The following software packages may be of some use in processing mass spectrometry and metabolomics data.
Automated Mass Spectral Deconvolution and Identification System (Windows only), is utilized primarily for the extraction of spectra from GC/MS data files.
The MS-DIAL software is able to utilize LC-MS/MS or GC-MS raw data from any vendor, including deconvolution, alignment, and compound identification.
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Mzmine 2 is an open-source software tool for mass spectrometry data processing, primarily for LC/MS data.
MetaboAnalyst is a free online tool for univariate and multivariate statistics, including data normalization and transformation.
Proteowizard is a modular and extensible set of open-source, cross-platform, tools and libraries for the processing of mass spectrometry data.