Martin,
The asterisk means that there is high homology between the top scoring
hit and lower hit(s) for that particular spectrum. It's an indication
that the best match reported by Mascot isn't that much better than the
second match. I.E. if you looked on a Mascot peptide report, the top
ranking hit for the query would have a score very similar to the second
rank hit.
By default PeptideProphet will penalise these hits, hence the low
probability. You can choose not to penalise these hits from the petunia
web interface, or on the command line using the l flag.
A common situation where you don't want to penalise hits like this is
that of phosphorylation studies. Often the top scoring hits given by
Mascot then correspond to the same peptide sequence, but with different
phospho site assignments, and you lose a lot of phosphopeptides if you
penalise them because of this.
DT
Martin R. wrote:
Hello
I just have a question. I'm comparing pep.xml files with each other
and there is this xml element
<search_score name="star" value="1"/>
and for the view of the pep.xml I get values similar to this line:
probability spectrum ionscore identityscore homologyscore
ions peptide
protein
0 spectrum.0000.2 14.44* 35.27 24.18 4/10 R.QDPN[115.03]PK.G
IPI00694111.3
Why is the probability for most of the asterisked ionscore value quite
low ? Is there any reason ?
Thanks in advance
Regards
Martin
--
Dr. David Trudgian
Bioinformatician in Proteomics
University of Oxford
Mon-Thu: CCMP, Roosevelt Drive
Tel: (+44) (01865 2)87784
Friday : Dunn School of Pathology, S. Parks Rd.
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