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bzhanglab / PepQuery

PepQuery: a targeted peptide search engine
http://pepquery.org
GNU General Public License v3.0
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Statistical evaluation of shuffled peptides with multiple (Iso)Leucine amino acids #54

Open HagemeijerRug opened 11 months ago

HagemeijerRug commented 11 months ago

I recently read the pepquery2 paper, I like many of the analyses you performed in the discussion to show its versatility, but I was left wondering about step4 (the shuffling of peptides).

If I understand correctly, you either make 10000 combinations, or all unique ones, in case the total number of combinations is lower than 10000. In my work I am seeing peptides with 4 or more I/L aminoacids, and after a cursory check of the source code I didn't find any code that takes their equal mass into effect for shuffling.

Is temporarily converting them to a "J" or some other character an option to rectify this for shuffling (and any other analyses where their equal mass matters. For example, does a reference match with an I instead of an L in the peptide or vice versa matter)?

If you already have any code aimed at handling this that I missed, could you link it? I would be very interested in reading it.

wenbostar commented 5 months ago

In this specific case, you could convert all I to L before you do the search using PepQuery.