Changing the default isotope envelope for multiple precursors?

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Changing the default isotope envelope for multiple precursors? ho-tak lau  2024-08-02 09:51
 

Hello Skyline Team,

Is there a way to change the isotope envelope of multiple peptide precursors?
I am working on some long glycopeptides with many precursors (see attached .png). So I wonder if the M+3, M+4 can be included by editing the .sky using a text editor.

Thanks in advance.
Ho-Tak

 
 
Nick Shulman responded:  2024-08-02 10:05
The way to tell Skyline how many isotope peaks should be included in the Targets tree is with the "Isotope Peaks Included" setting at:
Settings > Transition Settings > Full Scan

You can also right-click on the Precursor in the Targets tree and choose "Pick Children" and unselect the filter button and choose the rest of the isotopes.
The highest isotope m/z that you can add is the monoisotopic mass plus 9 Daltons. Also, any isotope m/z must have a predicted abundance which is at least 1% of the most abundant isotope m/z.

By the way, regardless of the "Isotope Peaks Included" setting at "Settings > Transition Settings > Full Scan", Skyline always extracts chromatograms for all of the precursors isotopes whose predicted abundance is at least 1% the abundance of the most abundant m/z, so, as soon as you add these precursor isotope transitions to the Targets tree you will see chromatograms for them.
-- Nick
 
ho-tak lau responded:  2024-08-02 11:21
I also tried to change it from count to percent. It helps a lot.

Thank you
Ho-Tak