Resources

The following publications will provide you with an overview of tools and approaches currently available for data analysis of tandem mass spectrometry:

Classical molecular networking in GNPS

Aron, A.T., Gentry, E.C., McPhail, K.L. et al. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc 15, 1954–1991 (2020). https://doi.org/10.1038/s41596-020-0317-5

Feature-based molecular networking in GNPS

Nothias, LF., Petras, D., Schmid, R. et al. Feature-based molecular networking in the GNPS analysis environment. Nat Methods 17, 905–908 (2020). https://doi.org/10.1038/s41592-020-0933-6

Preparing your metadata with ReDU template

Jarmusch, A.K., Wang, M., Aceves, C.M. et al. ReDU: a framework to find and reanalyze public mass spectrometry data. Nat Methods 17, 901–904 (2020). https://doi.org/10.1038/s41592-020-0916-7

Pre-processing your data with MZmine3

Schmid, R., Heuckeroth, S., Korf, A. et al. Integrative analysis of multimodal mass spectrometry data in MZmine 3. Nat Biotechnol 41, 447–449 (2023). https://doi.org/10.1038/s41587-023-01690-2

Damiani T, Heuckeroth S, Smirnov A, Mokshyna O, Brungs C, Korf A, et al. Mass spectrometry data processing in MZmine 3: feature detection and annotation. This content is a preprint and has not been peer-reviewed. ChemRxiv. 2023; doi:10.26434/chemrxiv-2023-98n6q 

Data analysis with FBmn-STATS GUIde

Pakkir Shah AK, Walter A, Ottosson F, Russo F, Navarro-Díaz M, Boldt J, et al. The Hitchhiker’s Guide to Statistical Analysis of Feature-based Molecular Networks from Non-Targeted Metabolomics Data. ChemRxiv. Cambridge: Cambridge Open Engage; 2023; This content is a preprint and has not been peer-reviewed. https://chemrxiv.org/engage/chemrxiv/article-details/6540eb2548dad23120c52242

Searching molecules across public datasets with MASST

Wang, M., Jarmusch, A.K., Vargas, F. et al. Mass spectrometry searches using MASST. Nat Biotechnol 38, 23–26 (2020). https://doi.org/10.1038/s41587-019-0375-9

Searching molecules across public datasets with microbeMASST

Zuffa, S., Schmid, R., Bauermeister, A. et al. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat Microbiol 9, 336–345 (2024). https://doi.org/10.1038/s41564-023-01575-9