent disclaims all warranties, United States and international copyright either express or implied, with regard laws.
  • Page 3 In This Guide This guide contains a step-by-step exercise to help you become familiar with your Agilent 7890A GC/5975 MSD with G1701EA MSD Productivity ChemStation software. To successfully use this book, you need the following: • GC Inlet: Split/Splitless Inlet with EPC (default inlet configuration) •...
  • Page 4 Recalibrate and Quantitate Unknowns Modify a sequence for recalibration and then use it to quantitate an unknown sample. Create a Cool Down Method Create and store a maintenance method. Shut Down the System Frequently Asked Questions Agilent G1701EA MSD Productivity ChemStation...
  • Page 5 7890A GC/5975 MSD. This information can be found on the Agilent Technologies GC and GC/MS Hardware User Information and Utilities DVDs that ship with your instrument. The Agilent Technologies GC and GC/MS Hardware User Information...
  • Page 6 Agilent G1701EA MSD Productivity ChemStation...

  • Page 7: Table Of Contents

    General Information for Editing the GC Parameters Open the GC edit parameters window Add a column to ChemStation local inventory Select and configure a column Upload parameters from the 7890A GC Customize the status panel view Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 8 Exit the Data Analysis Program Create a SIM Quantitation Method Introduction Create a SIM Method Simultaneously Acquire Scan and SIM Data (SIM/Scan Mode) SIM/Scan Mode Cycle Frequency Run a Sequence Prepare the Samples Create the Sequence Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 9 Run the Sequence Create a Cool Down Method Create the Cool Down Method Use the Cool Down Method Shut Down the System Shut Down the MS Shut Down the GC Frequently Asked Questions Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 10 Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 11: Start Up The System

    With the instruments off and the G1701EA MSD Productivity ChemStation not running, the instruments are started and the MSD is pumped down. Finally, a method is loaded in preparation for bringing all instrument parameters to settings required for data acquisition.

  • Page 12: Start Up The Hardware

    Open the MSD analyzer top cover. Close the MSD vent valve. Press the Power button on the front of the MSD to power it on. The foreline pump will make a gurgling noise. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 13 The pumpdown is completely automatic and does not require operator actions. After the turbo pump starts and the ion gauge value reaches 100 mTorr, allow the MSD to operate for a minimum of 2 hours before acquiring sample data. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 14: Run The Chemstation Software

    OK. The screen will appear repeatedly until the temperatures are reached. Set the default printer to PDF Printer, if a PDF writer like Adobe Acrobat is installed on the computer. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 15: Select The Tune File

    From the Files list, select atune.u. The atune.u file contains the optimal MSD parameter settings determined during the last autotune run. Select OK. The atune.u tune file is loaded and the dialog box closes. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 16: Load The Method

    Select View > Instrument Control to close the Tune and Vacuum Control…. and display the Enhanced ChemStation Instrument Control window. Select the Load Method button, . The Load Method dialog box opens. Navigate to and select default.m in the msdchem/1/methods directory. Select OK. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 17: Tune The Ms

    Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Tune the MS Introduction Run Autotune Evaluate the Autotune Results Tune History Trends This chapter provides a brief introduction to tuning and explains how to run an autotune on the instrument. An autotune report is generated as well as a report to evaluate the autotune results.

  • Page 18: Introduction

    Please see the ChemStation online help for details on using manual tune. The autotune program described in this section adjusts the MS for good performance over the entire mass range and is recommended for most applications. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 19: Run Autotune

    69, 219, and 502 profile scans are displayed with abundance and peak widths noted. See Figure 1. The tune report is also generated as shown in Figure 2 on page 21. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 20 Tune the MS Figure 1 Profile scan results for mass 69, 219, and 502 Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 21 Tune the MS Figure 2 Autotune report Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 22: Evaluate The Autotune Results

    23 where the report shows a high ratio of mass 18 to 69. This report warns of a high amount of water in the system and a corrective action to be taken. Figure 3 Passing system verification tune report Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 23 Tune the MS Figure 4 Failing system verification tune report Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 24: Tune History Trends

    Tune the MS Tune History Trends Select View > Instrument Control. Select Checkout > View Previous Tunes... to display the Tuneplot window plotting the results of recent tune parameters. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 25: Create A Method For Qualitative Analysis

    Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Create a Method for Qualitative Analysis Introduction Edit the Entire Method General Information for Editing the GC Parameters This chapter describes how to create an acquisition method that will be used later to identify all compounds in an Agilent standard sample.

