omssa compatibility

[jonas]

Hello scaffolders

As announced on the proteome software page Scaffold 2.1 should be able
to process OMSSA data (Open Mass Spectrometry Search Algorithm). I'm
running omssa from commandline with the following options:
./omssacl -d myfastadb.fasta -fm myinputmgf.mgf -v 1 -w -ht 20 -he
100000 -mf 3 -mv 1 -te 0.1 -ox outputname.xml
--> the important parameters which they mention on the webpage are: -
he 100000, -ht 20
--> also -ox produces the XML file and -w to include the spectra in
the xml file..

Nevertheless it directly throws an error upon selecting the files
(ready to be imported)
"No files added -- Scaffold could not load any valid MSMS data from
the selected files. No files were added to the loading queue."

- Does anybody having already experience with omssa-search-results in
Scaffold 2.1?
- Anybody knows the holy parameter set to create an importable file?

thanx & cheers - jonas

[Sheryl Macy]

Morning Jonas,
Did you get the information you needed from Chris Mason? If not, let me know. If so, we'd love to hear how Scaffold 2.1 is performing on OMSSA data.
Sheryl Macy

[jonas]

Dear Sheryl

Yes I did get the information and in the meanwhile I have a parameter-
xml file which I can run omssa with in order to get an output which
can then be imported into Scaffold.
I havent finished all the comparsions yet and I cannot tell you the
performance of scaffold with omssa results compared to mascot yet ..
but hopefully soon -
cheers - jonas

[Sheryl Macy]

Jonas
Thanks for the update. Keep us posted.
Sheryl