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Apr 1, 2011 (Vol. 31, No. 7)

Serum Profiling Making Mark on Predictive Medicine

Treasure Trove of Information Being Uncovered Is Advancing Field Rapidly

  • From Discovery to the Clinic

    ProFACT Proteomics has developed a set of tools for biomarker and drug target discovery that generates a profile of serum proteins based on their functional characteristics. The company’s SeraFILE™ platform comprises a multidimensional surface library and sequential separation protocols that reduce the complexity of the serum proteome and creates subproteome molecular profiles based on functional activity—typically enzymatic activity. SeraFILE protocols utilize mild binding and elution conditions to maintain protein function throughout the separation process. They incorporate a variety of surfaces for proteome subfractionation.

    Matthew Kuruc, co-founder and president of ProFACT, describes the company’s Functional Proteome Prospecting™ approach as being complementary to conventional mass spectrometry-based proteome analysis strategies that emphasize protein identification.

    “You can often detect functional features even before you can identify a protein,” says Kuruc. By monitoring the level of protein function relative to the total protein content in the various subproteomes, “you can monitor where a function goes in the different subfractions and select the fractions that have the most enrichment for that function.”

    Each separation step provides further enrichment. Throughout this iterative process, each subproteome is scored for a desired activity using a variety of techniques including enzyme bioassay, post-translational analysis, and mass spectrometry.

    ProFACTS’ partner in research consumables, Biotech Support Group develops products for proteomic sample preparation and enrichment, such as AlbuVoid™ for albumin depletion. The chemistry underlying AlbuVoid selectively inhibits binding of albumin, allowing the albumin-containing fraction to flow across the separation surface and into a collection vessel. The advantage of this strategy, rather than selectively binding the albumin, says Kuruc, is the ability simultaneously “to capture and concentrate the underlying proteins on the surface.”

    Alphylase, a CRO that provides protein-analysis services to companies involved in research and clinical development of protein pharmaceuticals, received GLP accreditation by the Danish Medicines Agency earlier this year for use of its bioanalytical assays in human and animal serum samples for preclinical and clinical pharmacokinetic/toxicokinetic applications. The company’s Alpha-Quant™ assays are based on stable isotope dilution LC-MS/MS and multiple reaction monitoring to perform absolute multiplex quantification of specific proteins and protein variants in complex samples without the need for antibodies.

    Ejvind Mørtz, Ph.D., COO at Alphalyse, reports “increasing interest from our clients in targeted protein biomarker quantification using LC-MS/MS methods. These methods can specifically quantify low nanogram protein amounts in a milligram protein serum sample within 15 percent accuracy.”

Readers' Comments

Posted 04/28/2011 by Aran Paulus

The life science community realized some time ago that finding biomarkers in biological samples is a daunting analytical task given that both total amount of proteins present and the dynamic range surpasses even the most advanced technologies. Therefore, sample fractionation is a must.

Bio-Rad’s ProteoMiner protein enrichment technology plays a critical role in biomarker discovery workflows as it lowers the absolute amount of high abundant proteins, thereby reducing the effective dynamic range. It is independent of the biological sample and works not only with serum and plasma but also other body fluids, tissues and cell lines.

The work of the University of Minnesota researchers demonstrates beautifully the current state-of-the-art in biomarker discovery workflows using saliva samples to look for differentially expressed proteins. The UM team shows that ProteoMiner technology is beneficial in PTM discovery workflows, in particular for phosphorylated and glycosylated proteins.

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