Thanks so much Jan! I am a newbie to both XCMS and LC-MS raw data in general (coming from a biostat background) so I appreciate your suggestions and your patience. Upon your recommendation, I did look at the raw data, but I am still pretty confused. First, I looked at the raw EIC for an rt range of 360 to 380 and an mzrange of 396 to 398 for 3 of the samples:
> xcmsRawSamp7 <- xcmsRaw(negFiles[7], profstep=1)
> xcmsRawSamp32 <- xcmsRaw(negFiles[32], profstep=1)
> xcmsRawSamp51 <- xcmsRaw(negFiles[51], profstep=1)
>
> par(mfrow=c(1,3))
> plotEIC(xcmsRawSamp7, rtrange=c(360,380), mzrange=c(396,398))
> plotEIC(xcmsRawSamp32, rtrange=c(360,380), mzrange=c(396,398))
> plotEIC(xcmsRawSamp51, rtrange=c(360,380), mzrange=c(396,398))
[attachment=0:20l8tcvj]rawEIC_neg_397_small.png[/attachment:20l8tcvj]
So it seems like all 3 samples would have a peak in that region, with the peak in the leftmost sample (#7 in dataset) being less clear than the other two and, of course, having a lower intensity...
However, it seems like no peak in that region is getting detected in the middle sample (#32 in the dataset) anywhere close to that m/z value:
> peaks32 <- findPeaks(xcmsRawSamp32,
+ method="centWave",ppm=10,snthr=10,peakwidth=c(5,10))
Detecting mass traces at 10 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
4357 m/z ROI's.
Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
802 Peaks.
> peaks32[abs(peaks32[,"rt"]-370) <= 10 &
+ abs(peaks32[,"mz"]-397) <= 10, ,drop=FALSE]
mz mzmin mzmax rt rtmin rtmax into intb maxo sn
The other 2 samples do have a detected peak very close to m/z=397:
> peaks7 <- findPeaks(xcmsRawSamp7,
+ method="centWave",ppm=10,snthr=10,peakwidth=c(5,10))
Detecting mass traces at 10 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
4574 m/z ROI's.
Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
810 Peaks.
> peaks7[abs(peaks7[,"rt"]-370) <= 10 &
+ abs(peaks7[,"mz"]-397) <= 10, ,drop=FALSE]
mz mzmin mzmax rt rtmin rtmax into intb maxo sn
[1,] 397.2064 397.2038 397.2075 368.427 366.541 372.055 1310.64 1305.079 589 55
>
>
> peaks51 <- findPeaks(xcmsRawSamp51,
+ method="centWave",ppm=10,snthr=10,peakwidth=c(5,10))
Detecting mass traces at 10 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
4617 m/z ROI's.
Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
703 Peaks.
> peaks51[abs(peaks51[,"rt"]-370) <= 10 &
+ abs(peaks51[,"mz"]-397) <= 10, ,drop=FALSE]
mz mzmin mzmax rt rtmin rtmax into intb maxo sn
[1,] 397.2052 397.2014 397.2081 369.064 365.292 374.578 15936.530 15741.280 5662.1758 62
[2,] 393.0016 393.0013 393.0024 375.835 373.949 377.092 1223.008 1220.493 664.7559 664
The middle sample, which does not have a detected peak, had an integrated peak intensity > 9.5 higher than the leftmost sample and somewhat smaller than that of the rightmost sample (after fillPeaks). I just can't figure out why no peak is detected since it seems much clearer than in the leftmost sample...
It's possible that I'm missing something super-obvious about the parameters or whatnot though...
Thank you again!
Best,
Maria
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