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XCMS / Re: Choose the best parameters to analyse UPLC-qTof data
Next it seems like all your peaks are extremely low. It can often be more easy to look at the base peak intensity (BPI) instead of the TIC. You can do that in masslynx also. Do you see more reasonable peaks there? Do you have a reasonably stable signal from the lockspray compound/trace? It doesn't look like it in your chromatogram. You need to understand if you have a reasonable data quality before there is a point in using XCMS.
For XCMS take a look at the parameters for centwave:
?findPeaks.centWave
Especially the default peakwidth parameter is not good for UPLC. You can try to use something like peakwidth=c(2,20).