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Mass spectrometry searches using MASST

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Fig. 1: MASST search, reporting and match visualization.

Data availability

All data used for testing and validating MASST are deposited in GNPS/MassIVE. MASST is a web-based application that is embedded in GNPS, which is a community service in which all public data are public. All data underlying figures present in the Supplementary Note are included as Supplementary Data 1 and 2. We cannot provide server installation, software engineers or administrator support for individual installations of MASST. The MASST platform is built as a workflow on top of the web repository workflow platform ProteoSAFe ( Each step of the MASST query is written in Python. Web rendering of the results is displayed by ProteoSAFe in the browser.

Code availability

For those who wish to build out MASST and recruit their own programmers, software engineers and system administrators, we have deposited the code at github ( The standalone MASST query interface is written in Python and Flask with a web front end written in HTML and JavaScript. It is open source ( and released under an LGPL-3 license.


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Conversion of data from different repositories was supported by R03 CA211211 on reuse of metabolomics data. The development of a user-friendly interface was in part supported by Gordon and Betty Moore Foundation through grant GBMF7622. The UC San Diego Center for Microbiome Innovation supported the campus wide SEED grant awards for data collection that enabled the development of much of this infrastructure. A.K.J. thanks the American Society for Mass Spectrometry for the 2018 Postdoctoral Career Development Award. We acknowledge C. O’Donovan and K. Haug for help with navigating the MetaboLights data repository. J.V.D.H. was supported by a ASDI eScience grant (ASDI.2017.030) from the Netherlands eScience Center (NLeSC). E.I.Z. and L.L.-B. were supported by NIH grants AI081923 and AI113923. A.M.C.R., K.E.K., S.P.P., J.L.K., M.J.B. and P.C.D. were supported by NSF grant IOS-1656475. A.B. was supported by National Institute of Justice Award 2015-DN-BX-K047. F.V. was supported by the Department of Navy, Office of Naval Research Multidisciplinary University Research Initiative (MURI) Award, award number N00014-15-1-2809. D.P. was supported by the German Research Foundation (DFG) with grant PE 2600/1. Additional support for data acquisition and data storage was provided by P41 GM103484 Center for Computational Mass Spectrometry, Instrument support though NIH S10RR029121. R.L. is supported by NIH grants R01DK106419, 5P42ES010337 and 5UL1TR001442, and NIH K01DK116917 to J.D.W. The development of the web interface and harmonization with Qiita was in part supported by the Sloan Foundation.

Author information

Authors and Affiliations



P.C.D. and M.W. came up with the concept of MASST. M.W. and N.B. performed the engineering to enable MASST. M.W., A.V.M., A.K.J., J.J.J.v.d.H., J.M.G., M.P., E.O.E., K.W., C.M.A., F.D.O., E.B., A.B., R.Q., M.C., N.S. and S.S. curated metadata. F.V., J.M.G., L.L.-B., K.W., E.B., A.A.A., R.Q., M.C. and C.S.C. generated data for the manuscript. E.C.G. synthesized the bile acids. P.C.D., M.W., D.P., J.D.W., M.J., L.F.N., J.M.G., E.I.Z., L.L.-B., K.E.K., S.P.P., A.M.C.R., A.V.M., F.V., K.W., A.A.A. and S.S. performed experiments and/or analysis for Box 1. P.C.D., D.P., L.F.N., J.J.J.v.d.H., J.M.G., A.A.A., A.M.C.R., F.V., K.W., A.B., F.D.O., M.E. and R.d.S. tested the MASST infrastructure and downloaded public data. P.C.D., N.B., E.I.Z., R.L., R.K., A.D.S., M.J.B. and J.L.K. provided supervision and funding for the project. P.C.D., A.K.J., D.P., J.J.v.d.H., M.E., J.M.G., A.A.A., A.M.C.R., R.K., J.L.K., L.F.N., N.B. and M.W. wrote and edited the manuscript.

Corresponding author

Correspondence to Pieter C. Dorrestein.

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Competing interests

M.W. is the founder of Ometa Labs LLC and consults for Sirenas, and P.C.D. is on the scientific advisory board of Sirenas.

Supplementary information

Supplementary Note

Supplementary Data for Supplementary Note Box Figure 1a

Underlying data for figure panel in the Supplementary Note.

Supplementary Data for Supplementary Note Box Figure 1c,d

Underlying data for figure panel in the Supplementary Note.

Supplementary Data for Supplementary Note Box Figure 2a

Underlying data for figure panel in the Supplementary Note.

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Wang, M., Jarmusch, A.K., Vargas, F. et al. Mass spectrometry searches using MASST. Nat Biotechnol 38, 23–26 (2020).

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