I have tried MSstats both from the Skyline external tool and from the R console. I think the dialogue window for QC, profile, and condition plots are not flexible enough (no choice for log transformation or normalisation method). Plus, from Skyline we cannot exploit the data as much, in R we can follow what is happening to our data and make comparison plots (volcano and heatmap). This is for my experience.
In R 3.0.1,I recently got a new error message that I do not understand as I have no zeros and no #N/A:
> quantData<-dataProcess(raw,logTrans=2, normalization=TRUE)
Missing feature intensities should be given by 'NA' in the abundance column.
Error in dataProcess(raw, logTrans = 2, normalization = TRUE) :
Also some people have been asking for clustering and PCA analyses.