  • Page 26: Introduction

    As seen in the table, the range of the molecular ions is from 0 to 270 so we will scan for ions from 0 to 300 in the method. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 27: Edit The Entire Method

    MS parts of the currently loaded method. We are not modifying the Data Analysis part of the method at this time. Select OK to close the Edit Method dialog box. Because Method Information was selected, the Method Information dialog box opens. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 28 In the MS Connected to area, select the location where your S/SL inlet is attached to the MS through the column. Select OK to close the Inlet and Injection Parameters dialog box and display the GC Edit Parameters window. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 29: Check The Gc Configuration

    With the Miscellaneous tab selected, set the Pressure Units to psi. Under Valve Configuration set all Valve Type fields to Not Installed, and verify that the MSD transfer line is shown as a Thermal Aux Type. Figure 5 Miscellaneous configuration tab Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 30 For the Inlet pressure for this column, select the Front or Back Inlet from the dropdown. For the column Outlet pressure select Vacuum for the MS For the column Heated By select Oven from the dropdown. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 31 Select He gas from the dropdown for the inlet connected to column 1. The system uses the properties of helium to obtain an accurate flow and pressure relationship for the column. Click the Apply button to download any edits to the GC. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 32: Set The Gc Readiness State

    Click Apply to download these selections to the GC. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 33: Set The Gc Oven Parameters

    300 °C at a rate of 35 °C/min. The column is then held at 300 °C for an additional 2 minutes. At this time the oven is cooled down to 50 °C to await the next data acquisition run. Figure 9 GC oven parameters Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 34 300 °C oven temperature for 2 minutes after the run is finished before cooling down to 50 °C for the start of the next run. Select Apply to download these settings to the GC. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 35: Set The Gc Column Parameters

    In the dropdown list, select Constant Flow. In the Post Run field, enter 1.0 mL/min. Select Apply to download these settings to the GC. Figure 10 GC columns parameters Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 36: Set The Gc Inlet Parameters

    In the Mode area: From the Mode drop down list, select Splitless. In the Purge Flow to Split vent area: 50 mL/min In the field, enter In the Start Time field, enter Select Apply. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 37 Create a Method for Qualitative Analysis Figure 11 GC inlet parameters Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 38: Set The Gc Injector Parameters

    Select the Advanced button, . Additional options are displayed in the window. In the Plunger Speed area, select Fast. In the Sampling Depth area, Mark the Enable checkbox. In the field, enter Select Apply. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 39 Create a Method for Qualitative Analysis Figure 12 ALS parameters Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 40: Set The Gc Aux Heaters Parameters

    Value °C field. Select Apply. Figure 13 GC aux heaters parameters Set the GC signals parameters Select the Signals button, In the Signal Source dropdown list, select None for all the signal sources. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 41 Figure 14 GC signals parameters Select OK to download the selected parameters to the GC and close the GC Edit parameters window. The GC Detector Data dialog box opens. See Figure 15 on page 42. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 42: Edit The Gc Real Time Plots To Display

    Parameters dialog box opens. In the MS Instrument area enter: 3.00 min In the Solvent Delay field, enter In the EMV mode drop down list, select Gain Factor. 1.00 In the Gain Factor field, enter Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 43 Select the Scanning Mass Range tab: Mark the Scan Group 1 checkbox. 50.00 In the Start at Mass field, enter 300.00 In the End at Mass field, enter This scan range includes all the expected ions. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 44 Create a Method for Qualitative Analysis Figure 18 Specify the scan range Select the Threshold and Sampling Rates tab: In the Threshold field, enter In the Sampling Rate field, enter Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 45 Under High Mass, enter Plot Window #1 was set to be a TIC so no plotting entry is required. Plot Window #2 is a spectrum including all ions found between 50 and 350 m/z. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 46: Save The Method

