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NCI Issues Report on Proteomics Initiative

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Five teams established by the US National Cancer Institute are currently trying to explain the reasons behind the wide variability in proteomic results, and to possibly devise ways to eliminate them, according to a report issued by the institute in August.

According to the report by the Clinical Proteomic Technologies for Cancer of the NCI, five teams of labs chosen in late 2006 to address the issue of reproducibility in proteomics experiments came up with wide differences in their analysis of a 20-protein mixture, and the labs are now determining "why there is so much variability between laboratories and even within laboratories in an effort to address the sources of variation."

The teams have chosen the yeast proteome as a more complex system to continue their work to analyze the reasons for the differences in results and to develop standard operating procedures, protocols, and strategies to reduce variability and thus increase the reproducibility of proteomics experiments.

"Although their work has only just begun, the ... teams have made significant progress in establishing a baseline for understanding and reducing intra-laboratory and inter-laboratory variability in the unbiased discovery stage of the proteomics pipeline," according to the report describing the first year of work done by the five labs. "In addition, valuable resources for the proteomics community have been identified: the NCI-20 protein sample and the yeast proteome sample."

The teams were put together under an initiative by CPTC, called the Clinical Proteomic Technology Assessment for Cancer, or CPTAC, program, under which the labs were awarded a total of $35.5 million over five years to assess proteomics technologies. Longer-range goals of CPTAC include the development of standard reference material such as samples, antibodies, data, and protocols for use by the general community.

—Tony Fong

Proteomics Notes

Proteome Systems is shutting down its drug-development business to focus on its biomarker-based diagnostics operations. The company had been trying to develop therapeutics since it merged with Eukarion in 2005.

The Whitehead Institute, the Proteomics and Mass Spectrometry Facility at the University of Massachusetts Medical School, and Harvard Medical School will be using Protein Forest's Mass Spec Results Analysis Tool to study data gathered with the company's digital ProteomeChip system. They are looking for biomarkers for glial tumors, prostate cancer, and MHC-linked diseases.

MDS reported its third-quarter revenue dropped by 4 percent from 2007.

Datapoint

2,000
The number of Antibodies developed by the Human Proteome Resource now available from Sigma-Aldrich.

Funded Grants

$310,932/FY 2008
Algorithms and Software for Difficult Proteomics Problems
Grantee: Marshall Wayne Bern, Palo Alto Research Center
Began: Jul. 1, 2008; Ends: Jun. 30, 2010
With this grant, Bern will be developing algorithms and software to aid peptide identification in proteomics samples, including ones that have been modified. Specifically, he aims to develop a way to statistically measure false discovery rate, to make software to identify oxidative footprinting, and to improve mutation and modification searching.

$192,500/FY 2008
Subtle Modification of Isotope Ratio Proteomics (SMIRP)
Grantee: Julian Whitelegge, University of California,
Los Angeles
Began: Mar. 22, 2008; Ends: Feb. 28, 2011
Whitelegge plans to improve upon current quantitative proteomic strategies. With this grant, he wants to develop an inexpensive way to code the quantitative differential expression information from a single isotopomer envelope. He says this project will be applicable to expression proteomics and turnover measurements in humans.

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