The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics
Open accessAbstract
Large-scale protein sequencing methods rely on enzymatic digestion of complex protein mixtures to generate a collection of peptides for mass spectrometric analysis. Here we examine the use of multiple proteases (trypsin, LysC, ArgC, AspN, and GluC) to improve both protein identification and characterization in the model organism Saccharomyces cerevisiae. Using a data-dependent, decision tree-based algorithm to tailor MS(2) fragmentation method to peptide precursor, we identified 92 095 unique peptides (609 665 total) mapping to 3908 proteins at a 1% false discovery rate (FDR). These results were a significant improvement upon data from a single protease digest (trypsin) - 27 822 unique peptides corresponding to 3313 proteins. The additional 595 protein identifications were mainly from those at low abundances (i.e., < 1000 copies/cell); sequence coverage for these proteins was likewise improved nearly 3-fold. We demonstrate that large portions of the proteome are simply inaccessible following digestion with a single protease and that multiple proteases, rather than technical replicates, provide a direct route to increase both protein identifications and proteome sequence coverage.
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Cites
Global analysis of protein localization in budding yeast
Huh, W.-K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., & O'Shea, E. K. (2003) · Nature · doi:10.1038/nature02026 · Cited by 4,248
Elias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925
Global analysis of protein expression in yeast
Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., & Weissman, J. S. (2003) · Nature · doi:10.1038/nature02046 · Cited by 3,750
Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry
Syka, J. E. P., Coon, J. J., Schroeder, M. J., Shabanowitz, J., & Hunt, D. F. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402700101 · Cited by 2,370
Self-citationInterpretation of Shotgun Proteomic Data
Nesvizhskii, A. I., & Aebersold, R. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r500012-mcp200 · Cited by 1,025
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
de Godoy, L. M. F., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C., & Mann, M. (2008) · Nature · doi:10.1038/nature07341 · Cited by 873
Large-scale phosphorylation analysis of mouse liver
Villén, J., Beausoleil, S. A., Gerber, S. A., & Gygi, S. P. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609836104 · Cited by 730
Cited by
Protein Analysis by Shotgun/Bottom-up Proteomics
Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491
MS-GF+ makes progress towards a universal database search tool for proteomics
Kim, S., & Pevzner, P. A. (2014) · Nature Communications · doi:10.1038/ncomms6277 · Cited by 1,098
Geiger, T., Wehner, A., Schaab, C., Cox, J., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.014050 · Cited by 797
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
Vlastaridis, P., Kyriakidou, P., Chaliotis, A., Van de Peer, Y., Oliver, S. G., & Amoutzias, G. D. (2017) · GigaScience · doi:10.1093/gigascience/giw015 · Cited by 733
Hebert, A. S., Richards, A. L., Bailey, D. J., Ulbrich, A., Coughlin, E. E., Westphall, M. S., & Coon, J. J. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.034769 · Cited by 528
“tensive fractionation (24) and triplicate analysis of each frac-”
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Metadata
- Authors
- Swaney, D. L., Wenger, C. D., & Coon, J. J.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2010-01-29
- Volume
- 9
- Issue
- 3
- Pages
- 1323-1329
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W1995638700
- Cited by
- 474
- References
- 7
- FWCI
- 12.99
- Type
- journal article
- Language
- en
- Open access
- green
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