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 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.
Jessani
Nadim
N
The Skaggs Institute for Chemical Biology and Department of Cell Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, California 92037, USA.
Niessen
Sherry
S
Wei
BinQing Q
BQ
Nicolau
Monica
M
Humphrey
Mark
M
Ji
Youngran
Y
Han
Wonshik
W
Noh
Dong-Young
DY
Yates
John R
JR
Jeffrey
Stefanie S
SS
Cravatt
Benjamin F
BF
D014408:Biomarkers, Tumor / Q000032:analysis / Q000378:metabolism*; D001943:Breast Neoplasms / Q000175:diagnosis / Q000201:enzymology*; D004867:Equipment Design; D019544:Equipment Failure Analysis; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D009363:Neoplasm Proteins / Q000032:analysis / Q000378:metabolism*; D020543:Proteome / Q000032:analysis / Q000378:metabolism*; D040901:Proteomics / Q000295:instrumentation* / Q000379:methods; D014407:Tumor Cells, Cultured
D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D020543:Proteome