Hello Pete, Use of decoys in the X!Tandem workflow is not strictly required but it is helpful. X!Tandem is one of a handful of search engines for which there exists a parametric mixture model for PSM-level validation. In my experience, using the parametric models may not always give you the best results in terms of validation, and the lack of decoys precludes the ability to compute decoy-based error rates (FDR). In this case you have to only the FDR as estimated by the PeptideProphet model, and you cannot compare this FDR to decoy-based estimates. The best results are usually obtained by using a database that includes some proportion of decoys. You can then validate the search results using PeptideProphet's semi-supervised semi-parametric models, which tend to estimate more accurate error rates. However you decide to search your data, I also suggest you also include iProphet in your validation analysis for peptide-level validation.
Cheers, -David On Tue, Jun 5, 2018 at 12:47 PM, <[email protected]> wrote: > Please can someone advise - is it recommended to include decoys in my > database when using X! for searches then peptide/protein prophet in TPP? > > > As I understand, X! recommends not including decoys in searches (when used > standalone) – however when I analyse X! identified peptides using > peptide/protein prophet, I assume that I will need decoy matches to help > pin down the correct distribution? > > > Thanks > > Pete > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
