Hi Eric, Thanks a lot for your reply! Yes, my example files were reduced too much. Your mzIdentML is exactely what I had in mind. We were thinking about improving the compatibility of (TPP) pepXML in OpenMS, but I think we should rather wait for the official mzIdentML support in TPP / idconvert.
I would be interested to test your improved idconvert binary. If it doesn't work on our machines, I can of course also wait for the official release. Best regards George On Thursday, May 8, 2014 1:33:24 AM UTC+2, Eric Deutsch wrote: > > Hi George, we are currently working on an improved version of idConvert > that fixes most of these problems. > > > > Attached is the output of our latest idConvert on your files. It does have > some probabilities in there. But the file isn’t quite valid. There are no > SpectrumIdentificationItems. I suspect your reduced example was reduced too > much?? > > > > Attached also is the result of a full run of the TPP. What do you think of > that? We could send some binaries if you’d like to test. For Linux at > least, although there may be library problems. Anyway, we’re not done yet, > still working on it. > > > > Regards, > > Eric > > > > > > *From:* [email protected] <javascript:> [mailto: > [email protected] <javascript:>] *On Behalf Of *George > Rosenberger > *Sent:* Tuesday, May 06, 2014 11:36 PM > *To:* [email protected] <javascript:> > *Subject:* [spctools-discuss] idconverter (prot/pepxml to mzid): Problems > with TPP > > > > Dear TPP Team, > > > > I'm using the TPP with PeptideProphet, iProphet and ProteinProphet to > combine identifications from different search engines. I encountered some > problems using idconvert (shipped with TPP 4.7.0 or standalone) when trying > to convert ProtXML files. PepXML files could be successfully converted. > > Please find attached reduced example files where this problem occured. Is > this a bug or a problem on my side? > > > > Further, the PeptideProphet/iProphet probabilities were not imported to > the mzIdentML. Is this something that can be enabled during conversion? > Also, is there a specific cutoff that can be set during conversion to only > allow identifications above a score threshold to be imported for the > mzIdentML conversion? > > Thank you very much for your help and best regards > George > > ---- > > $ idconvert Example.pep.xml > format: mzIdentML > outputPath: . > extension: .mzid > > filenames: > Example.pep.xml > > processing file: Example.pep.xml > writing output file: ./Example.pep.mzid > > $ idconvert Example.prot.xml > format: mzIdentML > outputPath: . > extension: .mzid > > filenames: > Example.prot.xml > > processing file: Example.prot.xml > [Ion::mz()] m/z with protonDelta=electronDelta is impossible > Error processing file Example.prot.xml > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected] <javascript:>. > To post to this group, send email to [email protected]<javascript:> > . > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
