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sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
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Representation of (different) Ion Mobility values in scanHeaders #276

Open sneumann opened 1 year ago

sneumann commented 1 year ago

Hi, as pointed out by @RogerGinBer in #275, there are a number of ways how ion mobility can be measured and included in mzML data. One is a scan attribute, where the ion mobility stuff is (hopefully) all below ion mobility attribute: https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1002892&lang=en&viewMode=All&siblings=false We currently add ion mobility drift time if present: https://github.com/sneumann/mzR/blob/48029f236c90e66992d8835e174b22d235c34c2d/src/RcppPwiz.cpp#L247 but what about other vendors/instruments ? Seems Bruker TIMS Data converted by msconvert uses inverse reduced ion mobility. => Should that go into the same header column ? Then users will have to know what actual value that column contains. => New column, potentially bloating our headers ? Yours, Steffen

jorainer commented 1 year ago

Good questions. I would maybe add a separate header column? it's true that we start to get pretty large header data.frames, but IMHO it would be bad to put it into the same column if we don't know that the values are equivalent (and have the exact same meaning).

Note that we have also the MsBackendTimsTof that supports direct import of data from the vendor files.