Abstract

The systematic and quantitative molecular analysis of mutant organisms that has been pioneered by studies on mutant metabolomes and transcriptomes holds great promise for improving our understanding of how phenotypes emerge. Unfortunately, owing to the limitations of classical biochemical analysis, proteins have previously been excluded from such studies. Here we review how technical advances in mass spectrometry-based proteomics can be applied to measure changes in protein abundance, posttranslational modifications and protein–protein interactions in mutants at the scale of the proteome. We finally discuss examples that integrate proteomics data with genomic and phenomic information to build network-centred models, which provide a promising route for understanding how phenotypes emerge.

Author affiliations

1. Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8093 Zurich, Switzerland.
2. Competence Center for Systems Physiology and Metabolic Diseases, Swiss Federal Institute of Technology (ETH) Zurich, 8093 Zurich, Switzerland.
3. Faculty of Science, University of Zurich, 8006 Zurich, Switzerland.
4. Institute for Systems Biology, 1221 N. 34th Street, Seattle, Washington 98103, USA.

Correspondence to: Ruedi Aebersold^1,2,3,4 Email: aebersold@imsb.biol.ethz.ch

Correspondence to: Matthias Gstaiger^1,2 Email: gstaiger@imsb.biol.ethz.ch

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