Hi Rob and everyone, in the future mzIdentML will be the intermediary. The scenario will be that after you have completed your analysis with TPP, you will invoke an exporter within TPP to write out your results into mzIdentML 1.1. This format will be the preferred format for important into PRIDE. I don't quite know when this will be working, but our aim is for the end of the year. The ISB TPP/PeptideAtlas and EBI PRIDE teams are already working together under ProteomeXchange to make sure that your workflow is supported and much less effort than it is today. Unfortunately, today there is no better workflow than what you are already doing. But there will be an improved replacement!
Regards, Eric > -----Original Message----- > From: [email protected] [mailto:spctools- > [email protected]] On Behalf Of Robert Winkler > Sent: Wednesday, July 06, 2011 10:24 AM > To: [email protected]; [email protected] > Subject: [spctools-discuss] Depositing TPP/X!Tandem/OMSSA results on > PRIDE > > 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 > > -- > You received this message because you are subscribed to the Google > Groups "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to spctools- > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
