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ABRF Gears Up for Protein Quantitation, Protein-Standard Identification Studies


The Association of Biomolecular Research Facilities' Proteomics Research Group is preparing samples for its fifth annual study, which will focus on evaluating the proteomics community's ability to quantify proteins, according to a PRG official.

"I think this study is very relevant for biomarker discovery — for comparing diseased versus normal states," said Christoph Turck, the chair of the PRG who is also the head of the clinical proteomics group at the Max Planck Institute of Psychiatry. "I think it's a very timely project." Turck spoke with ProteoMonitor at the HUPO Fourth Annual World Congress, held in Munich last week.

The PRG hopes that at the end of the study, it will learn what methods of relative quanititation are used within the proteomics community, what are the success rates of each of the methods, and how well established relative quantitation methodologies are within the community.

In addition, the group hopes to find the major applications of relative protein quantitation within laboratories, and how feasible it is to do relative protein quanititation within core facilities.

"I think this study is very relevant for biomarker discovery — for comparing diseased versus normal states. I think it's a very timely project."

Researchers who choose to participate in the study will be asked to identify the proteins within two protein mixtures, and also to determine the relative amounts of the proteins present within each mixture. All academic researchers can participate in the study, but instrument vendors and other members of industry are sometimes excluded.

Turck said each mixture will consist of four to five proteins from a variety of species. The proteins will differ in concentration by a range of about two orders of magnitude.

"In disease research, the dynamic range is much bigger," Turck acknowledged, "But we're technically not there yet to prepare samples with [a range in concentration] above two orders of magnitude."

The proteins in the mixtures will come from a variety of commercial sources, Turck said.

Enough sample will be sent out so that laboratories that choose to analyze the proteins using 2D gels will be able to do so without running out of sample. Along with the protein mixtures, each participating laboratory will be sent an extensive questionnaire that will ask what conditions were used to do the analysis; what quantification kits, if any, were used; what the laboratory usually quantifies proteins for; and a host of other questions.

"I have a feeling that a lot of people will use the stable isotope labeling approach," said Turck. "Label-free quantitation is not as established, but it's something that's coming up."

Turck said the PRG expects to send out protein mixtures for relative quantitation analysis around mid- or late-October. Laboratories will have about two months to do the quantitative analysis, and will be asked to submit results by the end of the year.

After receiving results, the PRG will analyze the data and present findings at next year's annual ABRF conference, which is scheduled to take place Feb. 11-14 in Long Beach, Calif. A written report of the study will later be published in the Journal of Biomolecular Techniques, which is the official journal of the ABRF.

It has not yet been decided if industry will be allowed to participate in the quantitation study, Turck said.

"A lot of companies are very interested in being included, and we hope we can include the vendors," Turck said. "We will be discussing that [within the PRG] soon."

One condition for vendor participation would be that the companies can not use results of the study in advertising, Turck said.

Proteomics Standards Research Group

In addition to the PRG's quantitation study, another ABRF study that focuses on evaluating the proteomics community's ability to identify proteins within a sample mixture of about 50 human proteins is being set up by a newly formed group called the Proteomics Standards Research Group, or sPRG.

Researchers that participate in the sPRG study will be sent a mixture of proteins designed to emulate a "real world sample." The proteins in the mixture will be highly purified, and will be present in a range of concentrations. They will vary within a range of different molecular weights and isoelectric points.

Turck said members of the sPRG are currently negotiating with an undisclosed company to form a deal where the company would make the mixture of human proteins for the ABRF to study for free. After the study is finished, the company will sell the mixture as a standard for evaluating a laboratory's ability to identify proteins.

The sPRG hopes to learn from its study what methods of protein identification are used in the community, what are the success rates of the individual methods, how well-established the protein-identification methodologies are within the community, and what the views of the participants are in terms of the practical usefulness of proteomics reference standards.

While differences in protein identification software algorithms will not be immediately addressed by the study, a second round of the sPRG study would probably be conducted to evaluate software, Turck said.

The sPRG is chaired by Jeffrey Kowalak, a staff scientist at the National Institute of Mental Health.

As with the PRG, the sPRG hopes to send out samples to laboratories in mid- or late-October, to receive results back by the end of the year, and to present findings at the February 2006 meeting of the ABRF.

— Tien-Shun Lee ([email protected])

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