The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.
PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification
Open accessAbstract
Many software tools have been developed for the automated identification of peptides from tandem mass spectra. The accuracy and sensitivity of the identification software via database search are critical for successful proteomics experiments. A new database search tool, PEAKS DB, has been developed by incorporating the de novo sequencing results into the database search. PEAKS DB achieves significantly improved accuracy and sensitivity over two other commonly used software packages. Additionally, a new result validation method, decoy fusion, has been introduced to solve the issue of overconfidence that exists in the conventional target decoy method for certain types of peptide identification software.
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Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
Perkins, D. N., Pappin, D. J. C., Creasy, D. M., & Cottrell, J. S. (1999) · Electrophoresis · doi:10.1002/(sici)1522-2683(19991201)20:18<3551::aid-elps3551>3.0.co;2-2 · Cited by 8,203
Eng, J. K., McCormack, A. L., & Yates, J. R. (1994) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(94)80016-2 · Cited by 6,484
Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr101065j · Cited by 5,500
Keller, A., Nesvizhskii, A. I., Kolker, E., & Aebersold, R. (2002) · Analytical Chemistry · doi:10.1021/ac025747h · Cited by 4,830
Elias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925
TANDEM: matching proteins with tandem mass spectra
Craig, R., & Beavis, R. C. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth092 · Cited by 2,536
Open Mass Spectrometry Search Algorithm
Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M., Maynard, D. M., Yang, X., Shi, W., & Bryant, S. H. (2004) · Journal of Proteome Research · doi:10.1021/pr0499491 · Cited by 1,431
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry
Ma, B., Zhang, K., Hendrie, C., Liang, C., Li, M., Doherty‐Kirby, A., & Lajoie, G. (2003) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.1196 · Cited by 1,379
Self-citationPepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling
Frank, A., & Pevzner, P. (2005) · Analytical Chemistry · doi:10.1021/ac048788h · Cited by 688
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
Self-citationA late Middle Pleistocene Denisovan mandible from the Tibetan Plateau
Chen, F., Welker, F., Shen, C.-C., Bailey, S. E., Bergmann, I., Davis, S., Xia, H., Wang, H., Fischer, R., Freidline, S. E., et al. (2019) · Nature · doi:10.1038/s41586-019-1139-x · Cited by 454
Chick, J. M., Kolippakkam, D., Nusinow, D. P., Zhai, B., Rad, R., Huttlin, E. L., & Gygi, S. P. (2015) · Nature Biotechnology · doi:10.1038/nbt.3267 · Cited by 425
Mills, R. H., Dulai, P. S., Vázquez-Baeza, Y., Sauceda, C., Daniel, N., Gerner, R. R., Batachari, L. E., Malfavon, M., Zhu, Q., Weldon, K., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-021-01050-3 · Cited by 385
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Metadata
- Authors
- Zhang, J., Xin, L., Shan, B., Chen, W., Xie, M., Yuen, D., Zhang, W., Zhang, Z., Lajoie, G. A., & Ma, B.
- Venue
- Molecular & Cellular Proteomics
- Publisher
- Elsevier BV
- Published
- 2012-04
- Volume
- 11
- Issue
- 4
- Pages
- M111.010587
- ISSN
- 1535-9476 (ISSN-L)
- OpenAlex
- W2135078307
- Cited by
- 1,081
- References
- 25
- FWCI
- 12.04
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Zhang, J., Xin, L., Shan, B., Chen, W., Xie, M., Yuen, D., Zhang, W., Zhang, Z., Lajoie, G. A., & Ma, B. (2012). PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification. Molecular & Cellular Proteomics. https://doi.org/10.1074/mcp.m111.010587
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