Resources

Below you will find some tutorials and workshops on some useful approaches for data analysis:

QC-MXP Demo by Prof. David Broadhurst

In this video, Prof. David Broadhurst (Edith Cowan University) kindly provided a demo about his recently developed app QC:MXP based on his 2018 paper. Watch the recorded session and discussion with him here: QC-MXP demo.

International Blended Summer School on Natural Products (day 2)

The International Blended Summer School on Natural Products, September 26th – 27th 2024, took place at the Italian Academic Center on Roosevelt Island in New York City. The discussion was followed by a MicrobeMASST workshop where Dr. Caraballo teaches how to find out if detected small molecules are of microbial origin. This session is available online: IBSSNP day 2.

The following publications will provide you with an background on molecular networking and recent useful approaches for data analysis:

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

Heuckeroth, S., Damiani, T., Smirnov, A. et al. Reproducible mass spectrometry data processing and compound annotation in MZmine 3. Nat Protoc 19, 2597–2641 (2024). https://doi.org/10.1038/s41596-024-00996-y 

Data analysis with FBmn-STATS GUIde

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