Fig. 1
Alignment of peptide HINATESVR on a simulated spectrum carrying two modifications. a On the left, the theoretical spectrum St of peptide HINATESVR is modeled only by its b-ion peaks, and below, the simulated spectrum Se is displayed with dummy intensities to mimic an experimental spectrum. However, note that intensities have no effect during the alignment with SpecGlobX. Se contains two modifications compared to St and only two b-ion peaks (represented in blue) are present in the spectrum. On the right, complementary peaks – below the x-axis—are added to Se, to generate the spectrum Sec; For example, one ‘original peak’ and its complementary peak are connected by a dotted line for better readability. b The score matrix was computed by SpecGlobX to align both spectra by dynamic programming. Masses have been rounded for simplification of the graphical representation; masses corresponding to complementary peaks are in green; transitions are numbered on the last row. The green (when SpecGlobX found an alignment) or orange arrows -when SpecGlobX found a realignment (with a mass shift)- delineates the path followed by the traceback step interpreting Se. c The interpretation of Se as HI[N][0.98]ATE[S][27.99]VR in terms of peptide sequence and mass shifts suggests a deamidation on “N” (mass increment of 0.98 Da) and a formylation on “S” (mass increment of 27.99 Da); non-aligned amino acids and mass shift values are in brackets. Original b-ion peaks are in blue in the interpreted Se and y-ions are in red