Abstract
PhospoPep version 2.0 is a project to support systems biology signaling research by providing interactive interrogation of MS-derived phosphorylation data from four different organisms. Currently the database hosts phosphorylation data from the fly (Drosophila melanogaster), human (Homo sapiens), worm (Caenorhabditis elegans), and yeast (Saccharomyces cerevisiae). The following will give an overview of the content and usage of the PhosphoPep database.
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References
Bodenmiller B., Campbell D., Gerrits B., Lam H., Jovanovic M., Picotti P., Schlapbach R., Aebersold R. (2008) PhosphoPep – a database of protein phosphorylation sites in model organisms. Nat. Biotechnol. 26, 1339–1340.
Kanehisa M., Goto S., Hattori M., Aoki-Kinoshita K. F., Itoh M., Kawashima S., Katayama T., Araki M., Hirakawa M. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354–D357.
Shannon P., Markiel A., Ozier O., Baliga N. S., Wang J. T., Ramage D., Amin N., Schwikowski B., Ideker T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504.
Lange V., Picotti P., Domon B., Aebersold R. (2008) Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 4, 222.
Picotti P., Aebersold R., Domon B. (2007) The implications of proteolytic background for shotgun proteomics. Mol. Cell. Proteomics 6, 1589–1598.
Picotti P., Lam H., Campbell D., Deutsch E. W., Mirzaei H., Ranish J., Domon B., Aebersold R. (2008) A database of mass spectrometric assays for the yeast proteome. Nat. Methods 5, 913–914.
Lam H., Deutsch E. W., Eddes J. S., Eng J. K., King N., Stein S. E., Aebersold R. (2007) Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7, 655–667.
Lam H., Deutsch E. W., Eddes J. S., Eng J. K., Stein S. E., Aebersold R. (2008) Building consensus spectral libraries for peptide identification in proteomics. Nat. Methods 5, 873–875.
Bodenmiller B., Malmstrom J., Gerrits B., Campbell D., Lam H., Schmidt A., Rinner O., Mueller L. N., Shannon P. T., Pedrioli P. G., Panse C., Lee H. K., Schlapbach R., Aebersold R. (2007) PhosphoPep – a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Mol. Syst. Biol. 3, 139.
Bodenmiller B., Mueller L. N., Mueller M., Domon B., Aebersold R. (2007) Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat. Methods 4, 231–237.
von Mering C., Jensen L. J., Kuhn M., Chaffron S., Doerks T., Kruger B., Snel B., Bork P. (2007) STRING 7 – recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35, D358–D362.
Chen F., Mackey A. J., Stoeckert C. J., Jr., Roos D. S. (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res. 34, D363–D368.
Desiere F., Deutsch E. W., Nesvizhskii A. I., Mallick P., King N. L., Eng J. K., Aderem A., Boyle R., Brunner E., Donohoe S., Fausto N., Hafen E., Hood L., Katze M. G., Kennedy K. A., Kregenow F., Lee H., Lin B., Martin D., Ranish J. A., Rawlings D. J., Samelson L. E., Shiio Y., Watts J. D., Wollscheid B., Wright M. E., Yan W., Yang L., Yi E. C., Zhang H., Aebersold R. (2005) Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 6, R9.
Obenauer J. C., Cantley L. C., Yaffe M. B. (2003) Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res. 31, 3635–3641.
Keller A., Eng J., Zhang N., Li X. J., Aebersold R. (2005) A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 1, 2005.0017.
Keller A., Nesvizhskii A. I., Kolker E., Aebersold R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383–5392.
Eng J. K., McCormack A. L., Yates J. R. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom. 5, 976–989.
Beausoleil S. A., Villen J., Gerber S. A., Rush J., Gygi S. P. (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 24, 1285–1292.
Elias J. E., Gygi S. P. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207–214.
Reiter L., Claassen M., Schrimpf S. P., Buhmann J. M., Hengartner M. O., Aebersold R. (2009) Protein identification false discovery rates for very large proteomics datasets generated by tandem mass spectrometry. Mol. Cell. Proteomics 8, 2405–2417.
Olsen J. V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635–648.
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Bodenmiller, B., Aebersold, R. (2011). Phosphoproteome Resource for Systems Biology Research. In: Wu, C., Chen, C. (eds) Bioinformatics for Comparative Proteomics. Methods in Molecular Biology, vol 694. Humana Press. https://doi.org/10.1007/978-1-60761-977-2_19
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DOI: https://doi.org/10.1007/978-1-60761-977-2_19
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