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Associate proteins after peptide refinement

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Associate proteins after peptide refinement Priya Ghodasara  2018-04-26 16:56
 
Dear Skyline team,

I am a new skyline user and I am using skyline for processing SWATH data in Skyline version 4.1. I have a library file from which I create a list of peptides for targeted data extraction (View > Library > Add all and I untick association with proteins). After I finish extracting SWATH data, I re-associate the peptides with proteins (Edit>Refine>Associate protein) but it seems like it associates all the proteins present in the background proteome file (FASTA file) irrespective of curated peptides. I was expecting the proteins from curated peptides only. I am not sure how this function will work. It would be great if you can give your suggestions on how to associate curated peptide list to the specific proteins.

I would really appreciate your advice on it.

Thank you,
Priya
 
 
Brendan MacLean responded:  2018-04-26 17:42
Hi Priya,
You can give Edit > Refine > Associate Proteins any FASTA file or the Background Proteome to use as a source of protein information. That is just the source it uses. It will not actually add all of the source proteins to the document. It will only add the proteins for the peptides in your Targets list. i.e the proteins from the source list that match a peptide in your Targets list.

I think that is what you were hoping for, right? Have you actually tried running the association and you feel like you got something different? If you haven't tried it, go ahead. Remember, you can always click Undo if you don't like the results.

If you have tried it and you feel Skyline is not working as I just explained, then I will need to get your files and steps to reproduce what you are seeing. Or if you want something entirely different, then I will need to understand what you are looking for.

Thanks for posting to the Skyline support board.

--Brendan