Thank you, Magnus! Is 1 a reasonable startpoint for Qualscore 'cutoff'? Previously I used 0.95 in peptideprophet for filtering, so I guess PeptideProphet max. threshold for unassigned = 0.95? Another question, if I get some new hits from iterative search, shall I simply add them to my original "good" hit from previous peptideprophet filtering, and go ahead to use proteinprophet to compile all peptide hits to protein hits, OR, rerun the peptideprophet to recalculate the peptideprobabilty for all hits before moving to proteinprophet? Thanks! Sun
On Tuesday, July 9, 2013 12:30:03 AM UTC+8, [email protected] wrote: > > Dear Sun, > > I think QualScore is designed for exactly this purpose. > > > Cheers, > > Magnus > > On Monday, 8 July 2013 02:29:03 UTC+2, [email protected] wrote: >> >> Dear TPP users, >> I'm wondering if there is any tools that can extract those spectra with >> high spectra quality but no hits from peptideprophet results? I usually >> convert the raw spectra to mzXML and run X!tandem within TPP environment. I >> would like to try other search algorithms or larger search space for a 2nd >> round iterative search. >> >> Thank you! >> >> Sun >> > -- 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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
