We present an improved version of parametric time warping, which enables the method to be used in LC-MS measurements in proteomics. The new features include a new similarity measure for comparing warped chromatograms, an insurance against peaks at the extremes of the chromatograms disappearing because of the warping, and the possibility to select and use multiple traces in searching the optimal alignment. Moreover, we present an alignment strategy combining global and individual alignments for aligning LC-MS data that exhibit different shifts within the same sample, at the same retention time. Using an LC-MS data set consisting of E. coil homogenates that were measured in several batches over a period of six months, we show the benefits of the improved algorithm and the merits of the new strategy. The algorithm is publicly available as the R package ptw. (C) 2010 Elsevier B.V. All rights reserved.