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

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 proteomic...

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Published inNature methods Vol. 2; no. 9; pp. 691 - 697
Main Authors Cravatt, Benjamin F, Jessani, Nadim, Niessen, Sherry, Wei, BinQing Q, Nicolau, Monica, Humphrey, Mark, Ji, Youngran, Han, Wonshik, Noh, Dong-Young, Yates, John R, Jeffrey, Stefanie S
Format Journal Article
LanguageEnglish
Published United States Nature Publishing Group 01.09.2005
Subjects
Biomarkers, Tumor - analysis
Biomarkers, Tumor - metabolism
Breast Neoplasms - diagnosis
Breast Neoplasms - enzymology
Equipment Design
Equipment Failure Analysis
Female
Gene Expression Profiling - methods
Humans
Neoplasm Proteins - analysis
Neoplasm Proteins - metabolism
Proteome - analysis
Proteome - metabolism
Proteomics - instrumentation
Proteomics - methods
Tumor Cells, Cultured
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Summary: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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ISSN:1548-7091
1548-7105
DOI:10.1038/nmeth778