Mapped Proteins, how to interpret result when decoy protein is mapped #225
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Hi again, I have a question regarding the interpretation of the psm.tsv result.
How should one interpret this psm? I would think it should e filtered out because it is a decoy hit, but I am not sure as I would expect philosopher to remove it 'for me'. Thanks |
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Replies: 2 comments
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What you see there is a peptide that was assigned (i.e. mapping), to a target protein. What you see on the Mapped Proteins columns is the list of alternative proteins that also maps to the same peptide sequence, in this case a decoy. Judging only by the attributes we can observe on your example, like the PeptideProphet Probability and the length of the sequence, this seems to be a confident hit and can be taken into consideration for downstream analysis. |
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Ok, thanks! |
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@pisistrato
What you see there is a peptide that was assigned (i.e. mapping), to a target protein. What you see on the Mapped Proteins columns is the list of alternative proteins that also maps to the same peptide sequence, in this case a decoy. Judging only by the attributes we can observe on your example, like the PeptideProphet Probability and the length of the sequence, this seems to be a confident hit and can be taken into consideration for downstream analysis.