Re: [spctools-discuss] Re: Exporting StPeter´s ng to mzid
Hello Valdemir, You can run the ProtXMLViewer on the command-line to do this. If you want one protein per line, with peptides as a comma-separated list: /FULL/PATH/TO/tpp/cgi-bin/ProtXMLViewer.pl -file -action ExportExcel If you want one peptide per line, with per-peptide stats as well: /FULL/PATH/TO/tpp/cgi-bin/ProtXMLViewer.pl -file -action ExportExcel -peps Just replace the start of the path to match the location of the viewer file on your system, and make sure you use the full path to the input protXML file; the output file will be named the same as the input, but with a *.tsv* extension instead of .xml (e.g. myfile.prot.tsv). Hope this helps, --Luis On Tue, May 11, 2021 at 5:00 PM mele...@gmail.com wrote: > 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 >> *Sent:* Monday, May 10, 2021 2:42 PM >> *To:* spctools...@googlegroups.com >> *Cc:* Eric Deutsch >> *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 *On >> Behalf Of *mele...@gmail.com >> *Sent:* Monday, May 10, 2021 2:30 PM >> *To:* spctools-discuss >> *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_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 > <https://groups.google.com/d/msgid/spctools-discuss/02a15827-d847-4f01-aee7-32fde03f5793n%40googlegroups.com?utm_medium=email_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/CACyS9brn5SEwpA31D6j9yK_-JN6XEFMPPZorXYGYjvXQUbsQvg%40mail.gmail.com.
Re: [spctools-discuss] Re: Exporting StPeter´s ng to mzid
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 > *Sent:* Monday, May 10, 2021 2:42 PM > *To:* spctools...@googlegroups.com > *Cc:* Eric Deutsch > *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 *On > Behalf Of *mele...@gmail.com > *Sent:* Monday, May 10, 2021 2:30 PM > *To:* spctools-discuss > *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_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.
RE: [spctools-discuss] Re: Exporting StPeter´s ng to mzid
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 *Sent:* Monday, May 10, 2021 2:42 PM *To:* spctools-discuss@googlegroups.com *Cc:* Eric Deutsch *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-discuss@googlegroups.com *On Behalf Of *mele...@gmail.com *Sent:* Monday, May 10, 2021 2:30 PM *To:* spctools-discuss *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-discuss+unsubscr...@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_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/05ecfe9ce78342fd8ff39e76bfc12c0b%40mail.gmail.com.
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-discuss@googlegroups.com *On Behalf Of *mele...@gmail.com *Sent:* Monday, May 10, 2021 2:30 PM *To:* spctools-discuss *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-discuss+unsubscr...@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_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/0c6601d6c8386536f65b969b33816770%40mail.gmail.com.
