This paper describes a new quantitation method called AQSES for short echo time magnetic resonance spectra. This method is embedded in a software package available online from www.esat.kuleuven.be/sista/members/biomed/new/ with a graphical user interface, under an open source license, which means that the source code is freely available and easy to adapt to specific needs of the user. The quantitation problem is mathematically formulated as a separable nonlinear least-squares fitting problem, which is numerically solved using a modified variable-projection procedure. A macromolecular baseline is incorporated into the fit via nonparametric modelling, efficiently implemented using penalized splines. Unwanted components such as residual water are removed with a maximum-phase FIR filter. Constraints on the phases, dampings and frequencies of the metabolites can be imposed. AQSES has been tested on simulated MR spectra with several types of disturbance and on short echo time in vivo proton MR spectra. Results show that AQSES is robust, easy to use and very flexible. Copyright (C) 2006 John Wiley & Sons, Ltd.