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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
90 stars 46 forks source link

Validate mzIdentML against HUPO mzidentML and PRIDE validator, as well as ProteoWizard, IDConvert, Skyline, IDPicker #52

Closed stefanks closed 6 years ago

stefanks commented 7 years ago

Use mzLib, and the included class generated from schema.

stefanks commented 7 years ago

Or maybe mzTab is the format we should be focusing on?

trishorts commented 7 years ago

we could get some/all of this code from morpheus

stefanks commented 7 years ago

I would prefer to use class files generated from xsd, that are already included in mzLib. Less possibilities to mess up, and will automatically conform to specifications. https://github.com/smith-chem-wisc/mzLib/tree/master/mzIdentML

trishorts commented 7 years ago

check the result against the HUPO mzidentML and PRIDE validator tools: https://github.com/HUPO-PSI/mzIdentML

chambm commented 7 years ago

Somebody reported a ProteoWizard idconvert failure on some MetaMorpheus mzIdentML. It has spectra (SIIs and SIRs), but no peptide or protein information in it at all! Work in progress, I assume? :)

The file also reports version 1.0.0.0, but I see no release corresponding to that so I assume it's a dummy value.

rmillikin commented 6 years ago

reorganized in #1125