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Human Proteome Project Revisited at HUPO


More than a year after a project to map out the human proteome was first proposed, members of the Human Proteome Project and attendees of the Human Proteome Organization's annual conference, which was held in Toronto in September, revisited the merits, challenges, and advisability of such a project.

In April 2008, HUPO first publicized its plans to launch the ambitious initiative as a follow-up to the Human Genome Project in order to "fill in the void between the genotype and the phenotype," a HUPO official said at the time.

The project was estimated then to last a decade and cost $1 billion. But indications that it would have trouble getting off the ground became clear at last year's HUPO conference when representatives from a wide swath of funding agencies, while appreciative of its ambitions, expressed skepticism about the price tag and its chances of attracting funding.

In the year since, not much has been publicly heard about the Human Proteome Project, until recently when organizers of the HUPO conference and some of the leading voices in proteomics debated how to best approach such an effort.

A session held to restart a dialogue on HPP kicked off with John Bergeron, a past president of HUPO and a professor of anatomy and cell biology at McGill University, saying that, in fact, HPP had already begun with Amos Bairoch's annotation and curation of more than 20,300 protein-coding genes a year ago at Swiss-Prot and Matthias Uhlen's continuing work on the Human Protein Atlas.

Bairoch, formerly director of the Swiss-Prot database, is now head of a new resource called Computer and Laboratory Investigation of Proteins of Human Origin. Uhlen is president and vice president of microbiology at the KTH Royal Institute of Technology.

The phase that has not begun, and the aspect that remains undetermined, is how the mass spectrometry community and the quantitative data it can provide fits into the picture, Bergeron says.

— Tony Fong

Proteomics Notes

Thermo Fisher Scientific sublicensed Proteome Sciences' isobaric mass tag technology out to Life Technologies. The Life Tech iTRAQ reagents, according to Proteome Sciences, are based on that TMT technology.

The journal Molecular & Cellular Proteomics says that researchers publishing in the journal must submit their raw data to a public repository. The new policy will take effect after January 1, 2010.

UK-based Cheshire will distribute Denator heat inactivation technology, Stabilizor T1, in the UK and Ireland. The system stabilizes tissue from sampling, eliminating degradative enzyme activity without any additives.


$3.9 million
Amount NIH awarded to Scripps Research Institute scientists to develop protein ligand screening technology

Funded grants

Phosphoproteomics of Opioid Tolerance
Grantee: George Latimer Wilcox, University of Minnesota Twin Cities
Began: May 15, 2009; Ends: Apr. 30, 2011

For this project, Wilcox plans to use mass spectral phosphoproteomic analysis to compare proteins phosphorylated in people with and without morphine tolerance. This also will test the hypothesis that agmatine blocks spinal morphine tolerance development through signal transduction pathways distinct from the NMDA-R/NOS cascade.

A Quantitative Proteomics Approach to Understand Viral Immune Evasion Strategies
Grantee: Michele Hardy, Montana State University
Began: Jun. 1, 2009; Ends: May 31, 2011

To study how viruses evade cellular antiviral responses, Hardy will use stable isotope labeling of amino acids in culture followed by high-resolution chromatographic separation and tandem mass spec of rotavirus-infected cells. "Changes in protein abundance will be analyzed to define NSP1 substrates and determine how these proteins integrate into antiviral networks," the abstract says.

The Scan

Comfort of Home

The Guardian reports that AstraZeneca is to run more clinical trials from people's homes with the aim of increasing participant diversity.

Keep Under Control

Genetic technologies are among the tools suggested to manage invasive species and feral animals in Australia, Newsweek says.

Just Make It

The New York Times writes that there is increased interest in applying gene synthesis to even more applications.

Nucleic Acids Research Papers on OncoDB, mBodyMap, Genomicus

In Nucleic Acids Research this week: database to analyze large cancer datasets, human body microbe database, and more.