Easier visual for Heavy and Light in "normalized" grid

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Easier visual for Heavy and Light in "normalized" grid waltteri hosia  2019-09-24
 

Hello,

Is there an easier way distinguish heavy and light versions of the same peptide in document grid? Looks like that total area is the only column that distinguishes them. At least with my settings, (double calibration curve, normalize to heavy), skyline doubles the rows with same calculated values for both, (which is slightly odd, heavy normalizing heavy should give 1, or?) In other words for those peptides that I have heavy peptide to use as ISTD I see in normalized grid 4 calibration sequences, from two sequences actually injected. But two of them have identical values, although total area reveals they are from the heavy ISTD. Modifying the "normalized" grid from "peptide modified sequence" does not quite work either. Choosing "show monoisotopic mass" shows the plain sequence for both light and heavy.

BR, Waltteri

 
 
Nick Shulman responded:  2019-09-24
Title: Easier visual for Heavy and Light in
When you have heavy and light versions of a peptide, Skyline calls each of those two variants as different "Precursors".
In the Document Grid, you can add the column "Isotope Label Type" in order to distinguish them.
You can find that column in the Customize Report dialog under:
Proteins > Peptides > Precursors

The "Peptide Modified Sequence" column shows you the sequence of the peptide without any isotope modifications applied. If you want to see the sequence with heavy modifications, that column is called "Modified Sequence" and it's also on the Precursor.

If you want to learn more about the Document Grid you should take a look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
-- Nick