Selected reaction monitoring (SRM) MS is a highly selective and , sensitive technique to quantify protein abundances in complex biological samples. SRM analyses are well supported by state-of-the-art software for both interactive data analysis (e.g., Skyline) and statistical validation of acquired data (e.g., mProphet). However, at present, there is no validated approach to automate the estimation of absolute protein quantities, and manual evaluation, which is widely used, is inherently biased and error-prone. Here, we present Ariadne, a Matlab® software solution supporting automated absolute and relative quantification of SRM data. Ariadne quantifies the targeted peptides listed in the transition lists. If an mProphet output is available for the current experiment, targets can also be filtered according to its statistical validation. Signal processing and statistical learning approaches are combined to provide relative ? and, if requested, absolute ? peptide quantifications. In order to robustly estimate absolute abundances, the external calibration curve method is applied ensuring linearity over the dynamic range.