Dear SPC-tools community,
Up to now, I was used to deposit my TPP results to the PRIDE server,
after conversion of the PeptideProphet/ProteinProphet files with the
PRIDE converter and using the mzXML raw files.
Unfortunately, in my last project I could convert only 1/3 of the TPP
result files successfully (with the thresholds I wanted.) and the error
tracking of the PRIDE converter tool is not sufficient to identify the
problems.
Also the conversion of X!Tandem files failed, without giving sufficient
information on how to fix the problem.
The Pride-support informed me, that in future versions,
PeptideProphet/ProteinProphet files will not be an option any more and
recommended me to use Mascot/SEQUEST...
1) Would it be possible to initiate a collaboration between the TPP
developers and the PRIDE team?
2) Is there an alternative, robust, converter TPP-> PRIDE XML?
3) Is there a repository, where I could submit my TPP/ X!Tandem (OMSSA,
pep.xml) data for publication (NCBI peptidome also died...)?
Actually I found the TPP a very powerful solution for processing my data
from different platforms and with high flexibility and reliability, and
on the other hand PRIDE an excellent possibility for data repository.
However, if those two cannot be married by a converter/ parser or
anything similar, we are in trouble and have to think.
I won´t go back to the times, where the proteomics data section of the
paper consists of an EXCEL table "Spot Accession Score.." only and the
raw data are stored/distributed on my laptop/ the mass spec/
collaborators PC ...
Discussion/ solutions are welcome,
Robert
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