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Prediction of Posttranslational Modifications Using Intact-Protein Mass Spectrometric Data
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Section:Abstract
We present a Web-based application that uses whole-protein masses determined by mass spectrometry to identify putative co- and posttranslational proteolytic cleavages and chemical modifications. The protein cleavage and modification engine (PROCLAME) requires as input an intact mass measurement and a precursor identification based on peptide mass fingerprinting or tandem mass spectrometry. This approach predicts mass-modifying events using a depth-first tree search, bounded by a set of rules controlled by a custom-built fuzzy logic engine, to explore a large number of possible combinations of modifications accounting for the experimental mass. Candidates are saved during a search if they are within a user-specified instrument mass accuracy; the total number of possible candidates searched is based on a specified fuzzy cutoff score. Candidates are scored and ranked using a simple probabilistic model. There is generally not enough information in an intact mass measurement to determine a single unique protein characterization; however, the program provides utility by expediting the identification of sets of putative events consistent with the mass data and ranking them for further investigation. This approach uses a simple, intuitive rule base and lends itself to discovery of unannotated posttranslational events. We have assessed the program with both in silico-generated test data and with published data from an analysis of large ribosomal subunit proteins, both from the yeast S. cerevisiae. Results indicate a high degree of sensitivity and specificity in characterizing proteins whose masses resulted from reasonable proteolysis and covalent modification scenarios. The application is available on the web at http://proclame.unc.edu.
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This article has been cited by 4 ACS Journal articles (4 most recent appear below).
PTMSearchPlus: Software Tool for Automated Protein Identification and Post-Translational Modification Characterization by Integrating Accurate Intact Protein Mass and Bottom-Up Mass Spectrometric Data Searches
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Mining Phosphopeptide Signals in Liquid Chromatography−Mass Spectrometry Data for Protein Phosphorylation Analysis
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Hsin-Yi Wu, Vincent Shin-Mu Tseng, and Pao-Chi LiaoJournal of Proteome Research2007 6 (5), 1812-1821Protein phosphorylation is a key post-translational modification that governs biological processes. Despite the fact that a number of analytical strategies have been exploited for the characterization of protein phosphorylation, the identification of ...
Integration of Multidimensional Chromatographic Protein Separations with a Combined “Top-Down” and “Bottom-Up” Proteomic Strategy
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Kevin M. Millea, Ira S. Krull, Steven A. Cohen, John C. Gebler, and Scott J. BergerJournal of Proteome Research2006 5 (1), 135-146In this paper, we present a combined top-down/bottom-up proteomic analysis workflow for the characterization of proteomic samples. This workflow combines protein fractionation (multidimensional chromatographic separation) with parallel online ESI-TOF−MS ...
Characterization of the 70S Ribosome from Rhodopseudomonas palustris Using an Integrated “Top-Down” and “Bottom-Up” Mass Spectrometric Approach
Michael Brad Strader, Nathan C. VerBerkmoes, David L. Tabb, Heather M. Connelly, John W. Barton, Barry D. Bruce, Dale A. Pelletier, Brian H. Davison, Robert L. Hettich, Frank W. Larimer, and Gregory B. HurstJournal of Proteome Research2004 3 (5), 965-978Characterization of the 70S Ribosome from Rhodopseudomonas palustris Using an Integrated “Top-Down” and “Bottom-Up” Mass Spectrometric Approach
Michael Brad Strader, Nathan C. VerBerkmoes, David L. Tabb, Heather M. Connelly, John W. Barton, Barry D. Bruce, Dale A. Pelletier, Brian H. Davison, Robert L. Hettich, Frank W. Larimer, and Gregory B. HurstJournal of Proteome Research2004 3 (5), 965-978We present a comprehensive mass spectrometric approach that integrates intact protein molecular mass measurement (“top-down”) and proteolytic fragment identification (“bottom-up”) to characterize the 70S ribosome from Rhodopseudomonas palustris. Forty-two ...
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- Published In Issue January 15, 2004
- Received for review July 4, 2003. Accepted October 23, 2003.
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