The DOI matches its Crossref record; 36 of the 36 references it cites were found in a registry or an index.
MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra
Open accessAbstract
Today's highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most widely used search engines were developed when high-resolution mass spectrometry data were not readily available for fragment ion masses, we have designed a scoring algorithm particularly suitable for high mass accuracy. Our algorithm, MS Amanda, is generally applicable to HCD, ETD, and CID fragmentation type data. The algorithm confidently explains more spectra at the same false discovery rate than Mascot or SEQUEST on examined high mass accuracy data sets, with excellent overlap and identical peptide sequence identification for most spectra also explained by Mascot or SEQUEST. MS Amanda, available at http://ms.imp.ac.at/?goto=msamanda , is provided free of charge both as standalone version for integration into custom workflows and as a plugin for the Proteome Discoverer platform.
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Cites
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
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
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
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
Activities at the Universal Protein Resource (UniProt)
(2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1140 · Cited by 1,735
Beausoleil, S. A., Villén, J., Gerber, S. A., Rush, J., & Gygi, S. P. (2006) · Nature Biotechnology · doi:10.1038/nbt1240 · Cited by 1,577
Olsen, J. V., de Godoy, L. M. F., Li, G., Macek, B., Mortensen, P., Pesch, R., Makarov, A., Lange, O., Horning, S., & Mann, M. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t500030-mcp200 · Cited by 1,510
Cited by
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
Cardioids reveal self-organizing principles of human cardiogenesis
Hofbauer, P., Jahnel, S. M., Papai, N., Giesshammer, M., Deyett, A., Schmidt, C., Penc, M., Tavernini, K., Grdseloff, N., Meledeth, C., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.034 · Cited by 588
The cGAS–STING pathway drives type I IFN immunopathology in COVID-19
Domizio, J. D., Gulen, M. F., Saidoune, F., Thacker, V. V., Yatim, A., Sharma, K., Nass, T., Guenova, E., Schaller, M., Conrad, C., et al. (2022) · Nature · doi:10.1038/s41586-022-04421-w · Cited by 538
Chen, Y.-J., Roumeliotis, T. I., Chang, Y.-H., Chen, C.-T., Han, C.-L., Lin, M.-H., Chen, H.-W., Chang, G.-C., Chang, Y.-L., Wu, C.-T., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.012 · Cited by 382
Queiroz, R. M. L., Smith, T., Villanueva, E., Marti-Solano, M., Monti, M., Pizzinga, M., Mirea, D.-M., Ramakrishna, M., Harvey, R. F., Dezi, V., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-018-0001-2 · Cited by 365
Metadata
- Authors
- Dorfer, V., Pichler, P., Stranzl, T., Stadlmann, J., Taus, T., Winkler, S., & Mechtler, K.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2014-06-26
- Volume
- 13
- Issue
- 8
- Pages
- 3679-3684
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2087934409
- Cited by
- 490
- References
- 36
- FWCI
- 12.24
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Dorfer, V., Pichler, P., Stranzl, T., Stadlmann, J., Taus, T., Winkler, S., & Mechtler, K. (2014). MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra. Journal of Proteome Research. https://doi.org/10.1021/pr500202e
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