Ideas fly at Proteomics 2011

“What is proteomics?” Answering this simple question was the motivation for the Proteomics 2011, an annual symposium hosted by Judith and Hanno Steen of the Steen & Steen lab and The Proteomics Center at Children’s, featuring global innovators and local advances in proteomics at Children’s Hospital Boston, held last week. As a video at the start of the symposium showed, it’s a question that elicits a wide range of answers:

Video courtesy of the Carino Agency.

Symposium host Hanno Steen gives his opening remarks. (Photo: Chewie Lin)

As noted in the symposium’s opening remarks, the word “proteome,” referring to whole sets of proteins, is only 17 years old, and already the field of proteomics has reached unprecedented scale. Mass spectrometry (mass spec for short), a key technology for proteomic research, can now be used to measure thousands of biomolecules simultaneously and do so in amounts that defy intuition (one part per quintillion, that’s 1 particle in 1,000,000,000,000,000,000!).

This combination of sensitivity and flexibility has enabled a wide range of discoveries in biology and medicine, and the symposium featured several of the latest advances. Ruedi Aebersold from the ETH Zurich in Switzerland and Michal Sharon from the Weizmann Institute in Israel presented new approaches to measuring the interactome, the whole set of molecular interactions in cells, both globally and specifically with respect to human diseases.

Ben Garcia from Princeton University talked about recent advances in epigenetics brought about by the development of functional proteomics, allowing the simultaneous profiling of hundreds of chemical modifications of proteins that affect gene expression.

Harvard Medical School's Dan Finley opens his talk on the proteasome. (Photo: Chewie Lin)

And Dan Finley from Harvard Medical School’s Department of Cell Biology described how enhanced understanding of the proteasome and mechanisms of protein degradation can be used to develop new drug treatments.

Members of The Proteomics Center and the Steen & Steen lab presented some their latest work as well. Sasha Singh discussed FLEXIQinase, a new assay based on the lab’s earlier FLEXIQuant assay that leaps beyond the conventional “on/off” methods used to study molecular switches like kinases. Marc Kirchner presented a transformative method for analyzing multiplex mass spec data, which should greatly enhance our ability to understand complex proteomes.

Sasha Singh listens to an audience question about FLEXIQinase. (Photo: Chewie Lin)

Finally, I presented latest results from a large collaborative project spanning several departments at Children’s Hospital on ways to use proteomics to improve the diagnosis and treatment of wide variety of human diseases. In particular, mass spec-based proteomics allowed my colleagues and me to identify new diagnostic markers of Kawasaki disease, a serious inflammatory and heart illness for which we have no definitive diagnostic test and which is mimicked by many childhood conditions.

In all, Proteomics 2011 suggested that “next generation proteomics” will enable unprecedented discovery of how proteins are regulated by functional modifications, how protein networks control biology, and how their study in patients could improve the diagnosis and treatment of a wide variety of human diseases.

The Proteomics 2011 speakers and hosts (L-R): Dan Finley, Reudi Aebersold, Michal Saron, Alex Kentsis, Judith Steen, Sasha Singh, Joao Paolo of the Steen & Steen lab, Ben Garcia, Marc Kirchner, Hanno Steen. (Photo: Chewie Lin)

[Ed. Note: Proteomics is still a growing field, and as greater analytic (read: computational and instrumental) power becomes available it should have immeasurable impact on our understanding of health and disease. Especially if in the future efforts to integrate molecular profiles with clinical and natural histories start to include proteomic data. So tell us: Where do you think the next generation of proteomic breakthroughs will come from?]