Using MS2

[Vidit Minda]

Hello,

I am trying to work with MS/MS data. I need to access individual fragmentation spectra by scan number or time. Essentially I need a table of m/z and corresponding intensity for fragmentation spectra (getting parameters will be a plus). 

I have a Shimadzu QTOF and can convert my data file to any format with Proteowizard. I believe that MS2 from Pyteomics will be able to help me but I am confused about its usage.

So if I go ahead and use pyteomics.ms2.read(*args, **kwargs)

I think I will be able to achieve this. However, the source probably needs an MS2 file format that seems to be a text format. How can I obtain the text format from an mzml file (or some similar format such as mzXML)?

Is there any video or documentation? I appreciate your help!

Thank you 

Sincerely,

Vidit Minda

[Joshua Klein]

The pyteomics.ms2.MS2 type in Pyteomics is for reading the plain text ms2 file format. If you have an mzML file, you should use pyteomics.mzml.MzML instead. If you want to retrieve a scan by its scan number, use reader[scan_number - 1], and for retention time reader.time[rt]. For more information about random access behavior, see https://pyteomics.readthedocs.io/en/latest/data.html#indexed-parsers and https://pyteomics.readthedocs.io/en/latest/data.html#rich-indexing.

Thank you,
Joshua Klein

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