Extract MS spectrum with the spectrum extraction tool

The behavior of the spectrum extraction tool can be adjusted. To change the behavior, click in the Chromatograms window, and adjust the settings in the Spectrum extraction page. In the following procedure, all options are enabled.

Preparations

• The injection is linked to a processing method that supports manual MS spectra extraction (method configurations MS or LC/MS Sample Purity).

• To be able to carry out the procedure as described, you need the privilege Data Processing > Do manual spectrum extraction . Privileges are configured in the Control Panel.

1. To automatically subtract background spectra: In the method, check the settings in the Extraction > Spectrum node in the MS tab.

   Depending on the spectrum that you extract, the settings for either Arbitrary spectra or for Peak spectra will apply.

2. In the Chromatograms window, click in the toolbar to activate the spectrum extraction tool.

3. Move the mouse over the chromatogram. The cursor changes dynamically, for example, if you move it over a peak apex or a baseline.

   

   Figure Spectrum extraction cursor at peak apex

4. To extract a time point spectrum, click at the required position.

   OR: To extract an average spectrum over a time range, click and drag the cursor over the required range.

5. When asked for confirmation, click or press ENTER to confirm the spectrum extraction. The spectrum extraction will occur without confirmation if you cleared the corresponding check box in the Chromatogram Properties.

   Confirmation dialog at peak apex

   Confirmation dialog at selected time point

   The extracted spectrum is shown in the MS Spectrum window, and it is listed under the details for the individual injection in the injection tree.

   If a background spectrum has been subtracted, the time point or time range used for subtraction is shown.

6. Save the data.

   Extracted spectra are saved together with the data.