Omssa usage

[Oded]

Hi,
I would like to use Omssa with the TPP and couldn't find much
documentation (BTE it seems that the Spctools search option is only
showing results from the last few months) other than this link in the
wiki:
http://tools.proteomecenter.org/wiki/index.php?title=Expert_search_and_TPP_usage
that hint that it is possible to search directly mzXML files.
Is that actually possible and if so how it should be defined?
I was trying to search mgf input and to use peptide prophet with omssa
pepXML output following the recent advice re defining trypsin as the
enzyme. I was able to get interact to work but the all the hits got pp
score of -2 and in addition I wasn't able to watch any of the spectra
(got an error message).
I'm using TPP v4.3 unstable dev prerelease, built on 20090409 on a
Mac.
In additon I think it might be very usefull for future users, if
somebody who is succesfully using Omssa will post his/her parameters
file as a template or post a link that can be used as a starting point
for setting the search parameters (so far the best info I got is
this:http://proteomicsresource.washington.edu/omssa.php).
Many thanks,
Oded

[Natalie Tasman]

Hi Oded,

If you're using new features like Omssa-with-TPP, you should really
update to the release version of 4.3.0. Yours is 4 months out of
date.

Best,
Natalie

[dctrud]

Hi Oded,

We have OMSSA being called from a script, which generates a command
such as:

omssacl -fm /cpfp_data/dev/submissions/500/560/B090717_002.mgf -d /
cpfp_data/temp_db/decoy_maxquant-kr-uniprot_sprot.v2009.04.23 -op /
cpfp_data/dev/search_results/2300/2334/B090717_002.pep.xml -he 1e6 -to
0.5 -te 0.01 -e 0 -v 3 -mf 200 -mv 201,202,203 -mx /cpfp_data/dev/
search_results/2300/2334/usermods.xml -hl 5 -zcc 1 -nt 4

The base_name in the resulting pepxml contains the .pep.xml extension,
which I don't think it should... so we then:

sed -i 's/\.pep\.xml//ig' $pepxmlFile

RefreshParser B090717_002.pep.xml /cpfp_data/temp_db/decoy_maxquant-kr-
uniprot_sprot.v2009.04.23.fasta

xinteract -Ninteract.pep.xml -ESUB130 -p0 -eT -dDECOY -O-P-d-p-A
*.pep.xml

This seems to work fine. I haven't seen any pp -2 score problems.

DT

[Oded]

Hi,
Thanks - that is what I was looking for.
Have you tried to use pepXML input for the search parameters (similar
to the one used by Omssa browser)?
Best,
Oded

[Dave Trudgian]

Oded wrote:
> Thanks - that is what I was looking for.
> Have you tried to use pepXML input for the search parameters (similar
> to the one used by Omssa browser)?
>

Nope, I'm afraid I've only called omssacl with command line params.

Regarding the parameters, I have a recollection that using -he to
specify a high e-value cut off is important so that peptide prophet has
enough poor quality matches to fit the negative model.

DT

--
Dr. David Trudgian
Bioinformatician in Proteomics
University of Oxford

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