Evaluating Peptide Mass Fingerprinting-based Protein Identification |
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Authors: | Senthilkumar Damodaran Troy D. Wood Priyadharsini Nagarajan Richard A. Rabin |
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Affiliation: | [1]Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA [2]Department of Chemistry, University at Buffalo, Buffalo, NY 14260, USA [3]Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA |
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Abstract: | Identification of proteins by mass spectrometry (MS) is an essential step in pro- teomic studies and is typically accomplished by either peptide mass fingerprinting (PMF) or amino acid sequencing of the peptide. Although sequence information from MS/MS analysis can be used to validate PMF-based protein identification, it may not be practical when analyzing a large number of proteins and when high- throughput MS/MS instrumentation is not readily available. At present, a vast majority of proteomic studies employ PMF. However, there are huge disparities in criteria used to identify proteins using PMF. Therefore, to reduce incorrect protein identification using PMF, and also to increase confidence in PMF-based protein identification without accompanying MS/MS analysis, definitive guiding principles are essential. To this end, we propose a value-based scoring system that provides guidance on evaluating when PMF-based protein identification can be deemed sufficient without accompanying amino acid sequence data from MS/MS analysis. |
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Keywords: | peptide mass fingerprinting Mowse Mascot ProFound proteomics Protein Identification Mass system guidance amino acid sequence data principles increase confidence reduce criteria identify However vast proteomic present instrumentation available practical analyzing |
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