    The Save Method As dialog box opens. See Figure Save the method demoscan.M in the Method File field. Enter Select OK to save the current ChemStation method as demoscan.m method. Figure 21 Saving the method Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 47: General Information For Editing The Gc Parameters

    Downloads any settings that have been changed to the GC and closes the GC Edit Parameters window. Cancel Discards any settings that have been changed and closes the GC Edit Parameters window. Help Displays help topics for the current parameter. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 48: Add A Column To Chemstation Local Inventory

    Column Catalog and add it to your Local Column Inventory. This example adds the supplied checkout column to local inventory. Select the Configuration icon to display the columns configured for the instrument. Figure 22 Columns configured for the instrument Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 49 Create a Method for Qualitative Analysis Click Inventory to display the Install Column 1 dialog box containing a list of columns in local inventory. Figure 23 The local inventory of columns Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 50 . Figure 25 Local inventory with the added column Columns added to local inventory can be quickly added and configured for the instrument. See “Select and configure a column” on page 51. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 51: Select And Configure A Column

    Figure 26 Columns configured for the instrument Click Inventory to display the Install Column 1 dialog box containing a list of columns in local inventory. Figure 27 The local inventory of columns Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 52 Under the Outlet heading dropdown, select the item the column outlet is attached to. For an MS select Vacuum. Under the Heated By heading dropdown, select the method for controlling the column temperature. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 53: Upload Parameters From The 7890A Gc

    To move an item up or down in the displayed list, select the item and then the up or down arrow buttons until it is in the desired position. Select Save to save the settings and return to the GC Edit Parameters window. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 54 Create a Method for Qualitative Analysis Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 55: Run The Scan Method

    Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Run the Scan Method Prepare the Sample Load the Method Run the Method Take a Snapshot View the Logbook In this chapter, a sample is prepared for data acquisition and the ALS is loaded with the sample, the solvent wash vial, and a solvent waste vial.

  • Page 56: Prepare The Sample

    Fill a solvent wash vial with isooctane and place it in injector turret location A for solvent wash mode A, B. Place a waste vial in turret location B specified for solvent wash mode A, B. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 57: Load The Method

    From the PC desktop, select the ChemStation shortcut icon, the Instrument Control window opens. Select the Load Method button, to open the Load Method window. Navigate to and select demoscan.M. Select OK to load the method and close the dialog box. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 58: Run The Method

    . The Start Run dialog box opens with the GC ALS, Inlet Location, and MS Connected to selections pre-populated. Figure 29 Start a single sample run In the Operator Name field, enter your name. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 59 During the solvent delay the system will prompt for you to override. When the time is up, the dialog box will close automatically. Observe the TIC real time plot and go to “Take a Snapshot” on page 61 after the second compound elutes. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 60 Run the Scan Method Figure 30 Instrument control window during single sample run Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 61: Take A Snapshot

    Analyze the compound of interest. Exit data analysis and return to the Instrument Control view. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 62: View The Logbook

    It is located in the instrument directory. Select the Logbook button, . The Logbook menu opens. Select Current Logbook to display the active log. Figure 32 The current logbook is open Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 63 Clear Logbook to delete the currently displayed logbook. • Save As Logbook to save the displayed logbook into a new • file. • Print Logbook to print the displayed logbook. Exit the Instrument Control program. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 64 Run the Scan Method Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 65: Qualitative Data Analysis

    Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Qualitative Data Analysis Integrate Peaks Edit the Method to Generate a Report Display Extracted Ion Chromatograms (EIC)s Enable or Disable the Right Mouse Click Context Menu Analyze Data Search the Spectral Library Print a Window, TIC, Spectrum, or Method...

