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Using Annotated Peptide Mass Spectrum Libraries for Protein Identification
Abstract
A system for creating a library of tandem mass spectra annotated with corresponding peptide sequences was described. This system was based on the annotated spectra currently available in the Global Proteome Machine Database (GPMDB). The library spectra were created by averaging together spectra that were annotated with the same peptide sequence, sequence modifications, and parent ion charge. The library was constructed so that experimental peptide tandem mass spectra could be compared with those in the library, resulting in a peptide sequence identification based on scoring the similarity of the experimental spectrum with the contents of the library. A software implementation that performs this type of library search was constructed and successfully used to obtain sequence identifications. The annotated tandem mass spectrum libraries for the Homo sapiens, Mus musculus, and Saccharomyces cerevisiae proteomes and search software were made available for download and use by other groups.
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Cited by
Gillet, L. C., Navarro, P., Tate, S., Röst, H., Selevsek, N., Reiter, L., Bonner, R., & Aebersold, R. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.016717 · Cited by 2,877
Lam, H., Deutsch, E. W., Eddes, J. S., Eng, J. K., King, N., Stein, S. E., & Aebersold, R. (2007) · PROTEOMICS · doi:10.1002/pmic.200600625 · Cited by 517
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis
Picotti, P., Clément-Ziza, M., Lam, H., Campbell, D. S., Schmidt, A., Deutsch, E. W., Röst, H., Sun, Z., Rinner, O., Reiter, L., et al. (2013) · Nature · doi:10.1038/nature11835 · Cited by 318
Reiter, L., Claassen, M., Schrimpf, S. P., Jovanovic, M., Schmidt, A., Buhmann, J. M., Hengartner, M. O., & Aebersold, R. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900317-mcp200 · Cited by 312
Assembling the Community-Scale Discoverable Human Proteome
Wang, M., Wang, J., Carver, J., Pullman, B. S., Cha, S. W., & Bandeira, N. (2018) · Cell Systems · doi:10.1016/j.cels.2018.08.004 · Cited by 201
Proteomic Insight into the Molecular Function of the Vitreous
Skeie, J. M., Roybal, C. N., & Mahajan, V. B. (2015) · PLOS ONE · doi:10.1371/journal.pone.0127567 · Cited by 93
Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics
Cifani, P., Li, Z., Luo, D., Grivainis, M., Intlekofer, A. M., Fenyö, D., & Kentsis, A. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00638 · Cited by 24
Metadata
- Authors
- Craig, R., Cortens, J. C., Fenyo, D., & Beavis, R. C.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2006-07-14
- Volume
- 5
- Issue
- 8
- Pages
- 1843-1849
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2113765377
- Cited by
- 301
- References
- 0
- FWCI
- 10.36
- Type
- journal article
- Language
- en
- Open access
- closed
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
