Multi-resolution LC-MS images alignment using dynamic time warping and Kullback-Leibler distance

Liquid chromatography mass spectrometry (LC-MS) is widely used in comparing proteomes for disease biomarker discovery. An LC-MS experiment produces a 2-D image, where the mass-to-charge ratio and the chromatographic retention time are the coordinates, and the signal intensities represent the abundance of detected peptides. However, there is always a non-linear retention time difference across replicate LC-MS images due to machine drift, such that synchronization of LC-MS images must be performed prior to any further analysis. In this paper, we propose a multi-resolution image alignment scheme to synchronize LC-MS images. Dynamic Time Warping (DTW) is used to reconcile the time differences among images and Kullback-Leibler distance (KLD) is used as a local distance measure. Our proposed scheme has been validated using two real data sets, and promising results have been obtained. © 2012 IEEE