  • Page 66: Integrate Peaks

    Start the data analysis program using the desktop Data Analysis icon, Figure 33 The initial data analysis window Select the Load Data File button, . The Select Data File dialog box is displayed. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 67 Qualitative Data Analysis Select Change Path. The Browse for Folder dialog box opens. Navigate to evaldemo.d. This is the data file from the scan analysis of our sample. Select OK. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 68 Qualitative Data Analysis In the Select Data File dialog box, select OK. The data file is loaded and the total ion chromatogram (TIC) is displayed. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 69: Edit The Integration Events

    The parameter is displayed in the Event field and the current setting is displayed in the Value field. Select the Value field. An Edit Integration Events confirmation message appears. Select Yes to change the setting. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 70: Save The Integration Events To The Method

    Select Yes to save the integration or No to continue without saving this integration to the method. If you selected Yes, a confirmation message appears displaying the saved auto integration parameter file name. Select OK to save the integration to the method. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 71: Manually Integrate Peaks

    Qualitative Data Analysis Figure 34 Integrated chromatogram Manually integrate peaks If required, “Edit the integration events” or load a saved integration events file. Select Tools > Options to display the Select DA Options dialog box. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 72: View The Integration Results In A Table

    If you want to delete an integrated peak, put the cursor on it and double-click the right mouse button. View the integration results in a table Select Chromatogram > Integrate Results…. The Tabulate window opens and lists the results. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 73 To print the integration table, select Print and navigate to your printer. To copy the table to your clipboard for use in another application, such as MS Excel, select Copy. Select Close to close the dialog box. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 74: Edit The Method To Generate A Report

    Check Percent Report and OK. Other report types can also be selected. The Percent Report Options dialog box opens. In the Destination pane, check where you want the report to be generated. Select OK. A confirmation message appears. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 75 Select Yes. The Save Method As dialog box opens. Select OK to save the setting to the current method. To interactively generate a report, select Chromatography > Percent Report. The report is displayed in a new window. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 76: Display Extracted Ion Chromatograms (Eic)S

    The default m/z range for each ion is -0.3 to +0.7 of the ion mass specified. You can change the range by entering the appropriate starting and ending values. Select OK. A window opens displaying a chromatogram for each ion. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 77 Qualitative Data Analysis Select the Merged Format button to toggle from a chromatogram that displays the ions separately to one that displays the ions superimposed. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 78: Enable Or Disable The Right Mouse Click Context Menu

    The enabled context menu is shown in Figure Figure 35 Right mouse click context menu Certain mouse actions like averaging peak spectra and manually editing the baseline of a peak require the standard mouse actions. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 79: Analyze Data

    Enlarge the first peak using a left mouse click and drag to create a rectangle around the peak. The chromatogram is enlarged for the selected area. This is the peak for the compound Dodecane. Figure 36 The enlarged peak Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 80 You must be using the standard mouse actions. Figure 37 The spectrum at the peak apex The Data Analysis Variable Watch Window now shows the peak spectrum in the X register. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 81: Subtract The Baseline Noise From The Spectra

    Y register. Select the Subtract button, . The difference (Y - X) will be displayed as a spectrum labeled with a [-] following its title. See Figure Figure 38 Subtracted spectrum for Dodecane Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 82: Select Target And Qualifier Ions

    SIM acquisition and quantitative analysis later. Table 4 Target and qualifier ion selections Compound Target Ion Qualifier Ion Dwell time Biphenyl Dodecane Chlorobiphenyl Methyl Palmitate Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 83: Search The Spectral Library

    81. Select the Select Library button, . The Library Search Parameters dialog box opens. Select Browse to open the Browse for Folder window. Navigate to the demonstration library demo.l and select it. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 84: Generate An Automated Library Search Report

    Double right-click on the spectrum. A search is performed and the results are displayed. Generate an automated library search report Open the data file. Select the Library Search Report button, . The Library Search Report Options dialog box opens. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 85 “Subtract the baseline noise from the spectra” on page 81. Select OK to generate the report. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 86: Print A Window, Tic, Spectrum, Or Method

    Select a printer Select File > Select Printer. Select printer from the list of printers on your system. Select OK. To change the page orientation Select File > Printer Setup. Select Orientation. Select OK. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 87: Select An Item To Print

    Save the Data Analysis Method Select the Save Method button, . The Save Method As dialog box opens. Enter a name for the method and select OK to save the updated parameters to this method. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 88: Exit The Data Analysis Program

    Exit the Data Analysis Program Select File > Exit. A warning message appears. Select Yes to close the program. If you have not saved your method, you will lose changes if you click Yes to exit now. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 89: Create A Sim Quantitation Method

    Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Create a SIM Quantitation Method Introduction Create a SIM Method Simultaneously Acquire Scan and SIM Data (SIM/Scan Mode) SIM/Scan Mode Cycle Frequency This chapter describes how to create a SIM method for our standard sample using the target and qualifier ions found during qualitative analysis.

