Note: these tools are not exhaustive, but are meant to be representative of software that is available to NTA researchers.
| Name | Access Type | Website | Description |
|---|---|---|---|
| enviMass | freely available for contributors; purchased through enviBee | https://www.envibee.ch/eng/enviMass/overview.htm | A versatile data-mining workflow for the automatized detection of patterns and compounds in hyphenated (LC or GC) or direct-injection mass spectrometry. The workflow includes a growing bundle of data mining functionalities such as targeted screening, non-targeted peak grouping, homologue series detection, quantification and statistical analysis. |
| enviPick | Open-source R package* | https://cran.r-project.org/package=enviPick | R package for "sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot." |
| ChromaTOF | LECO Corporation | https://www.lecosoftware.com https://www.leco.com/product/chromatof-software | Commercial software |
| Competitive Fragmentation Modeling (CFM-ID) | open-source | https://cfmid.wishartlab.com/ | Created by the Wishart lab at the University of Alberta and provides a platform for MS-spectra prediction, MS-spectra annotation, and MS-based compound identification. |
| Compound Discoverer | Thermo Fisher Scientific | https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/compound-discoverer-software.html https://planetorbitrap.com/compound-discoverer https://mycompounddiscoverer.com/ | Commercial software |
| DEIMOS/ISiCLE/DarkChem | open-source | https://availabletechnologies.pnnl.gov/technology.asp?id=507 | Tools that the researchers at Pacific Northwest National Laboratory are developing to advance standards-free metabolomics—the identification of small molecules without reliance on standards—using calculated chemical properties and associated matching with multiple experimental attributes. |
| GNPS | open-source | https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp | A web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS). GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition/analysis to post publication. |
| LabSolutions Insight Explore | Shimadzu | https://www.shimadzu.com/an/products/liquid-chromatograph-mass-spectrometry/quadrupole-time-of-flight-lc-msms/lcms-9030/option.html | Commercial software |
| MassHunter Profinder | Agilent Technologies | https://www.agilent.com/en/product/software-informatics/mass-spectrometry-software/data-analysis/mass-profiler-professional-software#howitworks | Commercial software |
| Mass Profiler Professional | Agilent Technologies | https://www.agilent.com/en/product/software-informatics/mass-spectrometry-software/data-analysis/mass-profiler-professional-software | Commercial software |
| MassHunter Qualitative Analysis | Agilent Technologies | https://www.agilent.com/en/product/software-informatics/mass-spectrometry-software/data-analysis/qualitative-analysis | Commercial software |
| MassHunter Quantitative Analysis | Agilent Technologies | https://www.agilent.com/en/product/software-informatics/mass-spectrometry-software/data-analysis/quantitative-analysis | Commercial software |
| MetFrag | open-source | https://ipb-halle.github.io/MetFrag/ | A freely available software for the annotation of high precision tandem mass spectra of metabolites. Candidate molecules of different databases are fragmented in silico and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment. |
| MS-DIAL | open-source | http://prime.psc.riken.jp/compms/msdial/main.html | A program for untargeted metabolomics that supports multiple instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and vendors. MS-DIAL has a version of Fiehn lab’s GC/MS database and in silico retention time- and MS/MS database for LC/MS/MS based lipidomics. |
| mzMine | open-source | http://mzmine.github.io/ | An open-source software for mass-spectrometry data processing, with the main focus on LC-MS data with the goal of providing a user-friendly, flexible and easily extendable software with a complete set of modules covering the entire LC-MS data analysis workflow. |
| nontarget | Open-source R package* | https://cran.r-project.org/package=nontarget | R package for "screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components." |
| ProteoWizard | open-source | http://proteowizard.sourceforge.net/tools.shtml | A number of applications for reading and converting vendor formats, viewing and analyzing data. |
| SCIEX OS | Sciex | https://sciex.com/products/software/sciex-os-software-x120805 | Commercial software |
| SIRIUS + CSI:FingerID | open-source, java-based (GUI and CLI or Command Line version) | https://bio.informatik.uni-jena.de/software/sirius/ | A software framework for discovering a landscape of de-novo identification of metabolites using single and tandem mass spectrometry. SIRIUS uses isotope pattern analysis for detecting the molecular formula and further analyses the fragmentation pattern of a compound using fragmentation trees. |
| The Metabolomics Association of North America Software and Data Exchange (MaNaSoDa) | free | https://sites.google.com/metabolomicsna.org/soda/home?authuser=0 | Assembles and promotes sharing of informatics resources among a broader metabolomics community. Listed datasets can be used for teaching, bench-marking, validation, meta-analysis and mega-analysis. |
| XCMS | open-source (online or via R script) | https://xcmsonline.scripps.edu/ | Created by the Siuzdak Lab at Scripps Research and is designed to be an easy way to analyze, visualize and share untargeted metabolomic data. |