1
XCMS Online / Re: XC-MS data analysis: MS/MS matching –replicates- and met
Although XCMS provides easy and comfortable tool for initial screening,I reckon that there is no way around re-checking MS spectra and peak integration individually, especially when you are not on top of controlling the XCMS parameters . Also, the MS-MS fragmentation patterns differ between instruments and conditions, so I'm not sure how well it will match yours.
I'll give you an example for non MSn data: out of ~800 peaks integrated in serum in one job, when I manually checked them on XCMS and Qual browser (the instrument software), I got rid of ~200 which were noise peaks, contaminants, funny products of big peaks, and tails of big peaks (there is always a compromise because not all peaks have the same characteristics for integration). Now, this was still after strict filtering, hence at least 50% of samples in one group has the peak; above s/n of 6, threshold intensity 5000 etc. I reckon it would have been better if I did blank subtraction before I imported the files to XCMS, but didn't due to the unstable background in the blanks. Also, there is a lot of work after you are given a putative id: some peaks that XCMS identified for me (not MS/MS data though) were fragments of others, and for quite a few peaks there was no hit because not all the possible metabolites exist in metlin.
good luck!