Hi Amy,
I'll take a stab at this but I highly recommend you read (and re-read)
the ProteinProphet paper (Nesvizhskii et al Anal Chem 2003, 75,
4646-4658).
I have no experience with iProphet so I'll stay away from that...
PeptideProphet.probability is, as you'd expect, the probability of the
PSM being correct in the context of your dataset.
ProteinProphet is designed to reward proteins having multiple
peptides. The nsp_adjusted probability stands for the score in context
of a peptide's "number of sibling peptides" for a given protein. For
example, if Protein A has peps {1,2,3}, the individual peptide scores
will be adjusted to reflect the fact that this is a multi-hit protein.
The initial probability you see in the ProteinProphet results is for
the max score for a given peptide. Check your PeptideProphet output
for additional PSMs for your peptide 'HGVQELEIELQSQLSK'. My guess is
that you'll find one with a score of 0.9990
Hope that helps
John
On Apr 22, 11:26 am, grassworm <[email protected]> wrote:
> so my question is, what do the 'peptideprophet probability' and
> 'interprophet probability' in pep.xml, and 'initial probability' and
> 'nsp_adjusted probability' in prot.xml stand for?
> Thanks a lot!
>
> Amy
>
> On Apr 19, 6:08 pm, grassworm <[email protected]> wrote:
>
> > hello everyone,
>
> > i'm starting to use TPP and would like to thanks the authors for this
> > great program! i yet have some questions about the meanings of several
> > probabilities in the pep.xml and prot.xml files.
>
> > first there's this 'peptideprophet_result probability' in the in the
> > pep.xml file, in lines that look like this:
> > <peptideprophet_result probability="0.6908"
> > all_ntt_prob="(0.0000,0.6967,0.6908)">.
> > at first i thought it was the same as the 'initial probability' in the
> > corresponding prot.xml (e.g.
> > <peptide peptide_sequence="HGVQELEIELQSQLSK"
> > initial_probability="0.9990" nsp_adjusted_probability="0.9999"
> > weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2"
> > n_sibling_peptides="8.20" n_sibling_peptides_bin="6" n_instances="23"
> > exp_tot_instances="22.05" is_contributing_evidence="Y">), and that the
> > interprophet_result probability in lines like
> > <interprophet_result probability="0.518555"
> > all_ntt_prob="(0,0.525484,0.518555)">
> > are the same as the nsp_adjusted_probability in the prot.xml. however
> > i checked the values of several peptides and found that they don't
> > always match. the peptide values are often smaller than the ones in
> > the prot.xml.
>
> > i'm not sure if this has been discussed before. appologies if i've
> > brought up a toooold question, and please direct me to the relevent
> > discussions or documentations. thanks for your help!
>
> > Amy
>
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