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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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MSFragger Result Viewer #300

Closed hcadre closed 2 years ago

hcadre commented 3 years ago

The more I work with MSFragger, the more I think I can appreciate the quality of the results obtained. Being a long time MaxQuant user though, I am missing the Viewer functionality that serves as a common platform to access all result files from one central point (peptides, proteins, modifications, MSMS spectra etc). Are there any plans to implement a similar tool also for MSFragger?

fcyu commented 3 years ago

Thanks for your kind words. We use PDV to view the spectra. For timsTOF data, you need to check 'write calibrate mgf' so that PDV can use the MGF later.

Best,

Fengchao

anesvi commented 3 years ago

This is a good, valid suggestion. However, we also do not want to write another big viewer program. Perhaps there is something already available where we can feed our data into? I have not looked at Peptide Shaker for a while. Not sure what else is there that is freely available

From: hcadre notifications@github.com Sent: Monday, February 1, 2021 11:42 AM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [Nesvilab/FragPipe] MSFragger Result Viewer (#300)

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The more I work with MSFragger, the more I think I can appreciate the quality of the results obtained. Being a long time MaxQuant user though, I am missing the Viewer functionality that serves as a common platform to access all result files from one central point (peptides, proteins, modifications, MSMS spectra etc). Are there any plans to implement a similar tool also for MSFragger?

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hcadre commented 3 years ago

Thanks for your suggestions! MSConvert is slow as molasses though in converting .d files to mgf format and converting dozens of files will take aeons then. And then I have access to the spectra only. But what about the combined.prot.xml file? Doesn´t it contain the all the combined protein data in a format that could be rendered accessible to PDV or maybe Peptide Shaker?

Best,

Hannes

fcyu commented 3 years ago

PDV supports psm.tsv and pep.xml. Not sure about PeptideShaker.

Best,

Fengchao

JurajLenco commented 3 years ago

PeptideShaker currently supports X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda, MetaMorpheus, Novor, DirecTag, and mzIdentML. It would be great if it works with MSFragger too. J. Lenco

anesvi commented 3 years ago

Thank you for the suggestion. Our problem is we need to convert the output to mzIdentML. We need to check the format, and I am hoping to find someone who can help us with the process a bit. Best, Alexey

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PeptideShaker currently supports X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda, MetaMorpheus, Novor, DirecTag, and mzIdentML. It would be great if it works with MSFragger too. J. Lenco

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hcadre commented 3 years ago

On the MZIdentML page of the Seattle Proteome Center (http://tools.proteomecenter.org/wiki/index.php?title=Software:MZIdentML) it says: "... The program idconvert which is part of the ProteoWizard suite is capable of converting a number of different formats into mzIdentml. When doing the conversion it is useful to have all of the source files available to the converter because the converter is smart enough to find multiple sources and to weave the data into a single document. In particular the combination of prot.xml and pep.xml is supported. If you use this combination it is a good idea to have the original sources used for the search available and in the same spots that they were used in the search because the pep.xml file will not contain the original spectra but only a reference to the file from which they were read.

Would that help or represent a part of the solution?