To whom it may concern, I am a student from University of Louisville, USA. I am currently doing some MALDI-TOF MS data analysis research with PROcess package. I am trying to use the batch functionality of the package to do pre processing on 286 spectra. The m/z values are not exactly the same throughout the spectra, which I think it is an assumption in PROcess package. I used the code below to do baseline correction for one spectrum at a time B.fs <- list.files(my.B.files, pattern = "\\.*csv\\.*", full.names = TRUE) nb.file <- length(B.fs) foo<-lapply(seq(nb.file), function(i) read.files(B.fs[i] )) f0<-lapply(seq(nb.file), function(i) foo[[i]][foo[[i]][,1]>0,]) basecorr<-lapply(seq(nb.file), function(i) bslnoff(f0[[i]], method = "loess", bw = 0.1)) I could not use "rmBaseline" function since the row-names of the returning matrix are the m/z values, which in my case, are not identical. Would you please give some suggestions on this issue? Best Regards, Farida