quick & dirty approach to import Bruker xml files.

importBrukerXml.R

## code to import peaks from Bruker xml files

importBrukerXml <- function(file) {
  require("MALDIquant")

  ## read file
  r <- readLines(file)

  ## remove useless stuff
  r <- gsub(pattern="^.*<ms_peaks>|</ms_peaks>.*$", replacement="", x=r)

  ## fetch mass (mz), intensity (i), snr (sn) and fwhm
  tags <- c("mz", "i", "sn", "fwhm")
  patterns <- paste(tags, "=\\\"[0-9.]+\\\"", sep="")
  results <- vector(mode="list", length=length(tags))
  names(results) <- tags

  for (i in seq(along=tags)) {
    ## grep pattern
    rx <- gregexpr(pattern=patterns[i], text=r)[[1]]

    ## extract numeric value
    ## start offset == nchar(tag) + 2 (e.g. mz=", offset == 4)
    ## end offset = 1
    num <- substring(text=r, first=rx+nchar(tags[i])+2,
                     last=rx+attr(rx, "match.length")-2)

    ## convert character to double
    results[[i]] <- as.double(num)
  }

  ## create MassPeaks object
  return(createMassPeaks(mass=results$mz, intensity=results$i, snr=results$sn,
                         metaData=list(file=normalizePath(file),
                                       fwhm=results$fwhm)))

#  ## if you really want to create a MassSpectrum object out of this file
#  return(createMassSpectrum(mass=results$mz, intensity=results$i,
#                            metaData=list(file=normalizePath(file),
#                                          fwhm=results$fwhm,
#                                          snr=results$sn)))
}