  • Page 90: Introduction

    • The best time to switch groups - Agilent recommends that you choose a time to switch groups where the peaks are well separated to avoid variations in retention time due to sample matrix effects. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 91: Create A Sim Method

    MS parameters in the method. Select OK to load the method and close the dialog box. Select the MS Parameters button, . The MS SIM / Scan Parameters dialog box opens. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 92 In the Edit Ion area enter the values for all 4 ions in the group 1 ions time segment. In the m/z and Dwell fields enter the ion values for these compounds from Table 5 on page 93. After each ion addition, select Add/Modify Ion. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 93 Select Close to save settings and return to the MS SIM / Scan Parameters dialog box. Select OK. Select the Save Method button, . The Save Method As dialog box opens. In the Method File field, enter demosim and select OK. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 94 Analysis and Instrument/Acquisition check boxes. Select OK. The Method Information dialog box opens. In the Method Comments field, enter a description of this method. In the Method Sections To Run area, mark the Data Acquisition check box. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 95 Create a SIM Quantitation Method Select OK. The Save Method As dialog box opens. Confirm that demosim is entered in the Method File field and select OK. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 96: Simultaneously Acquire Scan And Sim Data (Sim/Scan Mode)

    Mark the Acquire Scan and SIM data check box. From the Acq. Mode dropdown box, select Scan. Select Scan Parameters. The Edit Scan Parameters dialog box opens and we can view our previous settings. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 97 Save the method with the name sim_scan.M. The individual cycle frequencies recorded here will be used to calculate the actual cycle frequency in the next section “SIM/Scan Mode Cycle Frequency” on page 98. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 98: Sim/Scan Mode Cycle Frequency

    For our example, Scan = 2.44 cycles/sec and SIM = 1.97 which results in an actual cycle time of 1.04 cycles/sec. To improve the number of data points, we could reduce the SIM dwell time, and increase the scan speed. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 99: 7 Run A Sequence

    Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Run a Sequence Prepare the Samples Create the Sequence Save the Sequence Load the Sequence Run the Sequence Print the Sequence Log This chapter describes how to create and run a sequence. A sequence is a list of samples to be analyzed and a designated method to be used for each analysis.

  • Page 100: Run A Sequence

    Fill a solvent wash vial with isooctane and place it in injector turret location A for solvent wash mode A, B. Place an empty waste vial in turret location B specified for solvent wash mode A, B. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 101: Create The Sequence

    Right mouse click and select Browse for Method. The Browse for Folder dialog box opens. Navigate to and select demoSIM. Select OK. The method name appears in the column. STD01 In the Data File column, enter Highlight rows 1 to 5. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 102 10 ng/mL. In row 4, under Sample column, change the value to 25 ng/mL. In row 5, under Sample column, change the value to 50 ng/mL. Select OK to close the Sample Log Table. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 103: Save The Sequence

    Save the Sequence Select the Save Sequence As… button, . The Save Sequence dialog box opens. eval In the File name field, enter Select Save. The dialog box closes and the sequence is saved. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 104: Load The Sequence

    Load the Sequence Select the Load Sequence button, . The Load Sequence dialog box opens. eval.s In the File Name field, enter Click Select to close the dialog box and load the sequence. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 105: Run The Sequence

    Use the controls on the bar to pause the sequence, access data analysis, or edit sequence sample entries that have not yet run. Figure 43 The sequence status bar Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 106: Print The Sequence Log

    Run a Sequence Print the Sequence Log Select the Print button, . The Select Items to Print dialog box opens. Mark the Sequence Log checkbox. Select OK. The Sequence log is displayed for printing. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 107: Set Up A Quantitation Database

    Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Set Up a Quantitation Database Add Compound Entries for the Database Add the Calibration Curve View or Edit an Existing Database This chapter describes how to add compounds to the database. After a compound is identified, quantitative data analysis...

