The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra
Abstract
Reliable identification of posttranslational modifications is key to understanding various cellular regulatory processes. We describe a tool, InsPecT, to identify posttranslational modifications using tandem mass spectrometry data. InsPecT constructs database filters that proved to be very successful in genomics searches. Given an MS/MS spectrum S and a database D, a database filter selects a small fraction of database D that is guaranteed (with high probability) to contain a peptide that produced S. InsPecT uses peptide sequence tags as efficient filters that reduce the size of the database by a few orders of magnitude while retaining the correct peptide with very high probability. In addition to filtering, InsPecT also uses novel algorithms for scoring and validating in the presence of modifications, without explicit enumeration of all variants. InsPecT identifies modified peptides with better or equivalent accuracy than other database search tools while being 2 orders of magnitude faster than SEQUEST, and substantially faster than X!TANDEM on complex mixtures. The tool was used to identify a number of novel modifications in different data sets, including many phosphopeptides in data provided by Alliance for Cellular Signaling that were missed by other tools.
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A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry
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Yates, J. R., Eng, J. K., McCormack, A. L., & Schieltz, D. (1995) · Analytical Chemistry · doi:10.1021/ac00104a020 · Cited by 1,253
PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling
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Self-citationNowak, S. J., & Corces, V. G. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.02.007 · Cited by 622
De Novo Peptide Sequencing via Tandem Mass Spectrometry
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Self-citationA method for reducing the time required to match protein sequences with tandem mass spectra
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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
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Kim, S., & Pevzner, P. A. (2014) · Nature Communications · doi:10.1038/ncomms6277 · Cited by 1,098
Self-citationLarge-scale proteomics and phosphoproteomics of urinary exosomes
Gonzales, P. A., Pisitkun, T., Hoffert, J. D., Tchapyjnikov, D., Star, R. A., Kleta, R., Wang, N. S., & Knepper, M. A. (2009) · Journal of the American Society of Nephrology · doi:10.1681/asn.2008040406 · Cited by 727
ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity
Xu, T., Park, S. K., Venable, J. D., Wohlschlegel, J. A., Diedrich, J. K., Cociorva, D., Lu, B., Liao, L., Hewel, J., Han, X., et al. (2015) · Journal of Proteomics · doi:10.1016/j.jprot.2015.07.001 · Cited by 511
Metadata
- Authors
- Tanner, S., Shu, H., Frank, A., Wang, L.-C., Zandi, E., Mumby, M., Pevzner, P. A., & Bafna, V.
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2005-06-09
- Volume
- 77
- Issue
- 14
- Pages
- 4626-4639
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W2075036506
- Cited by
- 567
- References
- 24
- FWCI
- 15.04
- Type
- journal article
- Language
- en
- Open access
- closed
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