Bioinformatic standards for proteomics-oriented mass spectrometry

Current Proteomics

Volumn 3, Issue 2, 2006, Pages 119-128

  Droit, Arnaud ^a   Fillon, Joël ^a   Morissette, Jean ^a   Poirier, Guy G ^a,b  

^a LAVAL UNIVERSITY   (Canada)

^b UNIVERSITÉ LAVAL   (Canada)

Author keywords

Bioinformatics; Open XML; Proteomics

Indexed keywords

EID: 33748448833     PISSN: 15701646     EISSN: None     Source Type: Journal    
DOI: 10.2174/157016406778194617     Document Type: Review

References (29)

1. Anderson, N.L., Matheson, A.D. and Steiner, S. (2000). Proteomics: applications in basic and applied biology. Curr. Opin. Biotechnol. 11: 408-12.
2. Baldwin, M.A. (2004). Protein identification by mass spectrometry: issues to be considered. Mol. Cell Proteomics 3: 1-9.
3. Ball, C.A., Awad, I.A., Demeter, J., Gollub, J., Hebert, J.M., Hernandez-Boussard, T., Jin, H., Matese, J. C., et al. (2005). The Stanford Microarray Database accommodates additional microarray platforms and data formats Nucleic Acids Res. 33: D580-2.
4. Boehm, A.M., Galvin, R.P. and Sickmann, A. (2004). Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing. BMC. Bioinformatics 5: 162.
5. Chalmers, M.J. and Gaskell, S.J. (2000). Advances in mass spectrometry for proteome analysis. Curr. Opin. Biotechnol. 11: 384-90.
6. Craig, R. and Beavis, R. (2004). TANDEM: matching proteins with tandem mass spectra. Bioinformatics 12: 1466-1467.
7. Craig, R., Cortens, J.P. and Beavis, R.C. (2004). Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 3: 1234-42.
8. Desiere, F., Deutsch, E.W., King, N.L., Nesvizhskii, A.I., Mallick, P., Eng, J., Chen, S., Eddes, J., et al. (2006). The PeptideAtlas project. Nucleic Acids Res. 34: D655-8.
9. Guldener, U., Munsterkotter, M., Oesterheld, M., Pagel, P., Ruepp, A., Mewes, H.W. and Stumpflen, V. (2006). MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res. 34: D436-41.
10. Han, D.K., Eng, J., Zhou, H. and Aebersold, R. (2001). Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19: 946-51.
11. Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., et al. (2004). IntAct: an open source molecular interaction database. Nucleic Acids Res. 32: D452-5.
12. Jones, P., Cote, R.G., Martens, L., Quinn, A.F., Taylor, C.F., Derache, W., Hermjakob, H. and Apweiler, R. (2006). PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 34: D659-63.
13. Keller, A., Eng, J., Zhang, N., Li, X.-J. and Aebersold, R. (2005). A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. Epub 2005.
14. Keller, A., Nesvizhskii, A.I., Kolker, E. and Aebersold, R. (2002). Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74: 5383-92.
15. Knudsen, T.B. and Daston, G.P. (2005). MIAME guidelines. Reprod. Toxicol. 19: 263.
16. Li, X.J., Zhang, H., Ranish, J.A. and Aebersold, R. (2003). Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal. Chem. 75: 6648-57.
17. MacCoss, M.J., Wu, C.C. and Yates, J.R., 3rd (2002). Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal. Chem. 74: 5593-9.
18. Nesvizhskii, A.I., Keller, A., Kolker, E. and Aebersold, R. (2003). A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75: 4646-58.
19. Orchard, S., Hermjakob, H. and Apweiler, R. (2003). The proteomics standards initiative. Proteomics 3: 1374-6.
20. Orchard, S., Hermjakob, H., Binz, P.-A., Hoogland, C., Taylor, C., Zhu, W., Julian, R. and Apweiler, R. (2005). Further steps towards data standardization: The Proteomic Standards Initiative HUPO 3rd annual congress, Beijing 25-27th October, 2004 5: 337-9.
21. Orchard, S., Hermjakob, H., Julian, R.K., Jr., Runte, K., Sherman, D., Wojcik, J., Zhu, W. and Apweiler, R. (2004). Common interchange standards for proteomics data: Public availability of tools and schema. Proteomics 4: 490-1.
22. Patterson, S.D. (2003). Proteomics: evolution of the technology. Biotechniques 35: 440-4.
23. Pedrioli, P.G., Eng, J.K., Hubley, R., Vogelzang, M., Deutsch, E.W., Raught, B., Pratt, B., Nilsson, E., et al. (2004). A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 22: 1459-66.
24. Perkins, D.N., Pappin, D.J., Creasy, D.M. and Cottrell, J.S. (1999). Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551-67.
25. Prince, J.T., Carlson, M.W., Wang, R., Lu, P. and Marcotte, E.M. (2004). The need for a public proteomics repository. Nat. Biotechnol. 22: 471-2.
26. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., et al. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13: 2498-504.
27. Taylor, C.F., Paton, N.W., Garwood, K.L., Kirby, P.D., Stead, D.A., Yin, Z., Deutsch, E.W., Selway, L., et al. (2003). A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat. Biotechnol. 21: 247-54.
28. Xenarios, I., Salwinski, L., Duan, X.J., Higney, P., Kim, S.M. and Eisenberg, D. (2002). DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30: 303-5.
29. Zanzoni, A., Montecchi-Palazzi, L., Quondam, M., Ausiello, G., Helmer-Citterich, M. and Cesareni, G. (2002). MINT: a Molecular INTeraction database. FEBS Lett. 513: 135-40.