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Messages - joergbuescher
Just wanted to post the solution that Stefan Neumann told me about and that is working beautifully for me:
This package reads SRM data from mzML files that were generated by Proteowizard. This is exactly what I was looking for.
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Looking at the forum, I'm not the only one who seems to struggle with parsing MRM data in R:
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,
I'm currently analyzing data that I recorded on an Agilent GC-MS (single quad) with XCMS and CAMERA. I use TMS derivatization and a temperature gradient that goes up to 300 C. Because of the temperature I see quite a bit of column bleeding towards the end of the chromatograms, most prominently the masses 207 and 281. Looking at the raw data the peaks that are detected in those two mass traces are quite high above zero, but only slightly above the local baseline. So as long as I do the analysis without peakfill and intb as intensity value, this is not much of an issue.
However if I use peakfill I have the impression that it only fills into. So it adds all those really high intensity signals with the effect that there is a high background signal even in blanks. I tried to get rid of those background signals using the correlation filtering function from CAMERA afterwards, but that did not help much.
I think that ideally peakfill would also do a baseline detection and fill the intb column. Is there a way to do that already?
Do you have any other suggestions how to tackle this issue?
Any hint is more than welcome.