It seems like a reasonable thing to test. I am not sure of the ultimate result but maybe you'll be able to make a few more identifications this way. Let me know what happens if you end up trying that.
-David On Tue, Jun 5, 2018 at 5:05 PM, <[email protected]> wrote: > Hi David, > > Thanks for your reply, that's very helpful. > > I've now tried including an equal number of decoys (reversed) in my > database, processing the same data through peptide prophet, iprophet and > protein prophet. My number of identified proteins has gone down, but the > PSMs are much more believable (judging from the spectra). > > As an aside - if I were to play with the proportion of decoys in the > database, (reducing the number to say 25% of the total database, rather > than 50%), in your experience would this reduction in the search space be > likely to have much of an effect on PSM / protein IDs? > > Thanks again, > Pete > > > On Tuesday, 5 June 2018 16:26:37 UTC-7, David Shteynberg wrote: >> >> 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. > -- 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.
