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Topics - nvinayav

1
XCMS / MRM data?
I have generated some MRM data from Agilent QQQ LC/MS.  I thought it would be useful to get the peak area for all of the peaks at once.  Is MRM data supported by xcms?  I have tried to use xcmsSet(), but it gave me the following messages:

> xs <- xcmsSet()
2_110927pos_wc-ptc1a: Error in seq.default(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) *  :
  invalid (to - from)/by in seq(.)
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
> traceback()
11: stop("invalid (to - from)/by in seq(.)")
10: seq.default(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) *
        step, by = step)
9: seq(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) * step,
      by = step)
8: .local(object, ...)
7: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">)
6: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">)
5: do.call(method, list(object, ...))
4: .local(object, ...)
3: findPeaks(lcraw, ...)
2: findPeaks(lcraw, ...)
1: xcmsSet()

I guess this is understandable, since the files contain mainly MS2 data, and not MS1.  Is there any way around this problem using xcmsSet()? 

Thank you very much.