title: A computational platform for MALDI-TOF mass spectrometry data: application to serum and plasma samples.
abstract: BACKGROUND
  Mass spectrometry (MS) is becoming the gold standard for biomarker discovery. Several MS-based bioinformatics methods have been proposed for this application, but the divergence of the findings by different research groups on the same MS data suggests that the definition of a reliable method has not been achieved yet. In this work, we propose an integrated software platform, MASCAP, intended for comparative biomarker detection from MALDI-TOF MS data.
  
  
  RESULTS
  MASCAP integrates denoising and feature extraction algorithms, which have already shown to provide consistent peaks across mass spectra; furthermore, it relies on statistical analysis and graphical tools to compare the results between groups. The effectiveness in mass spectrum processing is demonstrated using MALDI-TOF data, as well as SELDI-TOF data. The usefulness in detecting potential protein biomarkers is shown comparing MALDI-TOF mass spectra collected from serum and plasma samples belonging to the same clinical population.
  
  
  CONCLUSIONS
  The analysis approach implemented in MASCAP may simplify biomarker detection, by assisting the recognition of proteomic expression signatures of the disease. A MATLAB implementation of the software and the data used for its validation are available at http://www.unich.it/proteomica/bioinf.
authors.affiliation: Istituto Tecnologie Avanzate Biomediche (ITAB), Fondazione G. d'Annunzio, Chieti, Italy.
authors.forename: Dante
authors.initials: D
authors.lastname: Mantini
authors.forename: Francesca
authors.initials: F
authors.lastname: Petrucci
authors.forename: Damiana
authors.initials: D
authors.lastname: Pieragostino
authors.forename: Piero
authors.initials: P
authors.lastname: Del Boccio
authors.forename: Paolo
authors.initials: P
authors.lastname: Sacchetta
authors.forename: Giovanni
authors.initials: G
authors.lastname: Candiano
authors.forename: Gian Marco
authors.initials: GM
authors.lastname: Ghiggeri
authors.forename: Alessandra
authors.initials: A
authors.lastname: Lugaresi
authors.forename: Giorgio
authors.initials: G
authors.lastname: Federici
authors.forename: Carmine
authors.initials: C
authors.lastname: Di Ilio
authors.forename: Andrea
authors.initials: A
authors.lastname: Urbani
mesh_terms: D000465:Algorithms; D001327:Autoimmune Diseases / Q000097:blood / Q000378:metabolism; D015415:Biomarkers / Q000032:analysis / Q000097:blood / Q000378:metabolism; D001774:Blood Chemical Analysis / Q000379:methods / Q000706:statistics & numerical data*; D001798:Blood Proteins / Q000032:analysis / Q000378:metabolism; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D006801:Humans; D010949:Plasma / Q000737:chemistry* / Q000378:metabolism; D044967:Serum / Q000737:chemistry* / Q000378:metabolism; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
chemical_list: D015415:Biomarkers; D001798:Blood Proteins