New Search Engine Opens Public Metabolomics Data to All

Researchers at University of California San Diego and University of California, Riverside have developed a free, web-based platform that makes public metabolomics data far more accessible. The tool, called StructureMASST, allows users to search across billions of chemical spectra spanning thousands of studies, with the potential to make big-data metabolomics as straightforward as a standard internet search. It can be used to discover new metabolites, track drug exposures, and connect specific molecules to diseases or environmental sources. The study was published in Nature Biotechnology. 

Metabolomics is the large-scale study of small molecules such as amino acids and lipids—the end products of cellular processes. It offers a holistic snapshot of what is happening inside a cell, tissue, organ, or entire organism, including biochemical changes driven by genetics, diet, environmental factors, or disease.

Until now, searching for specific molecules in public repositories required expert knowledge and was limited to isolated datasets.

StructureMASST enables researchers, clinicians, and even members of the public to type in a chemical name, a SMILES string (text that represents 2D and 3D molecular structures), or a sub-structure pattern to instantly locate where those molecules have been documented across human, animal, plant, and environmental samples—from recently extinct animals and long-dead dinosaurs to microbial communities on the International Space Station.

"It will tell you what organs it's found in, which organisms can produce it, what health conditions it's associated with, and what molecules are connected to it," said senior author Pieter C. Dorrestein.

The platform draws on a massive knowledge base integrating data from all major public metabolomics repositories. The team used indexing technology to tag each chemical spectrum with its known associations, including organism, health condition, sample type, geography and environment, sex, and experimental design. "Search engines allow you to input text and quickly retrieve all the information associated with it because the entire worldwide web has been indexed," said Dorrestein. "We do essentially the same thing that these web search engines have done, but for molecules."

The tool returns results in seconds to minutes, supports searches by disease, and includes built-in quality control features that flag erroneous data in public libraries. StructureMASST has already surfaced patterns ranging from caffeine appearing in human blood and microbial cultures to bacterial iron-scavenging compounds in patients with chronic conditions.