Fig. 1.

Meta-SPS Procedures. A, Green arrows denote procedures previously described in (1) and red arrows denote procedures described here. The SPS step involves spectral clustering by MSCluster (34), PepNovo+ PRM scoring (35), and assembly of mass spectra into contigs (1). B, An alignment between two PRM spectra is represented as the shift of the second spectrum wrt the first that yields the highest possible score. The displayed scoring function takes the minimum matched/overlapping intensity ratio and multiplies by the number of matching peaks (denoted by MP(A) for alignment A〈S_i,S_j〉 between contig PRM spectra S_i and S_j). Matched and overlapping intensities for each spectrum are displayed as red and blue boxed regions, respectively. Sequences are not known in advance; shown only for illustration purposes. C, Here aligned SPS contigs are assembled into meta-contigs by iteratively merging the highest scoring alignment until remaining alignments have a low score. By merging the highest scoring alignment at every iteration, it is guaranteed that all inconsistent alignments that were removed have a lower score. D, Green arrows denote merged alignments and numbers correspond to the order in which they alignments are merged. Initially, every contig was in its own meta-contig. The 6 meta-contigs were then merged by five alignments, yielding a single meta-contig PRM spectrum and its meta-contig sequence.