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Figure 9 | BMC Research Notes

Figure 9

From: Label-free peptide profiling of Orbitrap™ full mass spectra

Figure 9

A practical example of Peptide profiling by Peptrix on a Orbitrap™ data set of in total 40 micro-dissected tissue samples, 10 spectra of glioma blood vessels (GV), 10 spectra of tissue surrounding the glioma vessels (GT), 10 spectra of normal endothelial vessels (EndV), and 10 spectra of endothelial tissue surrounding the normal vessels (EndT). A graphical representation of the results of the Wilcoxon-Mann-Whitney tests on peak intensities of masses when comparing the four groups, GV, GT, EndV, and EndT. The peptide profile matrix contains in total 26025 peak masses and 40 samples. The heights of the bars represent the total number of peak masses within a specific p-value interval, whereas the black bar indicates the number of peak masses that were predominantly present in the first mentioned group, and the white bar indicates the number of peaks masses predominantly present in the second mentioned group. The number of peaks masses found for each p-value after 10 times randomization is represented by the red line, which can be viewed as a baseline. Any low p-value bar that exceeds the height of the baseline indicates statistically significant differences in that particular comparison, which means a large number of masses with different peak intensities between both groups. The comparison of GT with GV (A) shows a faint but significant skewing to the left of the p-value range indicates that some peptide masses significant differ in peak intensities between both groups. The same pattern can be seen in (B) but more skewed for the comparison of GT with EndT, which means more significant differences between both groups. Also significant differences can be observed in the comparison of EndV with GV in (C). The comparison of EndV with EndT (D) does not show significant differences.

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