A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate

Background: A JavaTM application is presented, which compares large numbers (n > 100) of raw FTICR mass spectra from patients and controls. Two peptide profile matrices can be produced simultaneously, one with occurrences of peptide masses in samples and another with the intensity of common peak masses in all the measured samples, using the peak- and background intensities of the raw data. In latter way, more significantly differentially expressed peptides are found between groups than just using the presence or absence in samples of common peak masses. The software application is tested by searching angiogenesis related proteins in glioma by comparing laser capture micro dissected- and enzymatic by trypsin digested tissue sections. Results: By hierarchical clustering of the presence-absence matrix, it appears that proteins, such as hemoglobin alpha and delta subunit, fibrinogen beta and gamma chain precursor, tubulin specific chaperone A, epidermal fatty acid binding protein, neut...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Mark K. Titulaer, Dana A. N. Mustafa, Ivar Siccama, Marco Konijnenburg, Peter C. Burgers, Arno C. Andeweg, Peter A. E. Sillevis Smitt, Johan M. Kros, Theo M. Luider
• Keywords: BMCBI 2008, Common Peak Masses, Peptide, Protein