Analysis of proteomics data: An improved peak alignment approach

Mass spectrometry (MS) data are becoming common recent years. Prior to other statistical inferential procedures, alignment of spectra may be needed to ensure that intensities of the same protein/peptide are accurately located/identified. However, the enormous number of peaks poses challenge in handling such data. Direct applications of available curve alignment methods often do not produce satisfactory results. In this work, we propose an Automated Pairwise Piecewise Landmark Registration (APPLR) method for aligning MS data. For a pair of spectra, the most prominent peaks are given the priority to be aligned first. A weighted Gaussian kernel based similarity score is used to test warp these top peaks and spectra are then aligned according to the best match. The algorithm is implemented in an iterative way until all spectra are aligned. We illustrated the new method and two other curve alignment methods to the unlabeled total ion count data.