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  • Slides of the training in January 2018, partI
  • Slides of the training in January 2018, partII


  • Exercise 1 Converting raw data from vendor format to open format (mzML) using msconvert tool of ProteoWizard
  • Exercise 2 Processing data: peak picking and peak matching
    Convert files to mzML format using msconvert of ProteoWizard (see exercise 1)
    Analyze the data in R/RStudio using the xcms package
  • Exercise 3
  • Exercise 4
  • Exercise 5


MS spectral library: take file GMD_20111121_MDN35_ALK_MSL.txt


Bioconductor and Bioconductor packages

  • Bioconductor
  • xcms for data processing
  • IPO to optimize the processing parameters of xcms
  • CAMERA to group peaks of ions of the same compound (peaks with equal elution time)
  • mz.unity further examination of CAMERA results
  • credential to remove contaminating peaks

Other software