Software

	NP Analyst NP Analyst (www.npanalyst.org) is a data integration platform for predicting bioactive metabolites from complex mixtures. It integrates mass spectrometry metabolomics data and results from high-throughput screening experiments to directly predict bioactive MS features from large extract libraries. It is supported by both a web server, and a stand-alone CLI version. Full documentation can be found here. The codebase can be found here.
	SNAP-MS SNAP-MS (www.npatlas.org/discover/snapms) is a platform for reference spectrum-free structural annotation of GNPS data. This tool uses structural similarity between compounds in the Natural Products Atlas database to identify candidate compound families for GNPS subnetworks sharing related MS distributions. It can be used either with full GNPS output files, or in stand-alone mode by providing lists of candidate masses for identification. It is supported by both a web server, and a stand-alone CLI version. Full documentation can be found here. The codebase can be found here.
	Multiplex MS MultiplexMS is a tool for rapid acquisition of untargeted metabolomics data for large extract libraries. The system is designed to generate sets of pooled samples for MS analysis, which are then computationally deconvoluted to give the MS features of the original individual mixtures. The advantage of this approach is that it is much faster than acquiring replicate data on individual samples in the set. It is supported by both a stand-alone software package (available here) that requires no programming experience to install. Full documentation can be found here. The codebase can be found here.
	Multivariate Pattern Analysis (MVPA) Multivariate Pattern ANalysis (MVPA; www.mvpashiny.org) is a statistical software package for multivariate analysis of complex samples with large numbers of confounding variables. It is particularly well suited to analyzing metabolomics data, and can be used to generate selectivity ratios for bioactive MS features. It is supported by both a Shiny web server built in R, and a stand-alone version available in R Studio. Full documentation can be found here. The codebase can be found here.
	MADByTE MADByTE (www.madbytenmr.com) is a software package for NMR-based metabolomics on complex mixtures. It uses TOCSY and HSQC data to create sets of detectable spin systems in individual mixtures, and then uses these spin systems to create networks that relate mixtures to one another based on their NMR features. It is supported by a stand-alone software package available here. Full documentation can be found here. The codebase can be found here.
	IsoAnalyst IsoAnalyst is a software package for connecting secondary metabolites to their cognate biosynthetic gene clusters using parallel stable isotope labelling. The software tool includes functions for all major steps of MS data processing and biosynthetic building block prediction. It is supported by stand-alone software package available here. Full documentation can be found here. The codebase can be found here.
	GitHub All of our software tools are available on GitHub. Come and check out what is going on in our lab at the public organization page here.