A Grid Service for Pattern Extraction from Mass Spectrometry Data

The paper presents a Grid Service allowing to detect and extract the longest common sub-spectrum among a set of mass spectrometry spectra data. The service is based on a novel pattern extraction algorithm named LCSS (Longest Common Spectra SubString) that adapts a very popular string matching technique based on Suffix Trees to spectra data. The core of the algorithm and a first performance evaluation of the related Grid Service are discussed.

[1]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[2]  David Ward,et al.  Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data , 2003, Bioinform..

[3]  Y. Yasui,et al.  An Automated Peak Identification/Calibration Procedure for High-Dimensional Protein Measures From Mass Spectrometers , 2003, Journal of biomedicine & biotechnology.

[4]  Dan Gusfield.  Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology , 1997 .

[5]  Mario Cannataro,et al.  Preprocessing of mass spectrometry proteomics data on the grid , 2005, 18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05).

[6]  Mario Cannataro,et al.  Using ontologies for preprocessing and mining spectra data on the Grid , 2007, Future Gener. Comput. Syst..

[7]  Nicholas R. Jennings,et al.  The Semantic Grid: A Future e‐Science Infrastructure , 2003 .

[8]  Mario Cannataro.  Next‐generation Grids: requirements and knowledge‐based services , 2006, Concurr. Comput. Pract. Exp..

[9]  Hugh M. Cartwright,et al.  SpecAlign - processing and alignment of mass spectra datasets , 2005, Bioinform..

[10]  Hai Zhuge,et al.  China's E-Science Knowledge Grid Environment , 2004, IEEE Intell. Syst..

[11]  Mario Cannataro,et al.  KNOWLEDGE GRID An Architecture for Distributed Knowledge Discovery , 2002 .

[12]  Mario Cannataro,et al.  The knowledge grid , 2003, CACM.

[13]  Neal O. Jeffries,et al.  Algorithms for alignment of mass spectrometry proteomic data , 2005, Bioinform..