The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Probability-Based Validation of Protein Identifications Using a Modified SEQUEST Algorithm
Abstract
Database-searching algorithms compatible with shotgun proteomics match a peptide tandem mass spectrum to a predicted mass spectrum for an amino acid sequence within a database. SEQUEST is one of the most common software algorithms used for the analysis of peptide tandem mass spectra by using a cross-correlation (XCorr) scoring routine to match tandem mass spectra to model spectra derived from peptide sequences. To assess a match, SEQUEST uses the difference between the first- and second-ranked sequences (ACn). This value is dependent on the database size, search parameters, and sequence homologies. In this report, we demonstrate the use of a scoring routine (SEQUEST-NORM) that normalizes XCorr values to be independent of peptide size and the database used to perform the search. This new scoring routine is used to objectively calculate the percent confidence of protein identifications and posttranslational modifications based solely on the XCorr value.
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Cites
Smoothing and Differentiation of Data by Simplified Least Squares Procedures.
Savitzky, A., & Golay, M. J. E. (1964) · Analytical Chemistry · doi:10.1021/ac60214a047 · Cited by 21,904
Cited by
Semi-supervised learning for peptide identification from shotgun proteomics datasets
Käll, L., Canterbury, J. D., Weston, J., Noble, W. S., & MacCoss, M. J. (2007) · Nature Methods · doi:10.1038/nmeth1113 · Cited by 2,424
Self-citationPeptide 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
Hornbeck, P. V., Kornhauser, J. M., Tkachev, S., Zhang, B., Skrzypek, E., Murray, B., Latham, V., & Sullivan, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1122 · Cited by 1,646
Proteomics by Mass Spectrometry: Approaches, Advances, and Applications
Yates, J. R., Ruse, C. I., & Nakorchevsky, A. (2009) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-061008-124934 · Cited by 1,078
Self-citationInsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra
Tanner, S., Shu, H., Frank, A., Wang, L.-C., Zandi, E., Mumby, M., Pevzner, P. A., & Bafna, V. (2005) · Analytical Chemistry · doi:10.1021/ac050102d · Cited by 567
Metadata
- Authors
- MacCoss, M. J., Wu, C. C., & Yates, J. R.
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2002-09-07
- Volume
- 74
- Issue
- 21
- Pages
- 5593-5599
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W2072000480
- Cited by
- 377
- References
- 1
- FWCI
- 17.67
- Type
- journal article
- Language
- en
- Open access
- closed
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