Fig. 2
Alignment of peptide HINATESVR on a simulated spectrum carrying two modifications and a neutral loss. a The simulated spectrum Se is the same as the one presented in Fig. 1a, except that the mass of the peptide has been increased by a neutral loss of 301.99 Da. As a result, complementary peaks in Sec –represented below the x-axis – are shifted by 301.99 Da compared to the complementary peaks displayed in Fig. 1c; For example, the peak 690.34 is connected to its complementary peak 668.16 (366.17 + 301.99) by a dotted line b The score matrix computed by SpecGlobX to align the peptide HINATESVR with Sec by dynamic programming; Masses have been rounded for simplification of the graphical representation; c After the traceback step, Sec is interpreted as [301.99]HI[N][0.98]ATE[S][27.99]VR and after the post-processing step, Se is interpreted as HI[N][0.98]ATE[S][27.99]VR_301.99, identifying peptide HINATESVR with two modifications (a deamidation on “N” and a formylation on “S”) and a non-aligned mass of 301.99 Da (neutral loss), which is the correct identification