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  3. Toxbase: A Multidimensional Toxcast Reference Database For High-throughput Human Exposome Analysis.
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  3. Toxbase: A Multidimensional Toxcast Reference Database For High-throughput Human Exposome Analysis.

Related Experiment Video

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
05:34

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

ToxBase: A Multidimensional ToxCast Reference Database for High-Throughput Human Exposome Analysis.

Ryan Nguyen1, Griffin Rangel1, Xingzhu Liu1

  • 1Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States.

Environmental Science & Technology
|June 9, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

ToxBase, a new multidimensional database, enhances human exposome research by providing crucial reference data for chemical exposure profiling. This resource enables high-confidence identification of chemicals in biological samples, advancing analytical standardization.

Keywords:
MS/MSToxCastcollision cross sectionexposomeion mobility-mass spectrometrysuspect screening

Related Experiment Videos

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
05:34

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

Area of Science:

  • Environmental chemistry
  • Analytical chemistry
  • Toxicology

Background:

  • High-resolution mass spectrometry (HRMS) is vital for human exposome research, but lacks standardized reference data for chemical identification.
  • Scarcity of collision cross-section (CCS) and MS/MS fragmentation data impedes accurate structural annotation of chemical exposures.

Purpose of the Study:

  • To develop ToxBase, a comprehensive multidimensional reference database for chemical exposure agents.
  • To facilitate high-confidence structural annotation and standardization in human exposome research.

Main Methods:

  • Generated a multidimensional database (m/z, retention time, CCS, MS/MS) for over 2,000 chemicals using high-throughput liquid chromatography-ion mobility-tandem mass spectrometry (LC-IM-MS/MS).
  • Assembled a high-quality MS/MS reference library using targeted data-dependent acquisition and a novel data extraction algorithm (DDARawProcessor).
  • Validated ToxBase using human plasma, urine, and fecal samples.

    • Main Results:

    • ToxBase contains 3,598 precursor ions for 2,075 compounds with high precision and cross-platform agreement.
    • Application to human samples enabled rapid identification of 42 high-confidence (Level 1) chemical exposures.
    • The database demonstrated excellent interday CCS precision (98.5% < 1% RSD).

    Conclusions:

    • ToxBase provides a valuable, freely available resource for standardized, large-scale exposome analysis.
    • The database supports vendor-agnostic suspect screening workflows via compatibility with the open-source Skyline platform.
    • ToxBase significantly advances confident structural annotation of chemical exposures in complex biological matrices.