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BioAnalyte supports FDA Intact Protein Expression Spectrometry (IPEx) Mass Spectrometry Approaches for Label-free Relative Quantitation and Biomarker Discovery.

Monday, June 18, 2007. Portland, ME -- BioAnalyte announced today that it supports the Intact Protein Expression (IPEx) mass spectrometry methods developed by the US FDA Center for Food Safety and Applied Nutrition (CFSAN). IPEx mass spectrometry is an enhancement of existing analytical methods for profiling complex mixtures of intact proteins using widely-available liquid chromatography mass spectrometry (LC/MS) instrumentation.

"IPEx mass spectrometry provides rapid assessment of protein expression, both from a qualitative and a quantitative standpoint," said Peter Leopold, Ph.D., president of BioAnalyte, Inc. "The FDA's refinements of these approaches make them easy to implement both in the lab and in data analysis. We are excited to bring the focus of the IPEx techniques into our ProTrawler and Regatta data analysis products."

Intact Protein Expression mass spectrometry leverages recent advances in intact protein separations using liquid chromatography with sensitive, accurate detection by quadrupole time-of-flight mass spectrometers. The methods were developed at the CFSAN site in College Park, MD, by Steven Musser, Ph.D. and Tracie Williams, Ph.D.

After moving to the the Center for Disease Control in Atlanta, Williams's research continues to refine the IPEx Spectrometry protocol for the analysis of glycoproteins.

Musser, Williams and colleagues employed the method to identify new protein biomarkers useful for distinguishing closely related strains of food-borne pathogens. In several published cases, presence-absence pairs led to the discovery of unique proteins that distinguish newly-emerging pathogenic forms of Escherichia coli and Vibrio parahaemolyticus.

After moving to the Centers for Disease Control and Prevention in Atlanta, Williams' continues to refine the IPEx mass spectrometry protocol for the analysis of glycoproteins.

"IPEx mass spectrometry is valuable for profiling whole protein mixtures for bacterial identification or pathogenic gene mutation, but it is also may be useful for detecting minor glycosylation changes in mixtures of glyoproteins," Williams said. "Changes in protein glycosylation and other post-translational modifications are being examined as possible contributors to increased virulence of certain infectious diseases. IPEx may help us make a quick identification of proteins that have been modified.

Peter Scholl, Ph.D., of the Johns Hopkins University School of Public Health, uses IPEx mass spectrometry to complement Difference Gel Electrophoresis (DIGE.) In a recent study, Scholl used IPEx to discover global protein expression patterns in rat liver treated with an anti-tumor drug triterpenoid CDDO-Im. The expression patterns will be used in elucidating the drug's mechanisms of anti-tumor action as well as other potential effects on liver function.

"IPEx mass spectrometry aligns the separation power of liquid chromatography with the mass accuracy and resolution of time-of-flight, creating a MALDI-like ease of use," Leopold said. "Easy to use methods lower the barriers to multiple analyses, which facilitates the running of replicates, which improves statistics tremendously."

In the Scholl rat liver study, Scholl obtained abundant information about relative protein expression with one set of experiments that ran overnight. With the IPEx results in hand, Scholl's group is now able to perform hypothesis-driven MS/MS sequencing.

About BioAnalyte Inc.

BioAnalyte delivers high performance bioinformatics software and services to leading laboratories worldwide. It offers cross-platform solutions to facilitate high-speed interpretation of proteomics and metabolomics data to improve research accuracy and productivity. BioAnalyte's flagship product, ProTrawler(tm), was developed in partnership with the Food and Drug Administration (FDA) and led to the landmark discovery of a protein biomarker for a deadly food-borne bacterium. ProTrawler eliminates the data processing bottlenecks that are common to laboratories using instrument vendor-supplied software, dramatically improving productivity and data accuracy. ProNets(tm), the innovative 'consumable' software license, makes ProTrawler software available on a per data set basis. Regatta(tm) is BioAnalyte's label-free quantitation tool kit, facilitating LC/MS alignment, dynamic binning, hierarchical clustering and principal component analysis for expression regulation.


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