• 25W4M/LC-MS - Upload files1
  • 27W4M/LC-MS - Pre-Processing2
  • 29W4M/LC-MS - Processing3
  • 55W4M/LC-MS - Statistical Analysis4
  • 31W4M/LC-MS - Annotation5

W4M/LC-MS - Pre-Processing

Liquid chromatography
Mass spectrometry
Ions extraction

How to extract relevant mass spectrometry features from the different raw acquisition files ?

At the end of the course, you will understand :

  • the different extraction steps
  • how the parameters impact the resulting matrix



  • Knowledge in liquid chromatograhy and mass spectrometry.
  • You know what is the retention time.
  • You know what is the ratio mass upon charge
  • Presentation of xcms software
  • What type of data are available in the LCMS files.
  • How is build an extract ion chromatogram.
  • First step : parallel extraction of ions in the different files
  • Grouping step : alignment among all files
  • Retention time correction step
  • Replacing missing data, fillpeaks step.
  • datamatrix creation step with CAMERA annotation

Summary of the key parameters defined at the differents extraction steps.

Bioconductor : opensource softaware for bioinformatics. (2018). Software packages : xcms (3.7). Repéré à http://bioconductor.org/packages/release/bioc/html/xcms.html
Smith, C. A., Want, E.J., O’Maille, G., Abagyan, R., Siuzdak, G. (2006). XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification. Analytical Chemistry, 78 (3), 779–787. https://doi.org/10.1021/ac051437y
Tautenhahn, R., Boettcher, C., Neumann, S. (2008). Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics, 9, 504. https://doi.org/10.1186/1471-2105-9-504