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  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.