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| - An Alternative to Tandem Mass Spectrometry: Isoelectric Point and Accurate Mass for theIdentification of Peptides
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| - The traditional approach to the identification of peptidesin complex biological samples integrally involves the useof tandem mass spectrometry to generate a uniquefragmentation pattern in order to accurately assign itsidentity to a particular protein. In this article we describethe theoretical basis for a new paradigm for the identification of peptides and proteins. This methodology employsthe use of accurate mass and peptide isoelectric point (pI)as identification criteria, and represents a change in focusfrom current tandem mass spectrometry-dominated approaches. A mathematical derivation of the false positiverate associated with accurate mass and pI measurementsis presented to demonstrate the utility of the technique.The equations for calculation of the experimental falsepositive rate allow for the determination of the validity ofthe data. The false positive rate issue examined in detailhere is not restricted to accurate mass-based approaches,but also has application to the tandem mass spectrometrycommunity as well. The theoretical proteomes of Escherichia coli and Rattus norvegicus are used to evaluatethe efficacy of this approach. The power of the techniqueis demonstrated by analyzing a series of peptides with thesame monoisotopic masses but with differing isoelectricpoints. Finally, the speed of algorithm when combinedwith the experimental peptide analysis has the potentialto rapidly accelerate the protein identification process.
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