Fig. 1

Spectrum graph generation. Illustration of spectrum graph generation using an example deconvoluted MS/MS spectrum of the protein LNRVSG. a In the spectrum, the mass of the N-terminal fragment LNR is missing, and there is a noise mass peak (bold) between the fragment masses of LNR and LNRV. b In the spectrum graph, each node corresponds to a peak in the spectrum. Two nodes are connected by a directed edge if the difference between their corresponding masses matches the residue mass of one amino acid; the edge is labeled with the amino acid. The sequence tag NVRS extracted from the spectrum is incorrect because of the noise mass peak and its node v₂. c In the spectrum graph, each node corresponds to a peak in the spectrum. Two nodes are connected by a directed edge if the difference between their corresponding masses is less than 400 Da and matches the residue mass of one or several amino acids; the edge is labeled by the mass difference. The mass sequence of a path is a blocked pattern of the spectrum. For example, the bold path v₀,v₁,v₃,v₄ corresponds to a blocked pattern 114.04, 255.17, 87.03, which matches a correct sequence tag NRVS because 255.07 is the sum of the mass 156.10 of R and the mass 99.07 of V