| Combination of Edman degradation of peptides with liquid chromatography/mass spectrometry workflow for peptide identification in bottom-up proteomics. | |
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MedLine Citation:
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PMID: 23280970 Owner: NLM Status: In-Data-Review |
Abstract/OtherAbstract:
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RATIONALE: High-throughput methods of proteomics are essential for identification of proteins in a cell or tissue under certain conditions. Most of these methods require tandem mass spectrometry (MS/MS). A multidimensional approach including predictive chromatography and partial chemical degradation could be a valuable alternative and/or addition to MS/MS. METHODS: In the proposed strategy peptides are identified in a three-dimensional (3D) search space consisting of retention time (RT), mass, and reduced mass after one-step partial Edman degradation. The strategy was evaluated in silico for two databases: baker's yeast and human proteins. Rates of unambiguous identifications were estimated for mass accuracies from 0.001 to 0.05 Da and RT prediction accuracies from 0.1 to 5 min. Rates of Edman reactions were measured for test peptides. RESULTS: A 3D description of proteolytic peptides allowing unambiguous identification without employing MS/MS of up to 95% and 80% of tryptic peptides from the yeast and human proteomes, respectively, was considered. Further extension of the search space to a four-dimensional one by incorporating the second N-terminal amino acid residue as the fourth dimension was also considered and was shown to result in up to 90% of human peptides being identified unambiguously. CONCLUSIONS: The proposed 3D search space can be a useful alternative to MS/MS-based peptide identification approach. Experimental implementations of the proposed method within the on-line liquid chromatography/mass spectrometry (LC/MS) and off-line matrix-assisted laser desorption/ionization (MALDI) workflows are in progress. Copyright © 2012 John Wiley & Sons, Ltd. |
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Authors:
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Anna A Lobas; Anatoly N Verenchikov; Anton A Goloborodko; Lev I Levitsky; Mikhail V Gorshkov |
Publication Detail:
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Type: Journal Article |
Journal Detail:
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Title: Rapid communications in mass spectrometry : RCM Volume: 27 ISSN: 1097-0231 ISO Abbreviation: Rapid Commun. Mass Spectrom. Publication Date: 2013 Feb |
Date Detail:
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Created Date: 2013-01-02 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 8802365 Medline TA: Rapid Commun Mass Spectrom Country: England |
Other Details:
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Languages: eng Pagination: 391-400 Citation Subset: IM |
Copyright Information:
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Copyright © 2012 John Wiley & Sons, Ltd. |
Affiliation:
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Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia; Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow region, Russia. |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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