Hi David, Thanks for the response. The release notes are helpful. And no, I haven't noticed increased decoy hits w/ higher prob...but then again I haven't really looked.
In addition to the release notes, is there any documentation about which features from Alexey's papers have made it into the prophets? For example, Choi, Gosh, & Nesvizhskii 2007 JPR discuss the benefits of "variable component mixture model and semiparametric mixture model". I would guess one of these models is invoked if I check the "Use non-parametric model" option but I'm just not sure. To be clear, I'm not asking for full compliance with the literature, I just want to know if PeptideProphet differs from it. Thanks, John On Sep 20, 1:24 pm, David Shteynberg <[email protected]> wrote: > 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 > noteshttp://tools.proteomecenter.org/wiki/index.php?search=release+notes&g... > > -David > > On Tue, Sep 14, 2010 at 7:45 AM, John Damask <[email protected]> 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 [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group > > athttp://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 [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
