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Topic: MRM data (Read 423 times) previous topic - next topic

  • joergbuescher
  • [*]
MRM data
Hi there,

Looking at the forum, I'm not the only one who seems to struggle with parsing MRM data in R:
http://www.metabolomics-forum.com/index.php?topic=177.msg2249#msg2249
http://www.metabolomics-forum.com/index.php?topic=569.msg2312#msg2312

However those posts are quite old, and I heard that there is now a package that can import LC-QqQ (aka MRM) data in R. Unfortunately I cannot find it. Any hint would be highly welcome.

My current workaround is to use Proteowizard to convert my .d files to .txt files, for which I then wrote a very simple parser in R. But this is obviously less nice than using a well defined file format like .mzML.

Thanks for your help,
Joerg
  • MPI for Immunobiology and Epigenetics

  • Jan Stanstrup
  • [*][*][*][*][*]
  • Administrator
Re: MRM data
Reply #1
Info about the backend issues with this: https://github.com/sneumann/mzR/issues/73

From the discussion there it seems mzR at least should be able to read something from those files.
Maybe Msnbase can even read the files but I don't know.

XCMS issues:
https://github.com/sneumann/xcms/issues/57
https://github.com/sneumann/xcms/issues/169
  • Steno Diabetes Center Copenhagen, Denmark
Blog: stanstrup.github.io

  • joergbuescher
  • [*]
Re: MRM data
Reply #2
Just wanted to post the solution that Stefan Neumann told me about and that is working beautifully for me:

https://github.com/wilsontom/sRm

This package reads SRM data from mzML files that were generated by Proteowizard. This is exactly what I was looking for.

Best
Joerg
  • MPI for Immunobiology and Epigenetics