Metabolomics

Slides

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

Exercises

• 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

Files

MS spectral library: take file GMD_20111121_MDN35_ALK_MSL.txt

Software

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

• ProteoWizard for file conversion
• AMDIS for peak identification
• CSI:FingerID