Mass spectrometry data processing

Mass spectrometry data processing

Target Audience:

General context

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.

  • 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 and quantifying 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
Required skills

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

Course materials


Lennart Martens

Dr. Lennart Martens is Professor of Systems Biology at Ghent University, and Group Leader of the Computational Omics and Systems Biology (CompOmics) group at VIB.

Contact Lennart Martens :
Lieven Clement

Lieven Clement is Associate Professor of Statistical Genomics at Ghent University.

Contact Lieven Clement :



09h30 - 11h00: Search engines (LM)

11h00 - 11h15: Break

11h15 - 12h00: Practical 1.3 - search engines + questions

12h00 - 12h30: Other identification strategies


12h30 - 13h30: Lunch


13h30 - 14h30: Identification reliability and protein inference

14h30 - 15h15: practical 1.4 & 1.5: identification reliability and protein inference

15h15 - 15h30: Break

15h30 - 16h00: MS1 Quantification with moFF

16h00 - 17h00: Practical: moFF


9u30-10u15: Preprocessing & Differential Analysis of experiments with simple designs

10u15-11u15: Tutorial 2.3: Impact of different summarisation methods

11u15-11u30: Break

11u30-12u30: Tutorial 2.4 - Tutorial 2.5


12u30-13u30: Lunch


13u30-14u30: Statistical Inference & Analysis of Experiments with Factorial Designs

14u30-15u30: Tutorial 3.3: Impact of Blocking

15u30-15u45: Break

15u45 - 16u30: Tutorial 3.4: Statistical inference for experiments with multiple factors

16u30 - 17u00: Wrap-up and Questions


VIB training
Tel: +32 9 244 66 11