Protein Decoy FDR’s?

There was a lot of discussion of the utility of protein decoy FDR’s at ASMS. Especially in light of the two Nature human proteme papers that only calculated peptide decoy fdr’s on the spectra level. I assume it was spectra and not peptide…Are these protein decoy FDR’s useful? Many people I talked to think they are somewhat BS and provide no useful info whatsoever. Scaffold will calculate the protein FDR’s so you probably see them in your data. In fact we usually filter on them using a 5% protein FDR cutoff! Does filtering on your protein decoy FDR’s make your data worse? Do they tell you anything useful about your data? …You would think the proteomics community would have this figured out by now, especially since protein ID is not new. But there is not a consensus on this. Just a word of caution when analyzing your data…

More to come…


Posted in Proteomics Blog
One comment on “Protein Decoy FDR’s?
  1. Williamrog says:

    Thank you ever so for you forum post. Really Cool. Schuur

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