PurposeAn enhanced version of the ProFit fitting tool was developed and validated to improve the quantification of two‐dimensional JRPESS spectroscopic data.MethodsThe proposed enhancements were achieved by flexible organization of prior knowledge, configurations for different situations, the inclusion of measured macromolecular baseline contribution, additional baseline splines and a model‐free lineshape based on self‐deconvolution. The new software was tested and tuned on simulated data and subsequently applied to in vivo intrasubject and intersubject data.ResultsFit results of simulated and acquired spectra show good overall quality suggesting the potential reliable detection of up to 18 metabolites on a 3T system yielding Cramer‐Lower‐Bounds below 20%.ConclusionThe proposed enhanced version of ProFit together with two‐dimensional J‐resolved spectroscopy offers the opportunity to reliably detect a wide selection of important brain metabolites on 3T. Magn Reson Med 71:458–468, 2014. © 2013 Wiley Periodicals, Inc.