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Molecular & Cellular Proteomics 7:509-518, 2008.
© 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

A Sequence-specific Exopeptidase Activity Test (SSEAT) for "Functional" Biomarker Discovery^*,S

Josep Villanueva^,, Arpi Nazarian, Kevin Lawlor, San San Yi, Richard J. Robbins^¶ and Paul Tempst^,,||

From the Protein Center and Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065 and ^¶ Department of Medicine, The Methodist Hospital, Houston, Texas 77030

One form of functional proteomics entails profiling of genuine activities, as opposed to surrogates of activity or active "states," in a complex biological matrix: for example, tracking enzyme-catalyzed changes, in real time, ranging from simple modifications to complex anabolic or catabolic reactions. Here we present a test to compare defined exoprotease activities within individual proteomes of two or more groups of biological samples. It tracks degradation of artificial substrates, under strictly controlled conditions, using semiautomated MALDI-TOF mass spectrometric analysis of the resulting patterns. Each fragment is quantitated by comparison with double labeled, non-degradable internal standards (all-D-amino acid peptides) spiked into the samples at the same time as the substrates to reflect adsorptive and processing-related losses. The full array of metabolites is then quantitated (coefficients of variation of 6.3–14.3% over five replicates) and subjected to multivariate statistical analysis. Using this approach, we tested serum samples of 48 metastatic thyroid cancer patients and 48 healthy controls, with selected peptide substrates taken from earlier standard peptidomics screens (i.e. the "discovery" phase), and obtained class predictions with 94% sensitivity and 90% specificity without prior feature selection (24 features). The test all but eliminates reproducibility problems related to sample collection, storage, and handling as well as to possible variability in endogenous peptide precursor levels because of hemostatic alterations in cancer patients.

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