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
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
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