Computational prediction of proteotypic peptides for quantitative proteomics

Nature Biotechnology

Volumn 25, Issue 1, 2007, Pages 125-131

  Mallick, Parag ^a,b,c   Schirle, Markus ^d   Chen, Sharon S ^c   Flory, Mark R ^a   Lee, Hookeun ^a,e   Martin, Daniel ^a   Ranish, Jeffrey ^a   Raught, Brian ^a   Schmitt, Robert ^d   Werner, Thilo ^d   Kuster, Bernhard ^d   Aebersold, Ruedi ^a,e  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b CEDARS SINAI MEDICAL CENTER   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d GLAXOSMITHKLINE   (United Kingdom)

^e UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATOGRAPHIC ANALYSIS; COMPUTATIONAL METHODS; MASS SPECTROMETRY; PROTEINS;

CODING SEQUENCES; PROTEOTYPIC PEPTIDES;

AMINO ACIDS;

FUNGAL PROTEIN; PEPTIDE;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CHROMATOGRAPHY; FRAGMENTATION REACTION; GENOMICS; IONIZATION; MASS SPECTROMETRY; ORGANISM; PEPTIDE ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS; VALIDATION PROCESS;

ALGORITHMS; GENE EXPRESSION PROFILING; MASS SPECTROMETRY; PEPTIDE MAPPING; PEPTIDES; PROTEOME; SEQUENCE ANALYSIS, PROTEIN;

EID: 33846133955     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt1275     Document Type: Article

References (30)

1. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198-207 (2003).
2. 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).
3. Ong, S.E., Foster, L.J. & Mann, M. Mass spectrometric-based approaches in quantitative proteomics. Methods 29, 124-130 (2003).
4. Wright, M.E. et al. Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells. Genome Biol. 5, R4 (2003).
5. Durr, E. et al. Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat. Biotechnol 22, 985-992 (2004).
6. Ranish, J.A. et al. The study of macromolecular complexes by quantitative proteomics. Nat.Genet. 33, 349-355 (2003).
7. Blagoev, B. et al. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 21, 315-318 (2003).
8. Andersen, J.S. et al. Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426, 570-574 (2003).
9. Marko-Varga, G. et al. Discovery of biomarker candidates within disease by protein profiling: principles and concepts. J.Proteome Res. 4, 1200-1212 (2005).
10. Old, W.M. et al. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol.Cell Proteomics 4, 1487-1502 (2005).
11. Flory, M.R., Griffin, T.J., Martin, D. & Aebersold, R. Advances in quantitative proteomics using stable isotope tags. Trends Biotechnol. 20, S23-29 (2002).
12. Kirkpatrick, D.S., Gerber, S.A. & Gygi, S.P. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 35, 265-273 (2005).
13. Kuster, B., Schirle, M., Mallick, P. & Aebersold, R. Innovation: Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol. (2005).
14. Keller, A. et al. Experimental protein mixture for validating tandem mass spectral analysis. Omics 6, 207-212 (2002).
15. Desiere, F. et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 6, R9 (2005).
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).
17. Marzolf, B. et al. SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7, 286 (2006).
18. Jones, P. et al. PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 34, D659-663 (2006).
19. Kawashima, S. & Kanehisa, M. AAindex: amino acid index database. Nucleic Acids Res. 28, 374 (2000).
20. De Strooper, B. et al. Deficiency of presenilin-1 inhibits the normal cleavage of amyloid precursor protein. Nature 391, 387-390 (1998).
21. Xing, Y. & Lee, C. Alternative splicing and RNA selection pressure-evolutionary consequences for eukaryotic genomes. Nat. Rev. Genet. 7, 499-509 (2006).
22. Eisenberg, D., Marcotte, E.M., Xenarios, I. & Yeates, T.O. Protein function in the postgenomic era. Nature 405, 823-826 (2000).
23. Rotzschke, O. et al. Exact prediction of a natural T cell epitope. Eur. J. Immunol. 21, 2891-2894 (1991).
24. Schwartz, D. & Gygi, S.P. An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat. Biotechnol. 23, 1391-1398 (2005).
25. Marques, J.T. et al. A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells. Nat. Biotechnol. 24, 559-565 (2006).
26. Schirle, M. et al. Proceedings of the 52nd ASMS Conference on Mass Spectrometry and Allied Topics, Nashville, Tennessee, May 23-27, 2004 (American Society for Mass Spectrometry, Santa Fe, NM 2004).
27. Tabb, D.L., Huang, Y., Wysocki, V.H. & Yates III, J.R. Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 76, 1243-1248 (2004).
28. Breci, L.A., Tabb, D.L., Yates III, J.R. & Wysocki, V.H. Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra. Anal. Chem. 75, 1963-1971 (2003).
29. Peng, J., Elias, J.E., Thoreen, C.C., Licklider, L.J. & Gygi, S.P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2, 43-50 (2003).
30. Gavin, A.C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636 (2006).