Most of the time xcms have been used for untargeted mass spectrometry data analysis. Can you use the xcms software for targeted analysis? Is it suitable for proteomics or for all (metabolomics, lipidomics, proteomics, glycomics)?

Note: Can xcms be used for targeted mass spectrometry analysis?

In principle yes. The big issue here is the poor connection between derived and raw data within the xcms framework (i.e. how to link MS2 scans to detected peaks etc.). My first stab at solving this is a rather convoluted and horrible package (it was my first R package) called pepmaps (https://github.com/thomasp85/pepmaps). It hasn't been tested or used after R v.2.15 so I don't think you'll be able to run it, but you might draw some inspiration from how MS2 peptide identifications were matched to peaks in an xcmsSet.

My second stab was creating a whole new package (MSsary - https://github.com/thomasp85/MSsary) that precisely solves all these problems, but development on this has stood still while I finish up my PhD. As far as I remember though, If you're fine with using massifquant for peak detection and do a bit of manual work, you should be able to get MSsary to work just as easy (or easier) than wrestling with xcms...

Hey Thomas,

Thank you for your suggestion. Can you please provide me your email address so that I can write to you if I have any queries related to R.

Thank you