Improved proteomics tools generated in multidisciplinary EU consortium

Published: 2012-04-02

[PRESS RELEASE 2012-04-02] New and optimized technological approaches are developed within the PROSPECTS project taking part in moving the proteomics field beyond the large-scale detection and analysis of proteins towards performing true quantitative measurements and to follow cells response to stress or drugs at a proteome-wide level.

“The proteomics field is now entering a third generation phase where large-scale protein analysis will provide unique quantifiable data on a subcellular level “ says one of the participants in the EU funded PROSPECTS project Dr. Emma Lundberg from the Science for Life Laboratory Stockholm. In the PROSPECTS project new or improved tools and approaches have been developed to enable absolute protein quantification, study of protein-protein interactions and protein complexes and the quantitative study of protein abundance and turnover rates in different subcellular localizations at a proteome-wide level.

One specific aim of the PROSPECT project is the development and application of proteomics methods that can address problems of clinical significance. In a collaborative study between the Science for Life Laboratory, Stockholm and the Max Planck Institute, Martinsried, Germany (published in the March Special Issue: Prospects in Space and Time, Molecular & Cellular Proteomics), a new method for quantitative proteomics was described demonstrating that the combination of recombinant human protein fragments and mass spectrometry allows precise analysis of quantitative levels of proteins in a systematic manner.

Entering the “third generation” phase of proteomics, the PROSPECTS group anticipates that current methods for routine protein analysis can be replaced by mass spectrometry-based quantitative proteomics. Decreased costs, increased analysis speed and easier access to mass spectrometry instruments and user-friendly software will have a major impact in cell biology research.

The PROSPECTS (Proteomics Specification in Time and Space) project brings together ten proteomics research groups from around Europe. This project started in 2008 and is a five-year collaborative project between research groups with complementary expertise, coordinated by Professor Mathias Mann from the Max Planck Institute. Four years into the project more than 80 manuscripts have been published, two new mass spectrometry instruments (Orbitrap ELITE and Q Exactive) have been developed, as well as new tools and software for handling large amount of proteomics data.


Angus I. Lamond, Mathias Uhlen, Stevan Horning, Alexander Makarov, Carol V. Robinson, Luis Serrano, F. Ulrich Hartl, Wolfgang Baumeister, Anne Katrin Werenskiold, Jens S. Andersen, Ole Vorm, Michal Linial, Ruedi Aebersold, and Matthias Mann (2012) “Advancing Cell Biology Through Proteomics in Space and Time (PROSPECTS)” Mol Cell Proteomics 2012 11: O112.017731

Marlis Zeiler, Werner L. Straube, Emma Lundberg, Mathias Uhlen, and Matthias Mann (2012) “A Protein Epitope Signature Tag (PrEST) Library Allows SILAC-based Absolute Quantification and Multiplexed Determination of Protein Copy Numbers in Cell Lines” Mol Cell Proteomics 2012 11: O111.009613.

The Science for Life Laboratory is a joint effort between four Swedish universities, Karolinska Institute, The Royal Institute of Technology (KTH), Stockholm University and Uppsala University, to build an infrastructure for high-throughput research in the areas of health and environment. This center was started in 2010.