A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation

Background: A Java™ 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, neutrophil gelatinase-associated lipocalin prec

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation-2

1154.7128 Da, represented by the grey lines, is as expected not present in Glioma vessels.<p><b>Copyright information:</b></p><p>Taken from "A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation"</p><p>http://www.biomedcentral.com/1471-2105/9/133</p><p>BMC Bioinformatics 2008;9():133-133.</p><p>Published online 1 Mar 2008</p><p>PMCID:PMC2323386.</p><p></p

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation-0

Ioma vessels with codes TH1 to TH10, 10 spectra of normal vessels with codes S1 to S10, and 10 spectra of tissue surrounding the normal vessels with codes TS1 to TS10 are included. Two "normal vessels" samples, S5 and TS5, were excluded because they could not be calibrated. The highlighted box in Figure 3 represents the hierarchical clustering order 490 with mass 1037.5355 Da to 789 with mass 1665.7891 Da as presented (see Additional file ).<p><b>Copyright information:</b></p><p>Taken from "A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation"</p><p>http://www.biomedcentral.com/1471-2105/9/133</p><p>BMC Bioinformatics 2008;9():133-133.</p><p>Published online 1 Mar 2008</p><p>PMCID:PMC2323386.</p><p></p

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation-4

<p><b>Copyright information:</b></p><p>Taken from "A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation"</p><p>http://www.biomedcentral.com/1471-2105/9/133</p><p>BMC Bioinformatics 2008;9():133-133.</p><p>Published online 1 Mar 2008</p><p>PMCID:PMC2323386.</p><p></p

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation-1

Phodiesterase at 1508.8739 Da represented by the grey lines is as expected not present in glioma vessels).<p><b>Copyright information:</b></p><p>Taken from "A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation"</p><p>http://www.biomedcentral.com/1471-2105/9/133</p><p>BMC Bioinformatics 2008;9():133-133.</p><p>Published online 1 Mar 2008</p><p>PMCID:PMC2323386.</p><p></p