mQuest automates the process of signal detection and scoring in MRM data [1]. A number of characteristics of MRM data are used to derive scores that can be used to judge the identity as well as the quality of the MRM signals (Fig. 1). The scoring schema is flexible and aims at extracting a maximum of information from any type of workflow. As an example, mQuest processes data where isotopically labeled reference peptides were spiked into the sample as well as reference free experiments. If references were used, additional scores are derived for the correlation of the reference with the endogenous peptide. mQuest will also derive a score if the fragment ion pattern of a peptide is already known.