Resources

Publications, case studies, and documentation to support your work.

Publications

Peer-reviewed research

Our team and collaborators publish across the metabolomics workflow — from algorithmic advances in spectral matching to large-scale library construction and retention time modelling.

Large-scale MS/MS spectral matching against 40,000 authenticated reference standards improves annotation rates in untargeted metabolomics
A. M. Chen, J. R. Kowalski, L. E. Park, S. V. Nakamura, T. H. Bergstrom
Analytical Chemistry · 2025
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A hybrid deep learning model for retention time prediction in reversed-phase LC-MS using molecular fingerprints and graph neural networks
S. V. Nakamura, K. L. Tran, J. R. Kowalski, M. A. Dubois
Journal of Proteome Research · 2025
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Three-gate verification: integrating accurate mass, retention time, and MS/MS spectral similarity for MSI Level 1a metabolite identification
J. R. Kowalski, A. M. Chen, L. E. Park, T. H. Bergstrom
Metabolomics · 2024
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Automated high-throughput metabolomics workflows: from raw feature extraction to authenticated compound identification
L. E. Park, K. L. Tran, S. V. Nakamura, A. M. Chen
Nature Protocols · 2024
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Spectral networking reveals structural families in plant metabolomics: bridging known and unknown chemical space
T. H. Bergstrom, M. A. Dubois, J. R. Kowalski, L. E. Park
Plant Physiology · 2024
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Building the world's largest measured LC-MS/MS library: strategies for authentic standard acquisition, curation, and quality control
M. A. Dubois, A. M. Chen, S. V. Nakamura, K. L. Tran
Scientific Data · 2023
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ESI polarity switching expands coverage in authenticated metabolomics: a systematic evaluation of 40,000 standards in positive and negative ionization modes
K. L. Tran, T. H. Bergstrom, J. R. Kowalski, M. A. Dubois
Rapid Communications in Mass Spectrometry · 2023
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Benchmarking MS/MS similarity metrics for metabolite identification: comparing cosine, entropy, and deep embedding approaches against authenticated reference data
J. R. Kowalski, L. E. Park, A. M. Chen, S. V. Nakamura
Journal of the American Society for Mass Spectrometry · 2023
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Case Studies

Real-world impact

See how research groups and industry teams use VeroMass to accelerate metabolite identification and publish with confidence.

Plant Metabolism

Identifying stress-responsive metabolites in Arabidopsis thaliana

A plant biology group used VeroMass to identify 340 stress-responsive features from an untargeted LC-MS study, achieving MSI Level 1a for 78% of putatively annotated compounds — a 3.2× improvement over library-free approaches.

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Pharmaceutical

Rapid metabolite profiling in early-stage drug discovery

A pharmaceutical R&D team integrated the VeroMass batch API into their screening pipeline, reducing per-compound identification time from 45 minutes to under 3 minutes across 2,000+ samples in a single study.

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Clinical Research

Authenticated biomarker discovery in human plasma metabolomics

A clinical metabolomics lab applied VeroMass three-gate verification to a cohort study of 600 patient plasma samples, confidently identifying 142 metabolites associated with metabolic syndrome progression.

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Documentation

Guides, tutorials & API reference

Everything you need to integrate VeroMass into your research workflow — from getting started to advanced batch processing.

Quick Start Guide

Get up and running in minutes. Learn how to upload data, run identification workflows, and interpret results.

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Tutorials

Step-by-step video and written tutorials covering compound identification, spectral networking, and target fishing.

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API Reference

Complete RESTful API documentation for the VeroMass batch identification endpoint, Python client, and authentication.

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Ready to explore the full platform?

Access our complete library, run identifications, and publish with MSI Level 1a confidence.