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pymzml / pymzML

pymzML - an interface between Python and mzML Mass spectrometry Files
https://pymzml.readthedocs.io/en/latest/
MIT License
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Add a feature to read ion current file(dispersion filed matrix file) #184

Closed kothawadegs closed 4 years ago

kothawadegs commented 4 years ago

Please add .df file reader to analyse the dispersion field matrix data. I tried to read using the function "pymzml.run.Reader(file)", but it's throwing an error. Please find attached for reference Screenshots.

error1 error2
MKoesters commented 4 years ago

Hi @kothawadegs ,

Could you give me some more information about the file you are using? It is a mzML file right? If so, could you upload an example so I could test why it does not work? Additionally, I don't really know what you mean with dispersion field matrix and where/how it is stored, could you give me some more information or a link to make this clearer?

Best, Manuel

kothawadegs commented 4 years ago

Hi @MKoesters ,

It's not a mzML file. It's dispersion field file generated by FAIMS system. Please find attached file in the zip folder. matrix_0001.zip Please let me know whether it is possible to read and process such file using pymzML.

Regards, Gajanan

StSchulze commented 4 years ago

While it would be great to add a feature that allow reading of dispersion field/ion mobility data, pymzML is specifically designed to read mzML files and it seems like the field has not yet adopted this standard file format in a way that allows an easy integration of ion mobility data. The workaround that seems to be most commonly used (from what I could find with a quick search) is to split the raw file into multiple mzML, one for each CF. (e.g.: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6145172/).

MKoesters commented 4 years ago

As Stefan said, pymzML is specifically designed for handling mzML files.

However I'd appreciate feedback, if you happen to to convert your .df file to mzML and use pymzML. Since I never seen an mzML generated from a .df file, a small example would help to make sure pymzML can handle these.

I'm closing this for now, if you run into problems with mzMLs generated from .df, feel free to open a new issue :)