Hi David, Great - I'll give that a go.
Thanks, Alastair Am Dienstag, 13. November 2018 17:47:41 UTC+1 schrieb David Shteynberg: > > Hello Alastair, > > The parameter you want for PeptideProphetParser is called MASSWIDTH= . I > have gotten good results setting it to 1000 for +-500Da MSFragger search > analysis. > > Cheers, > David > > On Tue, Nov 13, 2018, 4:44 AM alastair.skeffington via spctools-discuss < > spctools...@googlegroups.com <javascript:> wrote: > >> Hello, >> >> In the MSFragger publication the authors adopt an extended mass model >> when processing the data with peptide prophet which allows >> mass-shift-dependent FDR estimation. >> >> I don't really see how you could implement this with the standard >> versions of peptide prophet - is the version of peptide prophet they used >> available? >> >> In addition, is this a valid option for a small dataset resulting in a >> couple of thousand PSMs only? The number of PSMs per dM bin might be quite >> small... >> >> Any help would be much appreciated, >> >> Alastair >> >> -- >> 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 spctools-discu...@googlegroups.com <javascript:>. >> To post to this group, send email to spctools...@googlegroups.com >> <javascript:>. >> 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
