High-Resolution Functional Proteomics by Active-Site Peptide Profiling

High-Resolution Functional Proteomics by Active-Site Peptide Profiling

Characterization and functional annotation of the large number of proteins predicted from genome sequencing projects poses a major scientific challenge. Whereas several proteomics techniques have been developed to quantify the abundance of proteins, these methods provide little information regarding...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS Vol. 102; no. 14; pp. 4996 - 5001
Main Authors: Okerberg, Eric S., Wu, Jiangyue, Zhang, Baohong, Samii, Babak, Blackford, Kelly, Winn, David T., Shreder, Kevin R., Burbaum, Jonathan J., Patricelli, Matthew P., Stubbe, JoAnne
Format: Journal Article
Language:English
Published: United States National Academy of Sciences 05-04-2005
National Acad Sciences
Subjects:
Animals
Binding Sites
Biological Sciences
Electrophoresis
Electrophoresis, Capillary
Enzyme activity
Enzymes
Fluorescence
Gels
Liver
Mice
Online searching
Pancreas
Peptide Mapping
Peptides
Peptides - analysis
Peptides - chemistry
Proteases
Proteomes
Proteomics
Proteomics - methods
Serine Endopeptidases - analysis
Serine Endopeptidases - chemistry
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Summary:Characterization and functional annotation of the large number of proteins predicted from genome sequencing projects poses a major scientific challenge. Whereas several proteomics techniques have been developed to quantify the abundance of proteins, these methods provide little information regarding protein function. Here, we present a gel-free platform that permits ultrasensitive, quantitative, and high-resolution analyses of protein activities in proteomes, including highly problematic samples such as undiluted plasma. We demonstrate the value of this platform for the discovery of both disease-related enzyme activities and specific inhibitors that target these proteins.
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To whom correspondence should be addressed. E-mail: mattp@activx.com.
Author contributions: E.S.O., J.W., K.R.S., J.J.B., and M.P.P. designed research; E.S.O., J.W., B.S., K.B., and M.P.P. performed research; B.Z., B.S., D.T.W., and M.P.P. contributed new reagents/analytic tools; E.S.O., J.W., K.B., and M.P.P. analyzed data; and M.P.P. wrote the paper.
Abbreviations: ABP, activity-based probe; CE, capillary electrophoresis; LIF, laser-induced fluorescence detection; LC, liquid chromatography; PF-PEG, fluorophosphonate polyethylene glycol; BODIPY FL, 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacine-3-propionic acid; TAMRA, carboxytetramethylrhodamine.
Communicated by JoAnne Stubbe, Massachusetts Institute of Technology, Cambridge, MA, February 15, 2005
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0501205102