Exporting StPeter´s ng to mzid

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mele...@gmail.com

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May 7, 2021, 8:03:11 PMMay 7
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Hello,
How can I  include StPeter´s quantifier (ng) during conversion from prot.xml to mzid?
Is there some tpp2mizd parameter? 
Thanks
Valdemir

Jason Winget

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May 8, 2021, 11:57:58 AMMay 8
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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

mele...@gmail.com

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May 10, 2021, 5:29:37 PMMay 10
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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

Eric Deutsch

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May 10, 2021, 5:41:39 PMMay 10
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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

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Eric Deutsch

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May 10, 2021, 6:10:09 PMMay 10
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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

mele...@gmail.com

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May 11, 2021, 8:00:01 PMMay 11
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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

Luis Mendoza

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May 12, 2021, 3:35:10 AMMay 12
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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 <full_path_to_protXML_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 <full_path_to_protXML_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


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