A common open representation of mass spectrometry data and its application to proteomics research (original) (raw)

References

  1. Patterson, S.D. & Aebersold, R.H. Proteomics: the first decade and beyond. Nat. Genet. 33 suppl., 311–323 (2003).
    Article CAS PubMed Google Scholar
  2. Spellman, P.T. et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 3, RESEARCH0046 (2002).
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. Baldwin, M.A. Protein identification by mass spectrometry: issues to be considered. Mol. Cell. Proteomics 3, 1–9 (2004).
    Article CAS PubMed Google Scholar
  13. 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
  14. 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
  15. 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

Download references

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).

Author information

Authors and Affiliations

  1. 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
  2. Insilicos LLC, 4509 Interlake Avenue North, no. 223, Seattle, 98103-6773, Washington, USA
    Brian Pratt & Erik Nilsson
  3. Albert Einstein College of Medicine, LMAP Room 405, Ullman Bldg., 1300 Morris Park Avenue, Bronx, 10461, New York, USA
    Ruth H Angeletti
  4. EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Rolf Apweiler, Henning Hermjakob, Chris F Taylor & Weimin Zhu
  5. Department of Anesthesiology, Center for Medical Informatics, Yale University School of Medicine, PO Box 208009, New Haven, 06520, Connecticut, USA
    Kei Cheung
  6. Boston University School of Medicine, 715 Albany Street, R-806, Boston, 02118-2526, Massachusetts, USA
    Catherine E Costello, Sequin Huang & Mark E McComb
  7. Lilly Research Laboratories, One Lilly Corporate Center, Indianapolis, 46285, Indiana, USA
    Randall K Julian Jr
  8. 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
  9. School of Biological Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
    Stephen G Oliver
  10. The University of Michigan Medical School, 1150 W. Medical Center Drive, Ann Arbor, 48109-0656, Michigan, USA
    Gilbert Omenn
  11. Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    Norman W Paton
  12. Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, PO Box 999, Richland, 99352, Washington, USA
    Richard Smith

Authors

  1. Patrick G A Pedrioli
    You can also search for this author inPubMed Google Scholar
  2. Jimmy K Eng
    You can also search for this author inPubMed Google Scholar
  3. Robert Hubley
    You can also search for this author inPubMed Google Scholar
  4. Mathijs Vogelzang
    You can also search for this author inPubMed Google Scholar
  5. Eric W Deutsch
    You can also search for this author inPubMed Google Scholar
  6. Brian Raught
    You can also search for this author inPubMed Google Scholar
  7. Brian Pratt
    You can also search for this author inPubMed Google Scholar
  8. Erik Nilsson
    You can also search for this author inPubMed Google Scholar
  9. Ruth H Angeletti
    You can also search for this author inPubMed Google Scholar
  10. Rolf Apweiler
    You can also search for this author inPubMed Google Scholar
  11. Kei Cheung
    You can also search for this author inPubMed Google Scholar
  12. Catherine E Costello
    You can also search for this author inPubMed Google Scholar
  13. Henning Hermjakob
    You can also search for this author inPubMed Google Scholar
  14. Sequin Huang
    You can also search for this author inPubMed Google Scholar
  15. Randall K Julian Jr
    You can also search for this author inPubMed Google Scholar
  16. Eugene Kapp
    You can also search for this author inPubMed Google Scholar
  17. Mark E McComb
    You can also search for this author inPubMed Google Scholar
  18. Stephen G Oliver
    You can also search for this author inPubMed Google Scholar
  19. Gilbert Omenn
    You can also search for this author inPubMed Google Scholar
  20. Norman W Paton
    You can also search for this author inPubMed Google Scholar
  21. Richard Simpson
    You can also search for this author inPubMed Google Scholar
  22. Richard Smith
    You can also search for this author inPubMed Google Scholar
  23. Chris F Taylor
    You can also search for this author inPubMed Google Scholar
  24. Weimin Zhu
    You can also search for this author inPubMed Google Scholar
  25. Ruedi Aebersold
    You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence toRuedi Aebersold.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

About this article

Cite this article

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

Download citation