The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
GutenTag: High-Throughput Sequence Tagging via an Empirically Derived Fragmentation Model
Open accessAbstract
Shotgun proteomics is a powerful tool for identifying the protein content of complex mixtures via liquid chromatography and tandem mass spectrometry. The most widely used class of algorithms for analyzing mass spectra of peptides has been database search software such as SEQUEST. A new sequence tag database search algorithm, called GutenTag, makes it possible to identify peptides with unknown posttranslational modifications or sequence variations. This software automates the process of inferring partial sequence "tags" directly from the spectrum and efficiently examines a sequence database for peptides that match these tags. When multiple candidate sequences result from the database search, the software evaluates which is the best match by a rapid examination of spectral fragment ions. We compare GutenTag's accuracy to that of SEQUEST on a defined protein mixture, showing that both modified and unmodified peptides can be successfully identified by this approach. GutenTag analyzed 33,000 spectra from a human lens sample, identifying peptides that were missed in prior SEQUEST analysis due to sequence polymorphisms and posttranslational modifications. The software is available under license; visit http://fields.scripps.edu for information.
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Fiat, A.-M., & Joll�s, P. (1989) · Molecular and Cellular Biochemistry · doi:10.1007/bf00421079 · Cited by 163
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-citationOmenn, G. S., States, D. J., Adamski, M., Blackwell, T. W., Menon, R., Hermjakob, H., Apweiler, R., Haab, B. B., Simpson, R. J., Eddes, J. S., et al. (2005) · PROTEOMICS · doi:10.1002/pmic.200500358 · Cited by 787
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
Self-citationChick, 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
JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy
Wang, X., Li, Y., Wu, Z., Wang, H., Tan, H., & Peng, J. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.039586 · Cited by 194
Data storage using peptide sequences
Ng, C. C. A., Tam, W. M., Yin, H., Wu, Q., So, P.-K., Wong, M. Y.-M., Lau, F. C. M., & Yao, Z.-P. (2021) · Nature Communications · doi:10.1038/s41467-021-24496-9 · Cited by 41
Metadata
- Authors
- Tabb, D. L., Saraf, A., & Yates, J. R.
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2003-10-18
- Volume
- 75
- Issue
- 23
- Pages
- 6415-6421
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W2035283832
- Cited by
- 274
- References
- 1
- FWCI
- 8.48
- Type
- journal article
- Language
- en
- Open access
- green
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