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Topic: XCMS and LC-MS/MS (Read 3270 times) previous topic - next topic

XCMS and LC-MS/MS

Hi, I'm sure this is a complete newbie question(s), but for the life of me I can't figure out how to proceed:

I have a (large?) data set with about 100 samples where we ran LC followed by tandem mass spec, for both positive and negative ions.  I've run the data through XCMS online, but I'd like to understand how to actually process the data myself, so I'm attempting to learn more about XCMS in R.  I'd also like to do a bit more sophisticated analysis, since the experimental design is not well suited to a simple t-test.

Please, by all means correct me if I'm wrong on any of this because I can't find a lot of guidance on tandem-MS data, but the best I can tell a typical workflow is:
1) Convert files to .mzXML format
2) Pre-process and pick peaks with xcmsSet()
3) Group between samples to find the same compounds with group()
4) Fill in missing peaks from raw data with fillPeaks() & original data files
5) Annotate peaks with CAMERA
6) Analyze and visualize results

So far I've converted my ABSciex .wiff data into .mzXML, and with the info about processing MSn data from the bioconductor website, I can read in individual files with xcmsRaw().  It seems that a normal workflow is actually going straight to xcmsSet() however, which would be helpful since I can't store more than a few samples in memory due to the several G/file size.  It appears I can process MS/MS data by using the xcmsSet(mslevel=2) argument, but I can't find a lot of documentation on this?  Am I even on the right track here?

Thanks!
-Will