Visualize and extract selected ions
Visualize selected ions
1. Before actually extracting the ions of interest into separate files you may like to review the ions in the measurements. When you have loaded one or more measurements you can select the tab „Options“ (below the Chromatogram Editor) and add the ions you like to visualize to the empty table „Add/Remove selected ions“. A magnification factor („Magnification“) is only useful if the differences of intensity of the ions is too large for visual comparison and needs adjustment.
2. Now to display the selected ions the appropriate view has to be opened. Almost for all operations in OpenChrom there are separate views/windows/tables – this way they can be optimized to their respective tasks. Via the icon „Select view“ you can choose the view „Selected Ion Chromatogram (Nominal)“.
3. You may zoom in to the RT region of interest either in the Chromatogram Editor or directly in the view „Selected Ion Chromatogram (Nominal)“. To get the legend displayed use the right mouse-click within the view.
Extract and integrate selected ions
1. Now to extract selected ion chromatograms from your measurements you can use the filter „Ion Remover“. The idea for your task is: Out of each measurement new selected-ion chromatograms will be created (two in the displayed example) and saved in separate batch processes. Here, one folder will contain the chromatograms of m/z 204 and the other the ones of m/z 207. The selected-ion chromatograms are created by removing all other ions. Within each batch process peak detection and integration will be performed on the „remaining“ chromatogram. The results are contained in the *.ocb files and in the *.txt report files which are saved at the end of the batch process. So after the processing you will need to retrieve your needed peak areas from the *.txt reports. You can access the settings for this filter via menu bar > Window > Preferences > A) Chromatography/Spectrometry > Filter > Filter MSD. Clear the list first.
3. Then scroll in the long list to the ion which you want to extract and quantify. Remove it from the list. In this case m/z 204 and 207 overlap. Therefore you should only remove m/z 204 for now. The whole procedure will have to be repeated for m/z 207, once the first batch process has been finished. Press „OK“ and close the preferences. Note, that there are also adjustable settings for peak detection and integration which are accessed via the Preferences. This may get important when you inspect the performance of the peak detection and integration and e.g. notice sub-optimal start and/or end-points of integration.