Figure 3
From: PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data
A diagram showing the concept behind the dynamic programming algorithm. Out of three candidate configurations, the site determining ions i.e. those fragment ions that would be specific for a particular phosphopeptide configuration, were established (b 4 to b 6 and y 6 to y 8, shown in top panel). The theoretical m/z of configuration 1 are shown. The observed m/z that only match (within a specified mass tolerance) to the theoretical site determining ions are then selected (indicated by red and blue arrows). The intensities of these site determining ions are then summed for each phosphopeptide configuration considered. Note that this diagram oversimplifies the problem because it ignores multiple charge states and neutral losses as discussed in text.