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 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 wrote:
> > The zipped pepXML file is in the attachment.
> >
> > Chuan-Qi Zhong
> >
> >
> > On Thu, Feb 13, 2014 at 7:05 PM, 钟传奇 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 spctools-discuss+unsubscr...@googlegroups.com.
> > To post to this group, send email to spctools-discuss@googlegroups.com.
> > 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 spctools-discuss+unsubscr...@googlegroups.com.
> To post to this group, send email to spctools-discuss@googlegroups.com.
> 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 spctools-discuss+unsubscr...@googlegroups.com.
To post to this group, send email to spctools-discuss@googlegroups.com.
Visit this group at http://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/groups/opt_out.
