A common open representation of mass spectrometry data and its application to proteomics research (original) (raw)
References
- Patterson, S.D. & Aebersold, R.H. Proteomics: the first decade and beyond. Nat. Genet. 33 suppl., 311–323 (2003).
Article CAS PubMed Google Scholar - Spellman, P.T. et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 3, RESEARCH0046 (2002).
- Li, X., Zhang, H., Ranish, J.A. & Aebersold, R. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal. Chem. 75, 6658–6665 (2003).
Article CAS Google Scholar - Han, D.K., Eng, J., Zhou, H. & Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946–951 (2001).
Article CAS PubMed PubMed Central Google Scholar - Purvine, S., Eppel, J.T., Yi, E.C. & Goodlett, D.R. Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 3, 847–850 (2003).
Article CAS PubMed Google Scholar - Eng, J.K., McCormack, A.L. & Yates, J.R. III. 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 (1994).
Article CAS PubMed Google Scholar - Perkins, D.N., Pappin, D.J., Creasy, D.M. & Cottrell, J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567 (1999).
Article CAS PubMed Google Scholar - 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 PubMed Google Scholar - Gygi, S.P. et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994–999 (1999).
Article CAS PubMed Google Scholar - 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 PubMed Google Scholar - Nesvizhskii, A.I., Keller, A., Kolker, E. & Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646–4658 (2003).
Article CAS PubMed Google Scholar - Baldwin, M.A. Protein identification by mass spectrometry: issues to be considered. Mol. Cell. Proteomics 3, 1–9 (2004).
Article CAS PubMed Google Scholar - Prince, J.T., Carlson, M.W., Wang, R., Lu, P. & Marcotte, E.M. The need for a public proteomics repository. Nat. Biotechnol. 22, 471–472 (2004).
Article CAS PubMed Google Scholar - Zhang, N., Aebersold, R. & Schwikowski, B. ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics 2, 1406–1412 (2002).
Article CAS PubMed Google Scholar - Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
Article CAS PubMed PubMed Central Google Scholar
Acknowledgements
This project was funded in part by federal funds from the National Heart, Lung, and Blood Institute, National Institutes of Health, under contract no. N01-HV-28179 and by grant no. 1R33CA93302 from the National Cancer Institute. The Institute for Systems Biology is supported by a generous gift from Merck and Co. We are grateful to SourceForge for hosting the project and Eugene Yi for providing the seven-protein mix data set. We would also like to acknowledge the following for endorsing the mzXML format: Philip C. Andrews, Tom Blackwell, Daniel Burns, Jayson Falkner, Panagiotis Papoulias, Abhik Shah, Peter Ulintz, Al Burlingame, Robert Chalkley, Karl Clauser, Bruno Domon, James Eddes, Robert Moritz, Daniel Figeys, Barry L. Karger, William Hancock, Tomas Rejtar, Peter James, Matthias Mann, Sanford Markey, Matthias Wilm, Ken Williams and Kratos Analytical Limited (a Shimadzu Group Company).
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Authors and Affiliations
- Institute for Systems Biology, 1441 North 34 Street, Seattle, 98103-8904, Washington, USA
Patrick G A Pedrioli, Jimmy K Eng, Robert Hubley, Mathijs Vogelzang, Eric W Deutsch, Brian Raught & Ruedi Aebersold - Insilicos LLC, 4509 Interlake Avenue North, no. 223, Seattle, 98103-6773, Washington, USA
Brian Pratt & Erik Nilsson - Albert Einstein College of Medicine, LMAP Room 405, Ullman Bldg., 1300 Morris Park Avenue, Bronx, 10461, New York, USA
Ruth H Angeletti - EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Rolf Apweiler, Henning Hermjakob, Chris F Taylor & Weimin Zhu - Department of Anesthesiology, Center for Medical Informatics, Yale University School of Medicine, PO Box 208009, New Haven, 06520, Connecticut, USA
Kei Cheung - Boston University School of Medicine, 715 Albany Street, R-806, Boston, 02118-2526, Massachusetts, USA
Catherine E Costello, Sequin Huang & Mark E McComb - Lilly Research Laboratories, One Lilly Corporate Center, Indianapolis, 46285, Indiana, USA
Randall K Julian Jr - Joint Proteomics Laboratory, Ludwig Institute For Cancer Research & The Walter and Eliza Hall Institute of Medical Research, Royal Melbourne Hospital, Parkville, Victoria, 3050, Australia
Eugene Kapp & Richard Simpson - School of Biological Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
Stephen G Oliver - The University of Michigan Medical School, 1150 W. Medical Center Drive, Ann Arbor, 48109-0656, Michigan, USA
Gilbert Omenn - Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
Norman W Paton - Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, PO Box 999, Richland, 99352, Washington, USA
Richard Smith
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Pedrioli, P., Eng, J., Hubley, R. et al. A common open representation of mass spectrometry data and its application to proteomics research.Nat Biotechnol 22, 1459–1466 (2004). https://doi.org/10.1038/nbt1031
- Published: 04 November 2004
- Issue Date: 01 November 2004
- DOI: https://doi.org/10.1038/nbt1031