Hannes, thanks for your reply. You are right. ConsensusID can process the data at peptide level, and I have done that successfully. However, consensusID lacks validation tool at protein level. According to a JPR paper, idXML can be converted to pepXML, which was subsequently subjected to TPP_proteinprophet analysis. I can not figure out how to use TPP_proteinprophet tool in openMS to analyze pepXML, so I just ask for help here.
So the question is how to validate results at protein level in openMS. Chuan-Qi On Thu, Feb 13, 2014 at 9:40 PM, Hannes Röst <[email protected]> wrote: > The main error seems to be that the processing engine is not recognized > > running: "/usr/local/apps/tpp/bin/PeptideProphetParser 'interact.pep.xml'" > (OpenMS/ConsensusID) > error: engine OpenMS/ConsensusID not recognized > > which seems to result from the attribute > search_engine="OpenMS/ConsensusID" > > however the file does contain peptideprophet_result tags so it seems > that you may have processed them with the OpenMS ConsensusID tool > which does something similar to peptideprophet > > http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/OpenMS-release/html/TOPP_ConsensusID.html > - is this the case? > > Hannes > > On 13 February 2014 12:08, 钟传奇 <[email protected]> wrote: > > The zipped pepXML file is in the attachment. > > > > Chuan-Qi Zhong > > > > > > On Thu, Feb 13, 2014 at 7:05 PM, 钟传奇 <[email protected]> wrote: > >> > >> I used openMS to process my data, and the results, idXML files, are then > >> converted to pepXML using IDconverter in openMS. > >> But these pepXML files cannot be processed by peptideprophet, and I > >> noticed that peptideprophet can handle pep.XML files, so there is any > >> difference between pepXML and pep.XML? > >> I have attached a pepXML file. > >> > >> How to fix this issue? > >> > >> Thanks a lot. > >> > >> Best, > >> > >> > >> Chuan-Qi Zhong > > > > > > -- > > 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/groups/opt_out. > > -- > 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/groups/opt_out. > -- 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/groups/opt_out.
