| Improve the coverage for the analysis of phosphoproteome of Hela cells by a tandem digestion approach. | |
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MedLine Citation:
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PMID: 22468782 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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Complete coverage of all phosphorylation sites in a proteome is the ultimate goal for large-scale phosphoproteome analysis. However, only use of one protease trypsin for protein digestion cannot cover all phosphorylation sites, because not all tryptic phosphopeptides are detectable in MS. To further increase the phosphoproteomics coverage of Hela cell, we proposed a tandem digestion approach by using two different proteases. By combining the dataset of the first Glu-C digestion and the second trypsin digestion, the tandem digestion approach resulted in the identification of 8062 unique phosphopeptides and 8507 phosphorylation sites in Hela cell. While the conventional trypsin digestion approach resulted in the identification of 3891 unique phosphopeptides and 4647 phosphorylation sites. It was found that the phosphorylation sites identified from the above two approaches were highly complementary. By combining above two data sets, totally we identified 10899 unique phosphopeptides and 11262 phosphorylation sites, corresponding to 3437 unique phosphoproteins with FDR < 1% at peptide level. We also compared the kinase motifs extracted from trypsin, Glu-C or second trypsin digestion data sets. And it was observed that basophilic motifs were more frequently found in the trypsin and the second trypsin digestion data sets, the acidic motifs were more frequently found in the Glu-C digestion data set. These results demonstrated that, our tandem digestion approach is a good complement to conventional trypsin digestion approach for improving the phosphoproteomics analysis coverage of Hela cell. |
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Authors:
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Yangyang Bian; Mingliang Ye; Chunxia Song; Kai Cheng; Chunli Wang; Xiaoluan Wei; Jun Zhu; Rui Chen; Fangjun Wang; Hanfa Zou |
Publication Detail:
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Type: JOURNAL ARTICLE Date: 2012-4-3 |
Journal Detail:
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Title: Journal of proteome research Volume: - ISSN: 1535-3907 ISO Abbreviation: - Publication Date: 2012 Apr |
Date Detail:
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Created Date: 2012-4-3 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 101128775 Medline TA: J Proteome Res Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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