Figure 1.
Degradation of a beta-2-microglobulin fragment observed via Mass Spectrometry.
Mass spectra generated during the degradation of a beta-2-microglobulin fragment by a mixture of urine proteins after 7 (upper) and 24 (lower) hours of incubation. Intensity is given in percent of maximal peak intensity. In the lower spectrum all fragments were annotated that could be verified by MS/MS identifications. Details of data acquisition and sample preprocessing are given in the results section. All raw spectra of this time series are shown in the Supporting Information (Figure S2).
Figure 2.
Complex proteolytic reaction visualized as graph.
Example protease system acting on a single peptide (SANSNPAMAPRERKAGCKNFF) and the resulting degradation products. The shown reactions are all artificial.
Figure 3.
Representation of the basic degradation graph structures.
(a) Exoprotease reaction, (b) Endoprotease reaction. See Figure 2 for an example containing both reaction types.
Figure 4.
Degradation graph of the degradation of fibrinopeptide A (FPA) as reported in [16].
Figure 5.
Effect of the different signal variability settings on the simulated signal intensities.
Shown are the extracted signal intensities for two peptides (a) DSGEGDFLAEGGGVR (left) and (b) EGDFLAEGGGVR (right) of the fibrinopeptide A system shown in Figure 4 with increasing signal variability values.
Figure 6.
Effect of the signal variability on the score .
Effect of the variability of the signal with respect to the intensity on the score computed by our method. Data was generated based on the fibrinopeptide A system shown in Figure 4.
Figure 7.
Effect of the signal variability on the the relative error of the estimated parameters.
The quality is given in terms of the relative deviation of the estimated from the real parameter . Data was generated based on the fibrinopeptide A system shown in Figure 4. The reaction parameters are numbered in the order of degradation (e.g., FPA
FPA-1
) shown in Figure 4.
Figure 8.
Degradation of endothelin-1 by multiple artificial endo- and exoproteases. (a) The mapping of indices to sequences. (b) The degradation graph. package.
Figure 9.
Degradation of angiotensin by multiple artificial endo- and exoproteases. (a) The mapping of indices to sequences. (b) The degradation graph.
Figure 10.
Degradation of somatostatin-28 by multiple artificial endo- and exoproteases. (a) The mapping of indices to sequences. (b) The degradation graph. package.
Table 1.
Parameter estimation error for the endothelin 1 system.
Table 2.
Parameter estimation error for the angiotensin system.
Table 3.
Parameter estimation error for the somatostatin 28 system.
Figure 11.
Intensity course for different fragments of the somatostatin-28 test system.
Shown is the intensity course of two peptide fragments compared with the predicted model intensities for the best somatostatin-28 degradation graph.
Figure 12.
Initial degradation graph for the beta-2-microglobulin fragment estimated from real data.
Shown is the degradation graph for the beta-2-microglobulin fragment which was initially estimated from a MALDI time series. (a) The mapping of indices to sequences. (b) The initial degradation graph. The dashed edges and nodes represent those reactions, that were not validated manually.
Figure 13.
Intensity course for different fragments of the manually validated degradation graph.
Intensity course for different fragments of the manually validated degradation graph. See text for more details.