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NEWS: The Scripps Center for Metabolomics is pleased to announce XCMS Online, a new user-friendly variant of XCMS for processing metabolomics data without installation.

Metabolite profiling in biomarker discovery, enzyme substrate assignment, drug activity/specificity determination, and basic metabolic research requires data preprocessing approaches to correlate specific metabolites to their biological origin. 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.

The XCMS software reads and processes LC/MS data stored in netcdf , mzXML, mzData and mzML files. It provides methods for feature detection, non-linear retention time alignment, visualization, relative quantization and statistics. XCMS is capable of simultaneously preprocessing, analyzing, and visualizing the raw data from hundreds of samples. XCMS is freely available under an open-source license.