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An LC/MS-based data analysis approach which incorporates novel nonlinear retention time alignment, feature detection, and feature matching. 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.
SimExTargId / Simultaneous metabolomic MS1-profiling Experiment and statistically relevant MS2 Target Identification
Permits users to realize autonomous and real-time analysis of metabolomic data. SimExTargId is an open source R package that provides an autonomous workflow that can also calculate data preprocessing in real-time, thereby alerting the user to signal degradation or loss. This method also facilitates real-time monitoring of liquid chromatography-mass spectrometry (LC-MS) data acquisition.
Aligns and calculates pairwise similarity scores among mass spectrometry (MS)/MS spectral data. MetCirc is an open-source package to make biological sense of mass spectral similarities from metabolomics data by providing a dedicated data analysis infrastructure and visualization interface to explore small molecules that mediate functionally important phenotypes. It can be used to pinpoint and formulate first structural hypothesis on previously non-characterized metabolites associated with a given phenotype.
Allows users to perform Two Dimensional Gas Chromatography-Mass Spectrometry (2D-GCMS) derived metabolite peak alignment and identification. R2DGC uses individual sample files including basic peak information to generate an alignment table which shows the peaks common to several samples and match the aligned one to a reference library. The pipeline also furnish a reference library gathering information about 298 peaks issued from over 125 metabolite standards and commonly observed background peaks.
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