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Workshop: Mass spectrometry-based proteomics

This workshop, organized by the Loewith lab, will cover the basics of peptide/protein identification and quantification by LC-MS/MS.


Programme of the workshop

We will discuss how to extract proteins from cells and provide practical sessions on how to perform proteolytic digestion, how to enrich phospho-peptides (if desired we will also touch on other post-translational modifications) and how to remove salts and interfering substances from samples. In shorter theoretical sessions we will introduce some basics of liquid chromatography, mass spectrometry and peptide analysis. Data analysis will be dealt with both in theory and in practice. We will be able to somewhat adjust the workshop to the need of. If there is enough interest, we can also touch on alternative quantification strategies and current developments in proteomics.

Practical sessions

  • From proteins to peptides
  • From buffer to interference-free solutions
  • From peptide mixtures to phospho-peptides
  • From spectra to identification and quantification


  • The scope: gel bands, IPs and complex samples
  • Chromatography and mass spectrometry (sensitivity, resolution, speed, mass accuracy)
  • The sample preparation workflow
  • Sample fractionation
  • Identifying peptide sequences
  • Quantifying peptides
  • Data post-processing (imputation, quality-control and multiple-testing correction) and what to do with protein-lists
  • Challenges in phospho-proteomics (neutral losses and isoforms)


More info

  • Participants: max. 6 (priority will be given to NCCR members)
  • Deadline to register: June 7, 2019
  • Only a basic knowledge about proteins is required. The workshop will be limited to beginner to intermediate level. Participation with a specific project in mind is encouraged.
  • Organizers: Dr. Michael Plank & Prof. Robbie Loewith, Department of Molecular Biology, UNIGE