Advertisement

SpecDB: A Database for Storing and Managing Mass Spectrometry Proteomics Data

  • Mario Cannataro
  • Pierangelo Veltri
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3849)

Abstract

Data produced by mass spectrometer (MS) have been using in proteomics experiments to identify proteins or patterns in clinical samples that may be responsible of human diseases. Nevertheless, MS data are affected by errors and different preprocessing techniques have to be applied to manipulate and gathering information from data. Moreover, MS samples contain a huge amount of data requiring an efficient organization both to reduce access time to data, and to allow efficient knowledge extraction. We present the design and the implementation of a database for managing MS data, integrated in a software system for the loading, preprocessing, storing and managing of mass spectra data.

Keywords

Spectrum Data Mass Spectrometry Data Preprocessing Technique Data Mining Tool Proteomics Experiment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Aebersold, R., Mann, M.: Mass spectrometry-based proteomics. Nature 422, 198–207 (2003)CrossRefGoogle Scholar
  2. 2.
  3. 3.
    Branden, C.-I., Tooze, J.: Introduction to Protein Structure, 2nd edn. Garland Publishing, Inc., New York (1998)Google Scholar
  4. 4.
    Cannataro, M., Cuda, G., Gaspari, M., Guzzi, P.H., Mazza, T., Tagliaferri, P., Tradigo, G., Veltri, P.: Mass Spectrometry Data Analysis for Early Detection of Inherited Breast Cancer. In: WIRN 2004 (2004)Google Scholar
  5. 5.
    Cannataro, M., Guzzi, P., Mazza, T., Oliverio, A., Tradigo, G., Veltri, P.: An Architecture for Managing Mass Spectrometry Data for a Distributed Proteomics Laboratory. In: Heterogeneous and Distributed Information Retrieval, 28th conf. on Research and Development Information Retrieval, SIGIR (2005)Google Scholar
  6. 6.
    Cannataro, M., Guzzi, P., Mazza, T., Tradigo, G., Veltri, P.: On the Preprocessing of Mass Spectrometry Proteomics Data. In: Apolloni, B., Marinaro, M., Nicosia, G., Tagliaferri, R. (eds.) WIRN 2005 and NAIS 2005. LNCS, vol. 3931, pp. 127–131. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  7. 7.
    Chen, L., Huang, Z., Ramakrishnan, R.: Cost-Based Labeling of Groups of Mass Spectra. In: SIGMOD 2004 (2004)Google Scholar
  8. 8.
    DuBois, P.: MySQL. 0-7357-1212-3, 2nd edn., Sams Developer’s Library (August 2004)Google Scholar
  9. 9.
    Petricoin, E.F., Ardekani, A.M., Hitt, B.A., Levine, P.J., Fusaro, V.A., Steinberg, S.M., Mills, G.B., Simone, C., Fishman, D.A., Kohn, E.C., Liotta, L.A.: Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359, 572–577 (2002)CrossRefGoogle Scholar
  10. 10.
    Thermo electrono corporation. Sample manager, http://www.thermo.com/com/cda/home
  11. 11.
    Research Collaborator for Structural Bioinformatics. Protein data bank (2004), http://www.rcsb.org/pdb/
  12. 12.
    Glish, G.L., Vachet, R.W.: The basic of mass spectrometry in the twenty-first century. Nature Reviews 2, 140–150 (February 2003)CrossRefGoogle Scholar
  13. 13.
    IBM. Proteomiq and ibm life sciences framework, http://www.proteomesystems.com/uploads/Proteomepartnerbrief.pdf
  14. 14.
    Lacroix, Z.: Terence: Bioinformatics: Managing Scientific Data. Learn how (2001)Google Scholar
  15. 15.
    Bujnicki, J.M.: Practical Bioinformatics, 1st edn., pp. 933–1891. Springer, Berlin (2004)Google Scholar
  16. 16.
    University of Waikato. Weka data mining tool, http://www.cs.waikato.ac.nz/ml/weka/
  17. 17.
    Proteomics Standard Initiative PSI. Psi, http://psidev.sourceforge.net/ms/
  18. 18.
    Nonlinear Bioinformatics Solutions. Non linear phoretyx, http://www.nonlinear.com/

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Mario Cannataro
    • 1
  • Pierangelo Veltri
    • 1
  1. 1.University Magna Græcia of Catanzaro Viale EuropaCatanzaroItaly

Personalised recommendations