Using Mass Spectrometers
Creating a PGM File for the MSQ

Use the Surveyor MSQ view of the PGM Editor (see Control  The PGM Editor) to create a new instrument method for the MSQ Mass Spectrometer as part of a PGM File. Open this view by clicking this icon on the shortcut bar in the left PGM Editor section:

 Tip:

If the PGM File was not created for a timebase that includes a mass spectrometer, neither an MS method nor the MSQ symbol will be available. To use such a PGM File for a timebase that includes a mass spectrometer, select Add MS Instrument Method on the Edit or context menu. This adds the Surveyor MSQ view. From the standard MS methods (Surveyor MSQ Templates) in the dialog box, select an MS method. The appropriate MS method depends on the ionization mode, the MS mode (Full Scan or SIM), and the polarity of the recorded ions. In addition, enter the following command in the Program (Commands view) at the time t = 0.000 min:

 0.000 Wait MS.Ready

 

The Surveyor MSQ view is part of the Xcalibur software and allows you to specify the method used by the MSQ mass spectrometer.

The upper left section shows a runtime preview of the single channels to record. In the Preview section, select:

For an overview of the defined channels, including their measurement parameters, select the Parameter option.

If a chromatogram was recorded with one MS channel only, you can also have the chromatogram displayed in the preview. Select Show Method Options to open the method options, and then select a sample by clicking the "..." button under Display.

On the top right, in the Per Method Parameters section, select ESI (Electrospray Ionization) or APCI (Atmospheric Pressure Chemical Ionization) as the ionization mode, depending on your MSQ installation. In addition, enter the nominal temperature on the ion source (range: 0 to 655°C).

In the Full/SIM Scan Events section, enter the MSQ-specific signal parameters for Mass Spectra acquisition:

In the Mass Range field, define the mass range (Full Scan). In the Mass field, define the mass. Define the corresponding bandwidth (SIM) in the Span field. In addition, define the duration of the data acquisition (Time Range), the data acquisition rate (Dwell Time (SIM) or Scan Time (Full Scan)), the Polarity, and the ionization voltage (Cone [V]).

 Note:

For a list of SIM masses for anions, cations, and amines in water, refer to Using Mass Spectrometers  SIM Mass Lists for IC-MS.

In the Scans section, select the Add Full option to add a new full-scan channel or Add SIM to add a new SIM channel. The settings from the preceding channel are adopted. Use the Create Group option to group all SIM channels that are recorded in the same retention time window. (To do so, hold down the CTRL key and click to select the SIM channels.) Select Ungroup to undo this action. To delete a channel, select the channel, and then click Delete.

 Tip:

This view of the PGM Editor is part of the Xcalibur software. The Xcalibur Help system provides detailed information about mass spectra acquisition. First, click the question mark (at the top right) and then click the option of interest to open the corresponding Help topic.

 Tip: 

When saving the PGM File, only use ASCII characters to name the entire path, i.e., including the datasource and the directories. If you use other characters, too, it may be impossible to start data acquisition.

For more information, refer to  Creating MSQ Channels with the MSQ PGM File.