A streamlined platform for high-content functional proteomics of primary human specimens

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Jessani, Nadim; Niessen, Sherry; Wei, BinQing Q; Nicolau, Monica; Humphrey, Mark; Ji, Youngran; Han, Wonshik; Noh, Dong-Young; Yates, John R 3rd; Jeffrey, Stefanie S; Cravatt, Benjamin F
Issue Date
Nature Publishing Group
Nat Methods. 2005 Sep;2(9):691-7
Breast Neoplasms/diagnosis/*enzymologyEquipment DesignEquipment Failure AnalysisFemaleGene Expression Profiling/*methodsHumansNeoplasm Proteins/analysis/*metabolismProteome/analysis/*metabolismProteomics/*instrumentation/methodsTumor Cells, CulturedTumor Markers, Biological/analysis/*metabolism
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.
1548-7091 (Print)
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College of Medicine/School of Medicine (의과대학/대학원)Surgery (외과학전공)Journal Papers (저널논문_외과학전공)
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