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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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Why is MS-GF+ not giving the pepXML output file format? #100

Open Jokendo-collab opened 4 years ago

Jokendo-collab commented 4 years ago

I am wondering on how to analyze the mzid output from the MS-GF+ for protein quantifications. Which software of tools can be used to quantify proteins identified by this pipeline? I am stuck and I am disperately asking for help

FarmGeek4Life commented 4 years ago

pepXML is another identifications output format, but mzid/mzIdentML is a standard format developed by HUPO's "Proteomics Standards Initiative". A comment here mentions that mzIdentML can combine in a single file more data than what is available in pepXML and protXML.

The ProteoWizard idconvert tool can convert between them, if you have a tool that only accepts pepXML input.

The addition of pepXML as an output file format for MS-GF+ is highly unlikely.

Jokendo-collab commented 4 years ago

Hi Gibbons,

I got a way of analyzing the downstream results by using the IDpicker software. I will also use the idconvert tool you have mentioned for the conversion.

Thanks, Javan Okendo

On Tue, Apr 14, 2020 at 1:03 AM Bryson Gibbons notifications@github.com wrote:

pepXML http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML is another identifications output format, but mzid/mzIdentML http://www.psidev.info/mzidentml is a standard format developed by HUPO's "Proteomics Standards Initiative". A comment here https://www.biostars.org/p/1894/ mentions that mzIdentML can combine in a single file more data than what is available in pepXML and protXML.

The ProteoWizard idconvert http://proteowizard.sourceforge.net/tools/idconvert.html tool can convert between them, if you have a tool that only accepts pepXML input.

The addition of pepXML as an output file format for MS-GF+ is highly unlikely.

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