Data Processing Software

The following software packages may be of some use in processing mass spectrometry and metabolomics data.

AMDIS

Automated Mass Spectral Deconvolution and Identification System (Windows only), is utilized primarily for the extraction of spectra from GC/MS data files.

MS-DIAL

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. 

XCMS

XCMS provides a framework for processing and visualization of chromatographically separated and single-spectra mass spectral data including untargeted metabolomic analyses. 

MZmine 3

Mzmine 3 is an open-source software tool for mass spectrometry data processing, primarily for LC/MS data.

MetaboAnalyst

MetaboAnalyst is a free online tool for univariate and multivariate statistics, including data normalization and transformation.

ProteoWizard

Proteowizard is a modular and extensible set of open-source, cross-platform, tools and libraries for the processing of mass spectrometry data.