Proteomics Rears Its Head for the First Time At TIGR s 13th GSAC in San Diego

For the first time in its 13 year history, the Genome Sequencing and Analysis Conference (GSAC) devoted a morning’s plenary session to proteomics, which included talks by Denis Hochstrasser, co-founder of GeneProt, Scott Patterson, vice president of proteomics at Celera, and Dolores Cahill, a protein array researcher at the Max-Planck Institute of Molecular Genetics in Berlin.

The three-day conference, organized by The Institute for Genomic Research (TIGR) and held this fall in San Diego Oct. 25-28, is traditionally the realm of sequencing —Craig Venter initiated the conference while at the NIH — but in recent years the conference has also emphasized emerging technologies, including microarry analysis, and now, proteomics.

Hochstrasser opened the proteomics session with a talk describing the clinical applications of proteomics, and the technology platform he helped develop at GeneProt for combing various kinds of biological samples to find novel proteins with potential as therapeutics or disease markers. As a faculty member of the University Hospital in Geneva, Hochstrasser also spoke on his academic research into developing a “molecular scanner” for analyzing proteins transferred to PVDF membrane with a mass spectrometer.

In addition to Patterson and Cahill, John Yates, a researcher at the Scripps Research Institute in La Jolla, Calif., presented his recent work to identify vaccine candidates in the human malarial parasite Plasmodium falciparum, and Ruedi Aebersold, of the Institute for Systems Biology in Seattle, described the inner workings of his ICAT (Isotope-Coded Affinity Tag) reagent technology for isotopically labeling cysteine residues in peptide fragments as a method for quantifying differences in protein expression.

Proteomics researchers also made their mark during the concurrent sessions, vying with talks on sequencing, bioinformatics, and microarray technology. Mathias UhlÈn of the Royal Institute of Technology in Stockholm, Sweden, described his efforts to express every protein encoded in human chromosome 21, and how he has used these expressed proteins to generate affinity reagents that have applications in protein antibody arrays.

In other proteomics talks, Celera Genomics researcher Paul Thomas presented Celera’s work to develop Panther, a simplified version of the publicly-available Gene Ontology for classifying proteins and assigning them to protein family trees. Lastly, Heather Pancio, a scientist at Incyte Genomics, described her company’s development of biotinylated antibody arrays and the use of resonance light scattering to detect when a binding event has occurred.

Researchers at TIGR will also soon cease to be immune from the growing influence of proteomics. A new functional genomics facility at the institute’s headquarters in Rockville, Md., will include proteomics when the building is completed in 2003, said TIGR President Claire Fraser in an interview. Fraser said the institute had not yet decided what technology to use in its future studies of proteins, but that she hoped to establish a next-generation platform that did not include 2D gel electrophoresis.

“I don’t think there’ll be any 2D gels,” she said. “That’s yesterday’s technology.”

— JSM