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XCMS / ms2 data with xcms
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:
> xs2
An "xcmsSet" object with 34 samples
Time range: 0.2-1980 seconds (0-33 minutes)
Mass range: 100.0756-999.96 m/z
Peaks: 152238 (about 4478 per sample)
Peak Groups: 0
Sample classes: .
Profile settings: method = bin
step = 0.1
Memory usage: 12.2 MB
I 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