MOTIVATION: Proteomics has particularly evolved to become of high interest for the field of biomarker discovery and drug development. Especially the combination of liquid chromatography and mass spectrometry (LC/MS) has proven to be a powerful technique for analyzing protein mixtures. Clinically orientated proteomic studies will have to compare hundreds of LC/MS runs at a time. In order to compare different runs, sophisticated preprocessing steps have to be performed. An important step is the retention time (rt) alignment of LC/MS runs. Especially non-linear shifts in the rt between pairs of LC/MS runs make this a crucial and non-trivial problem. RESULTS: For the purpose of demonstrating the particular importance of correcting non-linear rt shifts, we evaluate and compare different alignment algorithms. We present and analyze two versions of a new algorithm that is based on regression techniques, once assuming and estimating only linear shifts and once also allowing for the estimation of non-linear shifts. As an example for another type of alignment method we use an established alignment algorithm based on shifting vectors that we adapted to allow for correcting non-linear shifts also. In a simulation study, we show that rt alignment procedures that can estimate non-linear shifts yield clearly better alignments. This is even true under mild non-linear deviations. AVAILABILITY: R code for the regression-based alignment methods and simulated datasets are available at http://www.statistik.tu-dortmund.de/genetik-publikationen-alignment.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.