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.
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References
Aebersold, R., Mann, M.: Mass spectrometry-based proteomics. Nature 422, 198–207 (2003)
Applied Biosystem, http://www.cmpharm.ucsf.edu/nomi/nnpredict.htm
Branden, C.-I., Tooze, J.: Introduction to Protein Structure, 2nd edn. Garland Publishing, Inc., New York (1998)
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)
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)
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)
Chen, L., Huang, Z., Ramakrishnan, R.: Cost-Based Labeling of Groups of Mass Spectra. In: SIGMOD 2004 (2004)
DuBois, P.: MySQL. 0-7357-1212-3, 2nd edn., Sams Developer’s Library (August 2004)
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)
Thermo electrono corporation. Sample manager, http://www.thermo.com/com/cda/home
Research Collaborator for Structural Bioinformatics. Protein data bank (2004), http://www.rcsb.org/pdb/
Glish, G.L., Vachet, R.W.: The basic of mass spectrometry in the twenty-first century. Nature Reviews 2, 140–150 (February 2003)
IBM. Proteomiq and ibm life sciences framework, http://www.proteomesystems.com/uploads/Proteomepartnerbrief.pdf
Lacroix, Z.: Terence: Bioinformatics: Managing Scientific Data. Learn how (2001)
Bujnicki, J.M.: Practical Bioinformatics, 1st edn., pp. 933–1891. Springer, Berlin (2004)
University of Waikato. Weka data mining tool, http://www.cs.waikato.ac.nz/ml/weka/
Proteomics Standard Initiative PSI. Psi, http://psidev.sourceforge.net/ms/
Nonlinear Bioinformatics Solutions. Non linear phoretyx, http://www.nonlinear.com/
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Cannataro, M., Veltri, P. (2006). SpecDB: A Database for Storing and Managing Mass Spectrometry Proteomics Data. In: Bloch, I., Petrosino, A., Tettamanzi, A.G.B. (eds) Fuzzy Logic and Applications. WILF 2005. Lecture Notes in Computer Science(), vol 3849. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11676935_29
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DOI: https://doi.org/10.1007/11676935_29
Publisher Name: Springer, Berlin, Heidelberg
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