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-discuss@googlegroups.com 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-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. > -- 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.
