For R package users, there is a nice R library called XCMS.
XCMS is an LC/MS-based data analysis approach which incorporates novel nonlinear retention time alignment, feature detection, and feature matching. Without using internal standards, the method dynamically identifies hundreds of endogenous metabolites for use as standards, calculating a nonlinear retention time correction profile for each sample. Following retention time correction, the relative metabolite ion intensities are directly compared to identify changes in specific endogenous metabolites, such as potential biomarkers.
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