Table 1.

Notations and Definitions

Notation	Definition
	m proteins within a non-trivial connected component of the protein configuration graph
	protein configuration: indicator variables of proteins' presences
	all n peptides from m proteins being considered
	indicator variables of peptide j belonging to protein i if peptide j is a peptide from protein i, Zij = 1; otherwise Zij = 0
	peptide configuration: indicator variables of peptides' presences if peptide j is present, yj = 1; otherwise yj = 0
	assigned scores of peptides if peptide j is not identified, sj = 0
	probabilities of peptides being correctly identified also the estimated probabilities of peptides' presences
	likelihood ratio between peptides's presences and absences
	prior probabilities of peptides to be identified from proteins if Zij = 1, dij = the detectability of peptide j from protein i; otherwise, dij = 0