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gygilab / Monocle

Monocle is a tool for monoisotopic peak and accurate precursor m/z detection in shotgun proteomics experiments.
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Produced mzML files does not follow the schema #25

Closed fcyu closed 4 years ago

fcyu commented 4 years ago

Thanks for your contribution to the community. When I am testing this tool using an outputted mzML file, neither MSFragger nor Comet can read it. A closer looking shows that it's format does not follow the schema.

Thanks,

Fengchao

mammmals commented 4 years ago

Hi Fengchao, Thanks for letting us know. Is there any indication of what params/nodes are violating the schemas when you run the Monocle output through MSFragger/Comet? Thanks, Devin

fcyu commented 4 years ago

Hi Devin,

The incorrect position of </cvList> was the first one we spotted. After correcting that by editing the mzML file, there was another error thrown from MSFragger and Comet. So, it looks like there are multiple ones and we don't have time to find all of them.

Best,

Fengchao

mammmals commented 4 years ago

OK, we'll go through and track those down ASAP. Best, Devin

rrad42 commented 4 years ago

Hi Fengchao,

I've updated Monocle to output mzML files that now seem to validate against the schema. I've also tried a search with the latest release of comet and it produces reasonable-looking results, but I havent tried MSFragger. Please give it another try and let us know if there are any more issues.

Ramin

fcyu commented 4 years ago

Hi Ramin,

Thanks for your fast fix. It works.

Best,

Fengchao