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Cited by 517Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsGenomics and Phylogenetic Studies

Development and validation of a spectral library searching method for peptide identification from MS/MS

Open access
Lam, Henry, Deutsch, Eric W., Eddes, James S., Eng, Jimmy K., King, Nichole, Stein, Stephen E., Aebersold, Ruedi·2007·PROTEOMICS
DOI 10.1002/pmic.200600625
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Abstract

A notable inefficiency of shotgun proteomics experiments is the repeated rediscovery of the same identifiable peptides by sequence database searching methods, which often are time‐consuming and error‐prone. A more precise and efficient method, in which previously observed and identified peptide MS/MS spectra are catalogued and condensed into searchable spectral libraries to allow new identifications by spectral matching, is seen as a promising alternative. To that end, an open‐source, functionally complete, high‐throughput and readily extensible MS/MS spectral searching tool, SpectraST, was developed. A high‐quality spectral library was constructed by combining the high‐confidence identifications of millions of spectra taken from various data repositories and searched using four sequence search engines. The resulting library consists of over 30 000 spectra for Saccharomyces cerevisiae. Using this library, SpectraST vastly outperforms the sequence search engine SEQUEST in terms of speed and the ability to discriminate good and bad hits. A unique advantage of SpectraST is its full integration into the popular Trans Proteomic Pipeline suite of software, which facilitates user adoption and provides important functionalities such as peptide and protein probability assignment, quantification, and data visualization. This method of spectral library searching is especially suited for targeted proteomics applications, offering superior performance to traditional sequence searching.

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  • PeptideAtlas reprocesses publicly uploaded MS/MS data deposited through ProteomeXchange using sequence search engines Comet, X!Tandem and SpectraST, and aggregates data using rigorous criteria including peptide spectral matching with FDR ~0.0009% in the latest build to achieve ≤1% FDR at the protein level.

    “PeptideAtlas (http://www.peptideatlas.org) uses sequence search engines Comet66, X!Tandem67 and SpectraST68 to reprocess publicly uploaded MS/MS data deposited through ProteomeXchange (PX). Data are aggregated using rigorous criteria including peptide spectral matching with FDR ~ 0.0009% in the latest PeptideAtlas build to achieve ≤1% FDR at the protein level.”

    From A high-stringency blueprint of the human proteome (2020) · cites this paper as [68]

