MetaboAnalyst contains a total of 12 modules organized into four general categories:
- Exploratory statistical analysis: general statistics, biomarker analysis, two-factor/time-series analysis, and power analysis
- Functional enrichment analysis: metabolite set enrichment analysis, metabolic pathway analysis, and pathway activity prediction from MS peaks (mummichog)
- Data integration & systems biology: biomarker meta-analysis, joint-pathway analysis, and network explorer
- Data processing & utility functions: compound ID conversion, batch effect correction, lipidomics, and links to several spectra analysis tools
To address the needs of modern Clinical Research, MultiQuant™ software has been designed with the goal of improving data processing efficiency, thereby accelerating the process of data review. Integrated within Analyst® software, MultiQuant™ 3.0 software enables the identification and quantification of chemicals of interest in complex samples from data files generated on AB SCIEX triple quadrupole, QTRAP®, and TripleTOF® systems.
Skyline is a freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), DIA/SWATH and targeted DDA quantitative methods and analyzing the resulting mass spectrometer data. Its flexible configuration supports All Molecules. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale quantitative mass spectrometry studies in life sciences.
LipidXplorer is the open source software that supports the quantitative characterization of complex lipidomes by interpreting large datasets of shotgun mass spectra. LipidXplorer processes spectra acquired on any type of tandem mass spectrometers; it identifies and quantifies molecular species of any ionizable lipid class by considering any known or assumed molecular fragmentation pathway independently of any resource of reference mass spectra