Figure 2

An example of different partially occupied phospho sites in one sequence. This peptide occurs in the sequence of DGLSP/B3A0P1/Lotgi1|162078 (Aspartate-, glycine-, lysine- and serine-rich protein, aa324-335). A, peptide variant with phosphotyrosine identified by an uninterrupted series of y-ions for the rest of the sequence and the very intense diagnostic pY immonium ion at m/z 216.042. Expert annotations [29] were omitted, except for the major peak at m/z 120.0809 (phenylalanine immonium ion), to keep the spectrum clear. The doubly charged peptide ion was measured with a mass error of −0.014 ppm. PEP and phosphphorylation site localization probability were calculated by MaxQuant to be 8.96e-93 and 0.999. B, this time S₄ was determined as the phosphorylation site in an uninterrupted series of y-ions from y1 to y11. The mass error was −0.490 ppm, PEP was 1.16e-54 and the localization probability was 1.00. Major peaks at m/z 120.0809 and 136.0756 were annotated by the MaxQuant Expert system as the phenylalanine immonium ion and the a1-ion. A major peak at m/z 192.1016 was not annotated. Expert annotations of most of the minor peaks are omitted for clarity. C, a third phosphorylation site at S₈ was detected with a localization probability of 1.00 in still another variant of this peptide measured with a mass error of 0.531 ppm and with a PEP of 3.28e-164. Again, most expert annotations are omitted. *, ions showing a loss of H₃PO₄ from phosphoserine. Y-ions are shown in red, b-ions are shown in blue, b-or y-ions with a loss of ammonia or water are in orange, the a₂ ion is shown in light blue, black identifies ions without annotation unless the annotation is shown on top of the peak.