  • Page 108: Add Compound Entries For The Database

    Select the Load Data File button, . The Select Data File dialog box opens. Select Change Path. The Browse for Folder window opens. Navigate to and select C:\msdchem\1\data\demosim. Select OK. The path is displayed in the Path field. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 109 Select OK. The TIC window opens. Select the Setup Quant button, . A confirmation message may appear. Select OK. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 110 If some compounds need different parameters they can be changed later in the database. MSD Sample Calibration Title- ng/uL Units of Concentration - Select Use RTEINT. The RTE integrator is recommended for MS data. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 111 Set Up a Quantitation Database Select OK to save the settings and open the Edit Compounds dialog box. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 112: Identify Compounds

    The Scan is displayed in the lower window and the RT is displayed for the Ret. Time in the Quant Setup dialog box. Target is selected in the Quant Setup dialog box. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 113 When all compounds are added, select Exit to return to the Edit Compounds dialog box. Review the compound list. If any corrections need to be made, double-click on the compound and reenter the information in the Quant Setup dialog box. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 114 Set Up a Quantitation Database Select Exit. A confirmation message appears. This procedure continues with the next section “Add the Calibration Curve” on page 115. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 115: Add The Calibration Curve

    Select Add Level. 2.500000 Compound Concentration enter In the Level IDs area, enter in the New Level ID field. Select Do Update. The Edit Compounds dialog box opens and displays the first calibration point. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 116 Select the Identification tab. In the Quantitation Options area, select: Identify by - All Hits Subtraction Method - Avg first & last Select OK. A confirmation message appears. Select OK to save the changes. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 117: Add Calibrator Levels 5, 10, 25, And 50 To The Calibration Curve

    ), and DEMOSIM05 (level = In the Level IDs area, enter for DEMOSIM02 (level = DEMOSIM03 (level = ), DEMOSIM04 (level = ), and ) the New Level ID field. DEMOSIM05 (level = Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 118 5, 10, 25, and 50 to the calibration curve” until all concentration levels are added. The completed calibration curve is shown in Figure Figure 45 The completed quant database Select OK to close the window. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 119: Save The Database

    Save the database Select the Save Method button, . The Save Method As dialog box opens with the name of the current method displayed in the Method Path and Method File fields. Select OK. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 120: View Or Edit An Existing Database

    The Sum? field allows you to add the response of the designated qualifier ion to the response of the target ion. This method is valid only in area quantitation using the extended area quantitation method. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 121 However, you may use this for any other number or information about the compound. • Surrogate / Matrix Spike Amount • Matrix A and B concentrations • Signal level minimum and maximum • MS database name • Reference Spectrum number Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 122 Set Up a Quantitation Database Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 123: Generate A Report

    Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Generate a Report Generate a Report Automatically After the Run Generate a Detailed Report for Previously Acquired Data This chapter explains how to modify your method to generate a report at the end of each sample run and how to interactively generate a report from the Data Analysis view.

  • Page 124: Generate A Report Automatically After The Run

    From the Instrument View, select the Edit Entire Method… button, . The Edit Method dialog box opens. Mark the Method Information and Data Analysis check boxes only. Clear the Instrument/Acquisition check box. Select OK. The Method Information dialog box opens. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 125 Data Analysis check boxes, and clear the Post-Run Macro/Commands check box. Select OK. The Select Reports dialog box opens. Mark the Quant Report check box and clear all other check boxes. Select OK. The Quant Report Options dialog box opens. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 126 Select OK. The Select RUNMETHOD printer dialog box opens. Select a printer and click Select. The Save Method As dialog box opens. Select OK to save the setting to the current method or enter a new file name for the method. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 127: Run The Method And Generate The Report

