ms2 data with xcms December 10, 2013, 09:29:12 AM Hello,I am hoping to get a little more guidance on analyzing ms2 data in xcms. I have data from multiple samples from FT-ICR MS. I would like to search for parent ions that have a fragmentation spectrum and be able to view the spectrum (or get list of m/z and intensity for fragments) - is this possible with xcmsFragments? I also wanted to check to make sure xcmsFragments is running properly and I am using correct code.Here is what I have done so far:When I ran xcmsSet using the method MS1: xs2=xcmsSet(mzdatafiles, method="MS1")I then got:> xs2An "xcmsSet" object with 34 samplesTime range: 0.2-1980 seconds (0-33 minutes)Mass range: 100.0756-999.96 m/zPeaks: 152238 (about 4478 per sample)Peak Groups: 0 Sample classes: . Profile settings: method = bin step = 0.1Memory usage: 12.2 MBI then ran xcmsFragments: > xfragment=xcmsFragments(xs2)It ran overnight but did not finish. I stopped it so that I could check some other things - should it take days to run with many samples?Any suggestions on the use of xcmsFragments and whether or not it will do what I need would be great. I looked over the user manual and the forum but I am hoping to get more info on this than what I have been able to find so far.Thank you!Cara Quote Selected