PeptideProphet
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Alicia
Jun 23, 2009, 7:03:51 AM6/23/09
to spctools-discuss
Hi,
Just a quick question - I have been using PeptideProphet (TPP 4.2.0)
for Mascot data and have noticed that there is a * next to many of the
ion scores (in both the viewer and the excel format). I have searched
the documentation and this discussion board, but I can't find what the
* means. The reason I ask this question is that many of these peptides
have a reasonably large ion score (e.g., ion score of 40, with an
identity score of 32), but the PeptideProphet probability score is
small (e.g., 0.1). Inspection of the corresponding spectra show that
the sequence is a good match and therefore I would expect the
PeptideProphet probability to be much higher. Can you please help me
understand what might be going on here.
Alicia
Just a quick question - I have been using PeptideProphet (TPP 4.2.0)
for Mascot data and have noticed that there is a * next to many of the
ion scores (in both the viewer and the excel format). I have searched
the documentation and this discussion board, but I can't find what the
* means. The reason I ask this question is that many of these peptides
have a reasonably large ion score (e.g., ion score of 40, with an
identity score of 32), but the PeptideProphet probability score is
small (e.g., 0.1). Inspection of the corresponding spectra show that
the sequence is a good match and therefore I would expect the
PeptideProphet probability to be much higher. Can you please help me
understand what might be going on here.
Alicia
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