Hi John,
Yes, the semi-supervised and semi-paramteric features from Alexey's
papers are implemented. Specifying a decoy tag to PeptideProphet
makes it semi-supervised and selecting the non-parametric model makes
it semi-parametric; the one remaining parameter in the distributions
is the apportionment of non-decoy hits among the positive and
negative distributions (which in this mode do not follow the shape of
a predetermined parametric distribution e.g. Gamma for negatives and
Gaussian for positives, but are learned using Kernel Density
Estimates).
-David
On Tue, Sep 21, 2010 at 7:31 AM, John Damask jbdam...@gmail.com wrote:
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 dshteynb...@systemsbiology.org
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+notesg...
-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
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