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  1. Patterson, S. D., Aebersold, R., Nat. Genet. 2003, 33, 311- 323.
  2. De Hoog, C. L., Mann, M., Annu. Rev. Genomics Hum. Genet. 2004, 5, 267-293.
  3. Anderson, N. L., Anderson, N. G., Mol. Cell. Proteomics 2002, 1, 845-867.
  4. Mann, M., Jensen, O. N., Nat. Biotechnol. 2003, 21, 255-261.
  5. Aebersold, R., Goodlett, D. R., Chem. Rev. 2001, 101, 269- 295.
  6. Aebersold, R., Mann, M., Nature 2003, 422, 198-207.
  7. Patterson, S. D. Nat. Biotechnol. 2003, 21, 221-222.
  8. Sadygov, R. G., Eng, J., Durr, E., Saraf, A. J. Proteome Res. 2002, 1, 211-215.
  9. Sadygov, R. G., Cociorva, D., Yates, J. R., III, Nat. Methods 2004, 1, 195-202.
  10. MacCoss, M. J., Curr. Opin. Chem. Biol. 2005, 9, 88-94.
  11. Eng, J. K., McCormack, A. L., Yates, J. R., III., J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
  12. Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S., Electrophoresis 1999, 20, 3551-3567.
  13. Craig, R., Beavis, R. C., Bioinformatics 2004, 20, 1466-1467.
  14. Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., J. Pro- teome Res. 2004, 3, 958-964.
  15. Zhang, N., Aebersold, R., Schwikowski, B., Proteomics 2002, 2, 1406-1412.
  16. Keller, A., Nesvizhskii, A. I., Kolker, E., Aebersold, R., Anal. Chem. 2002, 74, 5383-5392.
  17. Domokos, L., Hennberg, D., Weimann, B., Anal. Chim. Acta 1984, 165, 61-74.
  18. Stein, S. E., Scott, D. R., J. Am. Soc. Mass Spectrom. 1994, 5, 859-866.
  19. Ausloos, P., Clifton, C. L., Lias, S. G., Mikaya, A. I. et al., J. Am. Soc. Mass Spectrom. 1999, 10, 287-299.
  20. Yates, J. R., III, Morgan, S. F., Gatlin, C. L., Griffin, P. R., Eng, J. K., Anal. Chem. 1998, 70, 3557-3565.
  21. Craig, R., Cortens, J. P., Fenyo, D., Beavis, R. C., J. Proteome Res. 2006, 5, 1843-1849.
  22. Frewen, B. E., Merrihew, G. E., Wu, C. C., Noble, W. S., Mac- Coss, M. J., Anal. Chem. 2006, 78, 5678-5684.
  23. Pedrioli, P. G., Eng., J. K., Hubley, R., Vogelzang, M. et al., Nat. Biotechnol. 2004, 22, 1459-1466.
  24. Desiere, F., Deutsch, E. W., Nesvizhskii, A. I., Mallick, P. et al., Genome Biol. 2004, 6, R9.
  25. Prince, J. T., Carlson, M. W., Wang, R., Lu, P., Marcotte, E. M., Nat. Biotechnol. 2004, 22, 471-472.
  26. Craig, R., Cortens, J. P., Beavis, R. C., J. Proteome Res. 2004, 3, 1234-1242.
  27. Kristensen, D. B., Brond, J. C., Nielsen, P. A., Andersen, J. R. et al., Mol. Cell. Proteomics 2004, 3, 1023-1038.
  28. Martens, L., Hermjakob, H., Jones, P., Taylor, C. et al., Prote- omics 2005, 5, 3537-3545.
  29. Desiere, F., Deutsch, E. W., King, N. L., Nesvizhskii et al., Nucleic Acids Res. 2006, 34, D655-D658.
  30. Kuster, B., Schirle, M., Mallick, P., Aebersold, R., Nat. Rev. Mol. Cell Biol. 2005, 6, 577-583.
  31. Keller, A., Eng., J. K., Zhang, N., Li., X., Aebersold, R., Mol. Syst. Biol. 2005, 1, 17.
  32. Marelli, M., Smith, J. J., Jung, S., Yi, E. et al., J. Cell Biol. 2004, 167, 1099-112.
  33. Smolka, M., Zhou, H., Aebersold, R., Mol. Cell. Proteomics 2002, 1, 19-29.
  34. Lopez-Ferrer, D., Capelo, J. L., Vazquez, J., J. Proteome Res. 2005, 4, 1569-74.
  35. Martin, D. B., Gifford, D. R., Wright, M. E., Keller, A. et al., Cancer Res. 2004, 64, 347-355.
  36. Yi, E. C., Lee, H., Aebersold, R., Goodlett, D. R. Rapid Com- mun. Mass Spectrom. 2003, 17, 2093-2098.
  37. Craig, R., Cortens, J. P., Beavis, R. C., Rapid Commun. Mass Spectrom. 2005, 19, 1844-1850.
  38. Kapp, E. A., Schutz, F., Reid, G. E., Eddes, J. S. et al., Anal. Chem. 2003, 75, 6251-6264.
  39. Elias, J. E., Gibbons, F. D., King, O. D., Roth, F. P., Gygi, S. P., Nat. Biotechnol. 2004, 22, 214-219.
  40. Huang, Y., Triscari, J. M., Tseng, G. C., Pasa-Tolic, L. et al., Anal. Chem. 2005, 77, 5800-5813.
  41. Elias, J. E., Haas, W., Faherty, B. K., Gygi, S. P., Nat. Methods 2005, 2, 667-675.
  42. Resing, K. A., Meyer-Arendt, K., Mendoza, A. M., Aveline- Wolf, L. D. et al., Anal. Chem. 2004, 76, 3556-3568.
  43. Kapp, E. A., Schutz, F., Connolly, L. M., Chakel, J. A. et al., Proteomics 2005, 5, 3475-3490.
  44. King, N. L., Deutsch, E W.., Ranish, J. A., Nesvizhskii, A. I. et al., Genome Biol. 2006, 7, R106.
  45. Steen, H., Mann, M., Nat. Rev. Mol. Cell Biol. 2004, 5, 699- 711.

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Authors
Lam, H., Deutsch, E. W., Eddes, J. S., Eng, J. K., King, N., Stein, S. E., & Aebersold, R.
Affiliations
  • Institute for Systems Biology (US)
  • National Institute of Standards and Technology (US)
  • University of Zurich (CH)
ORCID
Venue
PROTEOMICS
Publisher
Wiley
Published
2007-03
Volume
7
Issue
5
Pages
655-667
ISSN
  • 1615-9853 (ISSN-L)
  • 1615-9861
DOI
10.1002/pmic.200600625
OpenAlex
W2073637473
Cited by
517
References
45
Citations by year
2026: 11 · 2025: 12 · 2024: 17 · 2023: 31 · 2022: 21 · 2021: 25 · 2020: 26 · 2019: 31 · 2018: 21 · 2017: 25 · 2016: 38 · 2015: 24 · 2014: 37 · 2013: 37 · 2012: 28
FWCI
15.29
Type
journal article
Language
en
Open access
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations
  • PROTEOMICS (publishedVersion)
  • PubMed (publishedVersion)
  • Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
Funders
  • National Institutes of Health (n01hv28179-12-0-0)
  • National Heart, Lung, and Blood Institute (N01-HV-28179)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
spectral library search, peptide identification, spectral library construction, sequence database searching, targeted proteomics, Saccharomyces cerevisiae
MeSH terms
Peptides, Software, Saccharomyces cerevisiae Proteins, Databases, Protein, Proteomics, Tandem Mass Spectrometry

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