Journal
NATURE METHODS
Volume 2, Issue 9, Pages 691-697Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/NMETH778
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Funding
- NCI NIH HHS [R01 CA087660-05, R01 CA087660, CA087660] Funding Source: Medline
- NHGRI NIH HHS [HG00030] Funding Source: Medline
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Achieving information content of satisfactory breadth and depth remains a formidable challenge for proteomics. This problem is particularly relevant to the study of primary human specimens, such as tumor biopsies, which are heterogeneous and of finite quantity. Here we present a functional proteomics strategy that unites the activity-based protein profiling and multidimensional protein identification technologies (ABPP-MudPIT) for the streamlined analysis of human samples. This convergent platform involves a rapid initial phase, in which enzyme activity signatures are generated for functional classification of samples, followed by in-depth analysis of representative members from each class. Using this two-tiered approach, we identified more than 50 enzyme activities in human breast tumors, nearly a third of which represent previously uncharacterized proteins. Comparison with cDNA microarrays revealed enzymes whose activity, but not mRNA expression, depicted tumor class, underscoring the power of ABPP-MudPIT for the discovery of new markers of human disease that may evade detection by other molecular profiling methods.
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