Hi John, The target is for the quality of the software to improve with subsequent releases. Do you notice that you have more incorrect (decoy) hits with higher probability? BTW, the latest version is 4.4 not 4.3. For more information you can check the release notes http://tools.proteomecenter.org/wiki/index.php?search=release+notes&go=Go
-David On Tue, Sep 14, 2010 at 7:45 AM, John Damask <jbdam...@gmail.com> wrote: > Hi, > We recently upgraded an old version of TPP (Squall v3.3) to v4.3 rev1. > We've noticed an increase in the number of high confidence (<1% FDR) > peptides and proteins. Digging into the pepXml files we've seen cases > where, for example, a peptide previously assigned a probability of < . > 5 now scores > .9. Note that the Mascot scores haven't changed > > Where can I learn about the differences between versions of the > Prophets? > Thanks > John > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
