Thank you Eric for the clarification. Exporting prot.xml to TSV would be palliative in my case. May I ask you if it is possible to export prot.xml to TSV by command line (I just know how to do it with Petunia)? I am grateful for your help. Valdemir
Em segunda-feira, 10 de maio de 2021 às 19:10:09 UTC-3, Eric Deutsch escreveu: > I should add that mzQuantML is almost universally unsupported and is not > recommended. > > > > mzTab is the PSI format recommended for quant data: > > https://pubmed.ncbi.nlm.nih.gov/24980485/ > > > > FYI, there is an effort underway to design an improved mzTab 2.0, but it > is a long ways off. > > > > Eric > > > > > > *From:* Eric Deutsch <edeu...@systemsbiology.org> > *Sent:* Monday, May 10, 2021 2:42 PM > *To:* spctools...@googlegroups.com > *Cc:* Eric Deutsch <edeu...@systemsbiology.org> > *Subject:* RE: [spctools-discuss] Re: Exporting StPeter´s ng to mzid > > > > Hi Valdemir, the tpp2mzid is indeed the preferred and recommended tool, > not idconvert. > > > > I think the problem quite simply is that mzIdentML is not capable of > handling quant data. mzIdentML is designed only for identifications. > mzQuantML and mzTab are designed for quant data. So, no tool can or should > put quant data in mzIdentML. > > > > https://pubmed.ncbi.nlm.nih.gov/22375074/ > > https://pubmed.ncbi.nlm.nih.gov/23599424/ > > > > Regards, > > Eric > > > > > > *From:* spctools...@googlegroups.com <spctools...@googlegroups.com> *On > Behalf Of *mele...@gmail.com > *Sent:* Monday, May 10, 2021 2:30 PM > *To:* spctools-discuss <spctools...@googlegroups.com> > *Subject:* [spctools-discuss] Re: Exporting StPeter´s ng to mzid > > > > Thanks for your suggestion Jason, > > StPeter´s quantifiers have been written in ProtXML but apparently are not > included in mzid. > > Unfortunately, idconvert is returning Error writing analysis 1: > [Config::outputFilename] no spectraData elements (I´ll report this error...) > > I´ve tried two Proteowizad versions including the latest one. > > Does anyone know a way to incorporate them in mzid? > > Thanks > > Valdemir > > > > Em sábado, 8 de maio de 2021 às 12:57:58 UTC-3, jwi...@gmail.com escreveu: > > StPeter writes the quantification results back to the ProtXML. Have you > tried using idconvert from Proteowizard to convert the ProtXML to mzID? > http://proteowizard.sourceforge.net/tools/idconvert.html > > On Friday, May 7, 2021 at 8:03:11 PM UTC-4 mele...@gmail.com wrote: > > Hello, > > How can I include StPeter´s quantifier (ng) during conversion from > prot.xml to mzid? > > Is there some tpp2mizd parameter? > > Thanks > > Valdemir > > -- > 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-discu...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/4938f8a0-fd4b-41d1-a684-fe12e7fa8413n%40googlegroups.com > > <https://groups.google.com/d/msgid/spctools-discuss/4938f8a0-fd4b-41d1-a684-fe12e7fa8413n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/02a15827-d847-4f01-aee7-32fde03f5793n%40googlegroups.com.