    In the Sample Name field, enter a sample name. Enter the Vial number for your sample location in the ALS. In the Method Sections to Run area, select Data Acquisition and Data Analysis. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 128 Generate a Report Select OK and Run Method. The method is run and the summary quantitation report is automatically generated after the run is completed. Figure 46 Summary quantitation report Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 129: Generate A Detailed Report For Previously Acquired Data

    From the Style drop down list, select Detailed. In the Destination area, mark the Printer check box and clear all the other check boxes. Select OK. The dialog box closes and the report is printed. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 130 Generate a Report Figure 47 Detailed quantitation report Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 131: Recalibrate And Quantitate Unknowns

    Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Recalibrate and Quantitate Unknowns Create a Recalibration Sequence Save the Sequence Run the Sequence Regular recalibration is required to account for changes in your system. The ChemStation can perform this recalibration automatically using the recalibration sequence described here.

  • Page 132: Create A Recalibration Sequence

    Under Update RT column, click in the cell to activate the drop down list and select Replace. Under Update QI column, click in the cell to activate the drop down list and select Replace. Highlight rows 1 to 5. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 133 In row 5, under Level column, change the value to 50. In row 6, enter an unknown sample for analysis as shown in the figure. Select OK to close the Sample Log Table. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 134: Save The Sequence

    Save the Sequence Select the Save Sequence As… button, . The Save Sequence dialog box opens. updatequant In the File name field, enter Select Save. The dialog box closes and the sequence is saved. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 135: Run The Sequence

    In the Data File Directory field, add to the path. Select Run Sequence. The calibration table of the demoSIM method is updated and the unknown sample results are calculated/reported with the recalibrated calibration curve. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 136 Recalibrate and Quantitate Unknowns Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 137: Create A Cool Down Method

    Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Create a Cool Down Method Create the Cool Down Method Use the Cool Down Method This chapter describes how to create and store a method to use for instrument maintenance tasks. Using this type of method helps prevent damage to the instrument electronics and columns and avoid injuries such as burns or shocks.

  • Page 138: Create The Cool Down Method

    Mark the Pressure check box. Column flow must be maintained to prevent damage to the column when hot. Select the AUX button, Clear the On check box for the Aux 2 Heater. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 139: Use The Cool Down Method

    Select Download Method to GC from the context menu. A confirmation message is displayed. Select OK to close the message and return to the GC Edit Parameters window. When the GC enters the Ready state, perform the maintenance. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 140 Create a Cool Down Method Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 141: Shut Down The System

    Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Shut Down the System Shut Down the MS Shut Down the GC This chapter describes how to shut down the MS and GC. Agilent Technologies...

  • Page 142: Shut Down The Ms

    You can close the dialog box by selecting Exit, however, the process continues. To reopen the Vent Cycle status window, select View > Vacuum Status. Select OK to close the dialog box. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 143: Shut Down The Gc

    Close the Edit GC Parameters window and exit the ChemStation. When the GC enters the Ready state turn off the power to the GC and the MS. Turn off the carrier gas. Power off the PC and all peripheral equipment. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 144 Shut Down the System Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...

  • Page 145: Frequently Asked Questions

    Agilent G1701EA MSD Productivity ChemStation Familiarization Guide Frequently Asked Questions How often should the MSD be tuned? Perform an Autotune on a regular basis: weekly or monthly depending on use of the MSD. Perform a Check Tune daily to validate the performance of your instrument. If needed, perform a Quick Tune.
  • Page 146 Because many factors affect the match quality and ordering of the compounds in the hit list, the list should be viewed as an interpretative guide to the unknown's identity. It is the chemist's responsibility to Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 147 The chromatographic peak is normally determined by the retention time window where the peak of interest would display. After a column change or maintenance, this retention time will shift. Perform a retention time update. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 148 Why would the chromatogram show a peak if the quantitation report shows a N.D? Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 149 (=area ratio). You can specify which way you would like the qualifier ion ratio to be calculated. See the online help for instructions. Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 150 Frequently Asked Questions Agilent G1701EA MSD Productivity ChemStation Familiarization Guide...
  • Page 152 Agilent Technologies © Agilent Technologies, Inc. Printed in USA, June 2012 *G1701-90070* G1701-90070...

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