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Additional Research Reports from the 5th Siena Meeting on Functional Proteomics

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Cellzome Updates Yeast Protein-Protein Interactions

As an update to the protein-protein interaction study in yeast published in January of this year in Nature, Bernhard K ster, Cellzome’s director of mass spectrometry, spoke to the meeting on his company’s progress in probing the depths of the yeast proteome. Since January, Cellzome researchers have attempted to express and purify 6,466 open reading frames (ORFs), in addition to the 1,739 attempted for the Nature paper, and managed to purify complexes associated with 2,002 of the 6,466 ORFs. Given this 30 percent purification success rate, Cellzome proceeded to identify 380 multiple protein complexes containing a total of 2,660 protein identifications.

Comparing the number of Cellzome’s total protein identifications with data collected by John Yates via his MudPIT technique and published data from MDS Proteomics, K ster said there are about 3,498 total non-overlapping protein identifications, giving a rough estimate of the size of the yeast proteome.

On average, Cellzome identified complexes with numbers of protein components ranging from two to 132, with an average size of nine proteins per complex.

K ster said Cellzome’s data analysis indicated that their measurements covered 75 percent of the protein complexes described in the literature, but that 86 percent of the complexes contained “novelties” not found in the prior art. Using a “guilt by association” strategy of classifying putative function, Cellzome had identified probable cellular roles for about 820 proteins that lacked any previous annotation in the literature.

The company has also had a look at the TNF- pathway, and built a protein-protein interaction map to help learn the mechanisms of action of particular protein compexes. When studying protein samples of organisms with completed genomes, Cellzome relies on MALDI-TOF mass spectrometers, but employs nano-LC MS/MS when studying mammalian cell samples, K ster said.

NextGen Sciences to Build Protein Expression, 2D Gel Analysis Platforms

NextGen Sciences is developing an automated system for protein expression, NextGen European Commercial Director Grant Cameron told ProteoMonitor. The system, while still in the early stages of design, is meant to perform all stages of protein expression, including induction and purification, Cameron added. In addition, the company is building an alpha version of a 2D gel analysis system for analyzing single gels, in formats as large as 30 cm by 30 cm, Cameron said. Because NextGen is currently filing patents on the technology, the company decided to pull the poster it planned to present at the 5th Siena functional proteomics meeting. NextGen is collaborating with LabVantage Solutions to build LIMS software and task scheduling capabilities into the systems under development, Cameron said.

Walsh’s Proteomeca Seeks Startup Funds

Brad Walsh, former facilities manager for the Australian Proteomics Analysis Facility in Sydney, has formed his own company, Proteomeca, as ProteoMonitor reported last week. The new company, based in Harbord, Australia, is seeking venture funding primarily from equipment manufacturers and other trade investors, rather than venture capitalists, Walsh said. Proteomeca is likely to pursue applications of proteomics in agriculture and bacteriology, using conventional proteomics tools such as 2D gel electrophoresis, multidimensional liquid chromatography, and MALDI and electrospray ionization mass spectrometry, he said. “To be both a toolmaker and apply the tools to biology doesn’t work,” he said.

– JSM

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