|export fasta of all verified proteins from Skyline||kguehrs||2021-07-15|
Hello Skyline team,
Perhaps this matter was already asked but I could not find any answer after I drastically limited my search to "export fasta".
I have done a DIA analysis of some special tissues from an model organism. The basis for the analysis was a rather large fasta database of not so good quality which I used as the background proteome. The analysis of the run data was done with Umpire/Fragpipe and imported into Skyline for visualization and curation. I did quite a bit of manual refinement and came up with a status in which I erased a lot of identified by the search engines proteins that do not match my quality restriction. Besides the generation of a spectral library I would like to also create a fasta file of either all or a specified fraction of the proteins remaining after the curation of the data. This fasta coould be used for other purposes or as a core background proteome that could be further expanded by additional data.
Is there any chance to export the proteins remaining after curation as a fasta file from Skyline. If there is no direct way, can you propose an other tool or procedure to do so from any Skyline generated report.