Table 1.

Definition of the main concepts used in the mineMS2 approach

Acronym	Name	Definition
DAG	Directed Acyclic Graph	Graph with directed edges and without cycle (used to represent the MS/MS spectrum; Sect. 3.2)
AFG	Acyclic Flow Graph	Rooted DAG with at least one path from the root to each vertex (structure of the mineMS2 pattern; Sect. 3.4.1)
k-LMDF form	k Left-Most Depth-First canonical form	Specific canonical form of an AFG defined by picking edges in a specific order in Depth-First Search (form actually mined by mineMS2; Sect. 3.4.2)
k-path tree	k-path tree	Data structure to efficiently mine AFGs by storing all potentially frequent paths of size k or less (Sect. 3.4.3 and Fig. 3)