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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 mzxml files doesn't read by Proteome Discoverer or MaxQuant #26

Closed RSN4ever closed 3 years ago

RSN4ever commented 4 years ago

Dear Developers,

Thank you so much for creating this important tool in correcting monoisotopic peak correction which definitely has huge implications on MS-based proteomic result outputs. The produced mzxml files by monocle were unable to initiate a search by Proteome Discoverer. MaxQuant does complete the search but gives just 28 IDs with a very low Andromeda score. I appreciate if you could fix this issue.

Best, Raja

rrad42 commented 4 years ago

Hi Raja

The latest now produces mzXMLs that validate against the schema and are searchable with comet.

I dont have access to PD right now, and I can't find an mzXML that works with MaxQuant. Files converted with msconvert or raw converter dont seem to work with MaxQuant either. If you have more information about what could be wrong, or if you have an mzXML file that works in MaxQuant, please share and I'll try to debug the issue further.

Ramin