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Batch MASST Search

Drop an .mzML/.mgf file or a table of USIs and search every spectrum against all public metabolomics data with fastMASST. File spectra are read in your browser (nothing is uploaded); each query is searched on the GNPS server, and the hits are compiled into a table you can download. By default, big runs checkpoint to CSV every 1,000 queries so memory stays flat — uncheck that to keep everything in a single download.

Domain-specific MASSTs

Searching one spectrum? The domain MASSTs intersect the hits with curated reference metadata to tell you what kind of sample the molecule was seen in — the microbe, food, plant, tissue, product, or microbiome behind each match — on an interactive taxonomy / ontology tree.

microbeMASST

Which microbes (NCBI taxonomy) the molecule was observed in.

foodMASST

Which foods, on the Global FoodOmics ontology.

plantMASST

Which plants, on the plant taxonomy.

tissueMASST

Which tissues / body sites and conditions.

personalCareProductMASST

Which personal-care product categories.

microbiomeMASST

Which microbiome sample groups and interventions.

Input file

Drop an .mzML or .mgf here

or click to choose · spectra are extracted locally, in your browser

…and / or a table of USIs

Drop a .csv / .tsv / .txt of USIs

any column of values starting with mzspec: · one search per USI

Search

Search against

Search parameters

Analog search (allow a precursor-mass delta)

Cosine threshold

Precursor tol (Da)

Fragment tol (Da)

Min peaks / spectrum

Parallel searches

Download results to CSV every 1,000 queries — keeps memory flat on big runs; uncheck to hold everything in memory until done, then download once

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Too large for the browser?

Very large files can exceed a browser tab's memory. Download a Python script that runs this same search on your own machine — it streams hits to a CSV as it goes, so file size is no longer a limit, and there's no cross-origin restriction. The script is pre-filled with your settings above (index, tolerances, min peaks, parallelism) and takes the same mzML/MGF files or USI tables as input.

then: pip install pyteomics pynumpress lxml · python batch_masst.py YOURFILE.mzML

Summary

By dataset

Dataset	Matches

Matches

Query	Query m/z	Cosine	Peaks	Δ mass	Dataset	Compound	Spectrum

Citations

If you use MASST or a domain MASST, please cite the original MASST paper and the relevant domain tool:

MASST — Wang, M. et al. Mass spectrometry searches using MASST. Nature Biotechnology 38, 23–26 (2020). link
microbeMASST — Zuffa, S., Schmid, R. et al. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nature Microbiology 9, 336–345 (2024). link
foodMASST — npj Science of Food (2022). link
plantMASST — bioRxiv (2024). link
tissueMASST — bioRxiv (2025). link
microbiomeMASST — bioRxiv (2026). link
personalCareProductMASST — part of the domainMASST family (Dorrestein Lab); no dedicated publication yet.

Contributors

The domain MASSTs and their reference metadata are developed by the Dorrestein Lab (UC San Diego) and collaborators, built on the GNPS2 / fast MASST search infrastructure from the Wang Lab (UC Riverside). Reference-tree and data code: robinschmid/microbe_masst.

Contributors include Robin Schmid, Simone Zuffa, Wilhan Nunes, Shipei Xing, Yasin El Abiead, Sydney Thomas, Helena Mannochio-Russo, Mingxun Wang, and Pieter C. Dorrestein (PI).

Each spectrum is searched independently on api.fasst.gnps2.org; there is no batch endpoint, so a big file means many searches on a shared public server — please be considerate. A hit means a public spectrum looks similar to one of your spectra, not a confirmed identification; verify with the mirror plot. Compound names come only from library hits. This page needs cross-origin access enabled on the API for apps.gnps2.org, else the searches fail with a network error.