An annotation of a spectrum by a tool is here considered as two pieces of data: a known molecule, considered by the tool as the closest molecule to the spectrum; and a match score (a number between 0 and 1) that represents the similarity between the spectrum and the molecule, as judged by the tool. This yields three match scores (one per tool), denoted by cg, cs, c i , and three pairs of known molecules (obtained by considering all three possibilities of picking two out of the three tools). Each such pair of known molecules is used in turn to obtain a supplementary value, that represents the degree of agreement between the two tools. We use the Tanimoto similarity to assess the matching between pairs of known molecules. The six values obtained so far, namely, the three match scores and the three Tanimoto values, are hereafter called MS2DECIDE's indicators. They are used to compute the knownness score denoted by k (Fig. ). The score in turn is used to rank all the candidate ions of a given extract by order of recommendation for isolation (corresponding to increasing values of knownness score).