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Scoring proteomes with proteotypic peptide probes

Abstract

Technologies for genome-wide analyses typically undergo a transition from a discovery phase to a scoring phase. In the discovery phase, the genomic universe is explored and all pertinent data are noted. In the scoring phase, relevant entities are screened to reveal groups of genes that are associated with specific biological processes or conditions. In this article, we propose that the transition from a discovery to a scoring phase is also essential, feasible and imminent for proteomics.

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Figure 1: Current approaches for scoring proteomes.
Figure 2: Experimental and computational approaches for the identification of proteotypic peptides.
Figure 3: Analysis platform for scoring proteomes.

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References

  1. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003).

    Article  CAS  Google Scholar 

  2. Patterson, S. D. & Aebersold, R. H. Proteomics: the first decade and beyond. Nature Genet. 33, 311–323 (2003).

    Article  CAS  Google Scholar 

  3. Steen, H. & Mann, M. The abc's (and xyz's) of peptide sequencing. Nature Rev. Mol. Cell Biol. 5, 699–711 (2004).

    Article  CAS  Google Scholar 

  4. Andersen, J. S. et al. Directed proteomic analysis of the human nucleolus. Curr. Biol. 12, 1–11 (2002).

    Article  Google Scholar 

  5. Blagoev, B. et al. A proteomics strategy to elucidate functional protein–protein interactions applied to EGF signaling. Nature Biotechnol. 21, 315–318 (2003).

    Article  CAS  Google Scholar 

  6. Bouwmeester, T. et al. A physical and functional map of the human TNF-α/NF-κB signal transduction pathway. Nature Cell Biol. 6, 97–105 (2004).

    Article  CAS  Google Scholar 

  7. Brand, M. et al. Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nature Struct. Mol. Biol. 11, 73–80 (2004).

    Article  CAS  Google Scholar 

  8. Rosenblatt, K. P. et al. Serum proteomics in cancer diagnosis and management. Annu. Rev. Med. 55, 97–112 (2004).

    Article  CAS  Google Scholar 

  9. Liotta, L. A., Ferrari, M. & Petricoin, E. Clinical proteomics: written in blood. Nature 425, 905 (2003).

    Article  CAS  Google Scholar 

  10. Shiio, Y. et al. Quantitative proteomic analysis of Myc oncoprotein function. EMBO J. 21, 5088–5096 (2002).

    Article  CAS  Google Scholar 

  11. Adams, M. D. et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651–1656 (1991).

    Article  CAS  Google Scholar 

  12. Sachidanandam, R. et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933 (2001).

    Article  CAS  Google Scholar 

  13. LaBaer, J. & Ramachandran, N. Protein microarrays as tools for functional proteomics. Curr. Opin. Chem. Biol. 9, 14–19 (2005).

    Article  CAS  Google Scholar 

  14. Desiere, F. et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 6, R9 (2005).

    Article  Google Scholar 

  15. Keller, A., Nesvizhskii, A. I., Kolker, E. & Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383–5392 (2002).

    Article  CAS  Google Scholar 

  16. Craig, R., Cortens, J. P. & Beavis, R. C. Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 3, 1234–1242 (2004).

    Article  CAS  Google Scholar 

  17. Gygi, S. P. et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol. 17, 994–999 (1999).

    Article  CAS  Google Scholar 

  18. Schirle, M., Heurtier, M. A. & Kuster, B. Profiling core proteomes of human cell lines by one-dimensional PAGE and liquid chromatography–tandem mass spectrometry. Mol. Cell. Proteomics 2, 1297–1305 (2003).

    Article  CAS  Google Scholar 

  19. Washburn, M. P., Wolters, D. & Yates, J. R. III . Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnol. 19, 242–247 (2001).

    Article  CAS  Google Scholar 

  20. Gavin, A. C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002).

    Article  CAS  Google Scholar 

  21. Kawashima, S., Ogata, H. & Kanehisa, M. AAindex: amino acid index database. Nucleic Acids Res. 27, 368–369 (1999).

    Article  CAS  Google Scholar 

  22. Pan, S. et al. High-throughput proteome-screening for biomarker detection. Mol. Cell. Proteomics 4, 182–190 (2005).

    Article  CAS  Google Scholar 

  23. Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W. & Gygi, S. P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl Acad. Sci. USA 100, 6940–6945 (2003).

    Article  CAS  Google Scholar 

  24. Lu, Y., Bottari, P., Turecek, F., Aebersold, R. & Gelb, M. H. Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags. Anal. Chem. 76, 4104–4111 (2004).

    Article  CAS  Google Scholar 

  25. Lipton, M. S. et al. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc. Natl Acad. Sci. USA 99, 11049–11054 (2002).

    Article  CAS  Google Scholar 

  26. Li, X. J. et al. A tool to visualize and evaluate data obtained by liquid chromatography–electrospray ionization-mass spectrometry. Anal. Chem. 76, 3856–3860 (2004).

    Article  CAS  Google Scholar 

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Correspondence to Bernhard Kuster or Ruedi Aebersold.

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FURTHER INFORMATION

International Protein Index

PeptideAtlas

PeptideProphet

RefSeq

Seattle Proteome Center: Proteomics Tools

Sigma–Aldrich

Swiss-Prot

Thermo Electron Corporation

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Kuster, B., Schirle, M., Mallick, P. et al. Scoring proteomes with proteotypic peptide probes. Nat Rev Mol Cell Biol 6, 577–583 (2005). https://doi.org/10.1038/nrm1683

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