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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Decoy peptide output #468

Open patruong opened 2 years ago

patruong commented 2 years ago

Hi,

I need decoys to run the protein quantification tool Triqler. Is there a way to get DIA-NN to output the decoy peptides?

Best, Patrick

vdemichev commented 2 years ago

Hi Patrick,

Unfortunately this is not supported.

Best, Vadim

KlemensFroehlich commented 2 years ago

hi patrick and Vadim, I am using special FASTAs with additional decoy entries to cotrol the FDR additionally. My output contains these decoys.

This might not be perfect as instead of having a "normal" FASTA and "DIANN decoys" in the DIANN analysis, we have "normal" and "FASTAdecoy" and "DIANN decoys" and "DIANN decoys corresponding to FASTA decoys". Hope this is understandable :)

Would this work for you, Patrick? Do you see a problem with that approach Vadim?

Best, Klemens

vdemichev commented 2 years ago

Hi Klemens, yes, perfectly possible. The only caveat is that sensitivity will be somewhat reduced due to the increased search space because of adding extra 'decoys'. Unless the proportion of the latter is low.

Vadim