Importing Thermo Biopharma Finder Search Results to Skyline

Importing Thermo Biopharma Finder Search Results to Skyline Yao Chen  2024-02-02 00:25

Dear Skyline Team

Would it be possible to create a targeted search list in Skyline from Thermo's BioPharma Finder search results?


Nick Shulman responded:  2024-02-02 07:38
As far as I know, Skyline cannot do anything with BioPharma Finder search results.
Here is the list of search result formats that Skyline can understand:

There have been a couple of Skyline support requests that mentioned BioPharma Finder:

I do not see any useful information in those support requests but you might understand what they were saying better than I do.
-- Nick
Yao Chen responded:  2024-02-02 09:47
Thanks Nick

I might write something to convert the BioPharma Finder's search report into what skyline could understand.

A quick question. For mass shifts from modifications, for example "TASEFDC[+123.4567]SAIO[+654.4321]AQDK", what mass accuracy should I provide? Also, if a modification is not in the current library, would this entry still be able to show in the peptide list?
Nick Shulman responded:  2024-02-02 10:23
If you want to convert your peptide search results into something that Skyline can understand, you might want to convert it to the "spectrum sequence list" (.ssl) format:

You must have at least one decimal digit of precision in your mass modifications, but you can have more if you want, especially if those extra digits of precision will disambiguate between your modifications.
When Skyline is trying to figure out the actual modification that is represented by a particular mass number, Skyline will use whatever digits of precision are there.
When you create a BiblioSpec spectral library (.blib file) from your peptide search results, the .blib file does not actually know anything about the modifications other than their mass. If you try to look at that spectral library in Skyline using the "View > Spectral Library" menu item, Skyline will try to guess what the modifications are based on their masses, and users will be prompted if those modifications do not currently appear in the lists at "Settings > Peptide Settings > Modifications".
-- Nick