Evidence map›Paper›PMID 42229419›Full record

ArticleCell reports methods2026

Ordering molecular diversity in untargeted metabolomics via molecular community networking.

Elizabeth A Coler, Alexey Melnik, Ali Lotfi, Dana Moradi, Ben Ahiadu, Paulo Wender Portal Gomes, Abubaker Patan, Vincent Charron-Lamoureux, Pieter C Dorrestein, Stephen Barnes and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. MS/MS Mass Spectrometry Filtering Tree for Bile Acid Isomer Annotation.bioRxiv : the preprint server for biology · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Elizabeth A ColerDepartment of Chemistry, University of Connecticut, Storrs, CT, USA.
Alexey MelnikDepartment of Chemistry, University of Connecticut, Storrs, CT, USA; Arome Science Inc., Farmington, CT, USA; BileOmix Inc, Farmington, CT, USA.
Ali LotfiDepartment of Chemistry, University of Connecticut, Storrs, CT, USA.
Dana MoradiDepartment of Chemistry, University of Connecticut, Storrs, CT, USA.
Ben AhiaduBileOmix Inc, Farmington, CT, USA.
Paulo Wender Portal GomesCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, San Diego, CA, USA.
Abubaker PatanCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, San Diego, CA, USA.
Vincent Charron-LamoureuxCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, San Diego, CA, USA.
Pieter C DorresteinCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, San Diego, CA, USA.
Stephen BarnesDivision 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.
Vladimir BoginskiDepartment of Industrial Engineering & Management Systems, University of Central Florida, Orlando, FL, USA.
Alexander SemenovDepartment of Industrial & Management Systems Engineering, University of South Florida, Tampa, FL, USA.
Alexander A AksenovDepartment of Chemistry, University of Connecticut, Storrs, CT, USA; Arome Science Inc., Farmington, CT, USA; BileOmix Inc, Farmington, CT, USA. Electronic address: aaksenov@uconn.edu.

Funding

Reverse Metabolomics for the Discovery of Disease Associated Microbial MoleculesR01DK136117 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PIETER C DORRESTEIN · 2023 to 2026
$2.9M
NIDDK NIH HHS R01 DK136117
6 · The paper itself

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.

Indexed as

MetabolomeMetabolomicsBile Acids and SaltsHumansMass SpectrometryReceptors, G-Protein-CoupledBile Acids and SaltsReceptors, G-Protein-CoupledCP: computational biologyCP: metabolismgas chromatography-mass spectrometryliquid chromatography-mass spectrometrymetabolomicsmolecular community networkingmolecular networking

Identifiers

PMID42229419
PMCPMC13390073

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.