Mass spectrometry data processing

Trainer Lennart Martens and Niels Hulsaert


Obtain a good understanding of the origins and properties of mass spec data
Obtain an understanding of the processing of mass spec data, aimed at identifying peptides and proteins
Gain sufficient understanding of the software tools and database used, and of the issues and caveats involved, to critically analyse and assess results from mass spectrometry based proteomics experiments


In this training session we start by reviewing the types of mass spectrometer, and what the properties of their output data are. Out of our understanding of the data, we learn to extract meaningful interpretations.


A basic understanding of mass spectrometry as applied to peptides and proteins is required by the participants.


See the TRAINING AT VIB website for a detailed schedule of this training.

Training material

  • Practicals by Lennart Martens
  • Video tutorials: Lectures on Computational Mass Spectrometry Proteomics - Basics (see slides deks below)
  • Slides: Introduction to mass spectrometry and proteomics by Lennart Martens
  • Slides: Peptide and protein identification by Lennart Martens
  • Slides: Assessing identification reliability by Lennart Martens
  • Slides: Databases and protein inference by Lennart Martens
  • Slides: Quantification with moFF by Andrea Argentini
  • Zip-file containing all training material: tools, text, data and databases (right-click and choose 'Save as...')
    The tools in the zip file are a bit outdated, please download and install the updated versions: To run the software you need a recent Java, at least 4GB RAM and a 64-bit operating system.


Scientific topics Mass spectrometry data, Proteomics, Spectral analysis
Target audience Life Science Researchers, PhD students, post-docs