Networks in the Life Sciences – Genomics, Proteomics and Systems Biology
14th EMBL PhD Symposium

25th–27th October 2012

Speaker: Prof. Dr. Ruedi Aebersold

  • ETH Zürich Institute of Biotechnology
  • Co-founder & faculty member, Institute for Systems Biology, Seattle
  • EMBO member


Ruedi Aebersold Principal investigator at ETH Zürich, as well as co-founder and faculty member at the Institute for Systems Biology in Seattle, Ruedi Aebersold is known for developing several widely used proteomics methods, including the Isotope Coded Affinity Tag (ICAT). He now focuses on cancer, using these tools to profile cells from different states and identify diagnostic markers.

Talk: Proteomics and network biology

A new paradigm is emerging in the life sciences that places networks of interacting molecules between genotype and phenotype. These networks are dynamically modulated by a multitude of factors and the properties emerging from the network as a whole determine observable phenotypes. Often, such networks are characterized by proteins (network nodes) that are connected to each other in different ways (indicated as network edges). This paradigm is usually referred to as systems biology, network biology or integrative biology.

Mass spectrometry based proteomics has made significant progress towards the identification, characterization and quantification of proteins in complex samples, i.e. towards the characterization of network nodes. The quantitative analysis of network edges has been considerably more difficult.

In this presentation we will discuss how quantitative mass spectrometry can be used to directly measure network edges as in the case of physical protein–protein interactions. We will also discuss emerging methods to generate proteomic datasets from which network edges can be inferred in cases where they are not directly measurable, e.g. for functional interactions. The technical advances will be illustrated with selected examples.


  1. Gillet LC, Navarro P, Tate S, Roest H, Selevsek N, Reiter L, Bonner R, Aebersold R. (2012) Targeted data extraction of the MS/MS spectra generated by data independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics. 2012 Jan 18. Mol Cell Proteomics. 2012 Jan 18.
  2. Bensimon A, Heck AJ, Aebersold R. (2012) Mass Spectrometry-Based Proteomics and Network Biology. Annu Rev Biochem. 2012 Mar 22. [Epub ahead of print]
  3. Herzog F et al. (2012) Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross linking and Mass Spectrometry. Science, in press