{
  "abstract": "Molecules in living systems are not random but are shaped by biological necessity. Mass spectrometry (MS) is a powerful tool for exploring these complex molecular landscapes. Molecular networking links metabolites by spectral similarity, but conventional methods leave many nodes disconnected. We introduce molecular community networking (MCN), which identifies natural molecular clusters and prunes them to keep the strongest links. The approach increases connectivity to about 95% of molecules and better captures structurally related compounds, including distinct ion forms and in-source fragmentation ions. MCN also improves the mapping of molecular space, helping distinguish true novel molecules from artifacts. Using MCN, we discovered dipeptide-conjugated bile acids associated with Bifidobacterium breve and proposed structures for previously unexplored N-acyl amides that interact with G protein-coupled receptors. We also built a global metabolome map from public GNPS/MassIVE data, covering about 8.4 million molecular features, creating a \"roadmap\" for molecular diversity.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Chemistry, University of Connecticut, Storrs, CT, USA",
    "Department of Chemistry, University of Connecticut, Storrs, CT, USA; Arome Science Inc., Farmington, CT, USA; BileOmix Inc, Farmington, CT, USA",
    "Arome Science Inc., Farmington, CT, USA",
    "BileOmix Inc, Farmington, CT, USA",
    "Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, San Diego, CA, USA",
    "Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, 3233, USA",
    "Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham BBRB 711, 845 19(th) St. S, Birmingham, AL 35244, USA",
    "Department of Industrial Engineering & Management Systems, University of Central Florida, Orlando, FL, USA",
    "Department of Industrial & Systems Engineering, University of Florida, Gainesville, FL, USA",
    "Department of Industrial & Management Systems Engineering, University of South Florida, Tampa, FL, USA",
    "Department of Chemistry, University of Connecticut, Storrs, CT, USA; Arome Science Inc., Farmington, CT, USA; BileOmix Inc, Farmington, CT, USA. Electronic address: aaksenov@uconn.edu"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 13,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Elizabeth Coler",
      "orcid": "0000-0002-2502-9665"
    },
    {
      "affs": [
        1,
        2,
        0
      ],
      "name": "Alexey V. Melnik",
      "orcid": "0000-0002-4645-8880"
    },
    {
      "affs": [
        0
      ],
      "name": "Ali Lotfi",
      "orcid": "0000-0001-6124-3338"
    },
    {
      "affs": [
        0
      ],
      "name": "Dana Moradi",
      "orcid": "0009-0000-2088-485X"
    },
    {
      "affs": [
        3
      ],
      "name": "Ben Ahiadu"
    },
    {
      "affs": [
        4
      ],
      "name": "Paulo Wender Portal Gomes",
      "orcid": "0000-0001-5478-2448"
    },
    {
      "affs": [
        4
      ],
      "name": "Abubaker Patan",
      "orcid": "0000-0003-1415-7829"
    },
    {
      "affs": [
        4
      ],
      "name": "Vincent Charron‐Lamoureux",
      "orcid": "0000-0001-9440-7036"
    },
    {
      "affs": [
        4,
        5
      ],
      "name": "Pieter C. Dorrestein",
      "orcid": "0000-0002-3003-1030"
    },
    {
      "affs": [
        6,
        7
      ],
      "name": "Stephen Barnes",
      "orcid": "0000-0001-6837-1674"
    },
    {
      "affs": [
        7,
        8
      ],
      "name": "Vladimir L. Boginski",
      "orcid": "0000-0002-1571-0481"
    },
    {
      "affs": [
        9,
        2,
        0
      ],
      "name": "Alexander Semenov"
    },
    {
      "affs": [
        10
      ],
      "name": "Alexander A. Aksenov",
      "orcid": "0000-0002-9445-2248"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/21pegwgtrvc5k.bib",
  "cited_by": 13,
  "doi": "10.1016/j.crmeth.2026.101468",
  "fulltext_url": null,
  "id": "21pegwgtrvc5k",
  "issns": [
    "2667-2375"
  ],
  "landing_url": "https://doi.org/10.1016/j.crmeth.2026.101468",
  "language": "en",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Metabolomics and Mass Spectrometry Studies"
    ]
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  "openalex": "W4401300962",
  "pdf_url": null,
  "pmcid": "PMC11312580",
  "pmid": "39131284",
  "published": "2026-06-02",
  "publisher": "Elsevier BV",
  "ris": "https://research.draconitic.com/paper/21pegwgtrvc5k.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:26:46Z",
      "native_id": "W4401300962",
      "source": "openalex",
      "url": "https://doi.org/10.1016/j.crmeth.2026.101468"
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  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Metabolomics and Mass Spectrometry Studies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Ordering molecular diversity in untargeted metabolomics via molecular community networking",
  "title_text": "Ordering molecular diversity in untargeted metabolomics via molecular community networking",
  "type": "peer-reviewed",
  "updated_at": "2026-11-06T13:20:28Z",
  "url": "https://research.draconitic.com/paper/21pegwgtrvc5k",
  "venue": "Cell Reports Methods",
  "versions": []
}