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Building consensus spectral libraries for peptide identification in proteomics

Nature Methods volume 5, pages 873–875 (2008)Cite this article

Abstract

Spectral searching has drawn increasing interest as an alternative to sequence-database searching in proteomics. We developed and validated an open-source software toolkit, SpectraST, to enable proteomics researchers to build spectral libraries and to integrate this promising approach in their data-analysis pipeline. It allows individual researchers to condense raw data into spectral libraries, summarizing information about observed proteomes into a concise and retrievable format for future data analyses.

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Figure 1: Library building functionalities of SpectraST.
Figure 2: Effects of library quality level and consensus spectrum creation.
Figure 3: Effects of library spectrum simplification.

References

  1. Steen, H. & Mann, M. Nat. Rev. Mol. Cell Biol. 5, 699–711 (2004).

    Article  CAS  Google Scholar 

  2. Eng, J.K., McCormack, A.L. & Yates, J.R., III. J. Am. Soc. Mass Spectrom. 5, 976–989 (1994).

    Article  CAS  Google Scholar 

  3. Patterson, S.D. Nat. Biotechnol. 21, 221–222 (2003).

    Article  CAS  Google Scholar 

  4. Domon, B. & Aebersold, R. Mol. Cell. Proteomics 5, 1921–1926 (2006).

    Article  CAS  Google Scholar 

  5. Yates, J.R., III, Morgan, S.F., Gatlin, C.L., Griffin, P.R. & Eng, J.K. Anal. Chem. 70, 3557–3565 (1998).

    Article  CAS  Google Scholar 

  6. Domokos, L., Hennberg, D. & Weimann, B. Anal. Chim. Acta 165, 61–74 (1984).

    Article  CAS  Google Scholar 

  7. Ausloos, P. et al. J. Am. Soc. Mass Spectrom. 10, 287–299 (1998).

    Article  Google Scholar 

  8. Lam, H. et al. Proteomics 7, 655–667 (2007).

    Article  CAS  Google Scholar 

  9. Craig, R., Cortens, J.C., Fenyo, D. & Beavis, R.C. J. Proteome Res. 5, 1843–1849 (2006).

    Article  CAS  Google Scholar 

  10. Frewen, B.E., Merrihew, G.E., Wu, C.C., Noble, W.S. & MacCoss, M.J. Anal. Chem. 78, 5678–5684 (2006).

    Article  CAS  Google Scholar 

  11. Keller, A., Eng, J., Zhang, N., Li, X.J. & Aebersold, R. Mol. Syst. Biol. 1, 17 (2005).

    Article  Google Scholar 

  12. Pedrioli, P.G. et al. Nat. Biotechnol. 22, 1459–1466 (2004).

    Article  CAS  Google Scholar 

  13. Deutsch, E.W. et al. Proteomics 5, 3497–3500 (2005).

    Article  CAS  Google Scholar 

  14. Tabb, D.L., Thompson, M.R. & Khalsa-Moyers, G. J. Am. Soc. Mass Spectrom. 16, 1250–1261 (2005).

    Article  CAS  Google Scholar 

  15. Flikka, K. et al. Proteomics 7, 3245–3258 (2007).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank all the data contributors to PeptideAtlas who have made this study possible. This study was supported in part by the US National Heart, Lung and Blood Institute, National Institutes of Health (N01-HV-28179).

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Authors and Affiliations

  1. Institute for Systems Biology, 1441 N. 34th Street, Seattle, 98103, Washington, USA

    Henry Lam, Eric W Deutsch, James S Eddes, Jimmy K Eng & Ruedi Aebersold

  2. Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong

    Henry Lam

  3. National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, 20899, Maryland, USA

    Stephen E Stein

  4. Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, Eidgenössische Technische Hochschule Hönggerberg, Wolfgang Pauli Str. 16, HPT, and Faculty of Natural Sciences, University of Zürich, Zurich, CH-8093, Switzerland

    Ruedi Aebersold

Authors
  1. Henry Lam
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  2. Eric W Deutsch
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  3. James S Eddes
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  4. Jimmy K Eng
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  5. Stephen E Stein
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  6. Ruedi Aebersold
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Contributions

H.L. developed the SpectraST software, performed all library building and validation studies and wrote the manuscript. E.W.D. built the Human Plasma PeptideAtlas from which the data were drawn for this study. J.S.E., J.K.E. and S.E.S. contributed ideas to algorithm development and library format design. R.A. conceived and supervised the project. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Henry Lam.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4, Supplementary Tables 1–4, Supplementary Methods (PDF 286 kb)

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Lam, H., Deutsch, E., Eddes, J. et al. Building consensus spectral libraries for peptide identification in proteomics. Nat Methods 5, 873–875 (2008). https://doi.org/10.1038/nmeth.1254

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