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Reporting MS1 monoisotopic peak areas in document/report

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Reporting MS1 monoisotopic peak areas in document/report sweaver4  2025-03-10 09:11
 

Hello,

I'm wondering if it is possible to report the areas for MS1 peaks using only the monoisotopic peak. In the attached screenshot I have the monoisotopic peak, the M+1 peak, and the M+2 peak. I believe that the area reported in the document grid for 'Total Area' and 'Total Area MS1' are both the combined areas of these three isotopic peaks (in the document for the attached example this value is ~209k which matches the value from the 'peak area replicate comparison' view). I would like to have this value along with a value reporting only the area of the monoisotopic peak (the blue XIC) if possible. I know I can get this if I change the transition settings/MS1 filtering to only look at 1 peak. But then I have to continually go back and forth between 1 and three peaks. Is there an additional field I can add to the report that has the peak areas split out by isotopic peak?

Let me know if I can clarify anything. Thank you!

Simon
 
 
Nick Shulman responded:  2025-03-10 09:31
If you want to create a report with just the monoisotopic precursor peak area you should create a report that shows the "Area" value from the Transition Result and that also has a filter so that it only shows rows for the monoisotopic transitions.

That is, the report should have the filter that the "Fragment Ion" column equals "precursor".
One thing that you could do is start with the "Transition Results" report that you can find in the Document Grid and then right-click on the "Fragment Ion" column and choose "Filter..." and set it like in the attached screenshot "SimpleFilter.png".

Alternatively, you could apply the filter in the report definition by doing "Edit Report" and then then setting the filter on the Filter tab of the Edit Report dialog.

The monoisotopic transition will have the Fragment Ion value of "precursor".
The other isotopes will have Fragment Ion values such as "precursor [M+1]"
Non-precursor transitions will have Fragment Ion values such as "y8++".

You can learn more about custom reports in this tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

Also, you can learn about the pivot editor on this page, which mentions the "Remember current layout" on page 10:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PivotEditor
-- Nick