Evidence map›Paper›PMID 39755959›Full record

ArticleJournal of the American Society for Mass Spectrometry2025

Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing.

Xinsong Du, Amanda Dobrowolski, Mathias Brochhausen, Timothy J Garrett, William R Hogan, Dominick J Lemas

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of the American Society for Mass Spectrometry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Xinsong DuDivision of General Internal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.ORCID 0000-0003-3713-3264
Amanda DobrowolskiDepartment of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida 32611, United States.
Mathias BrochhausenDepartment of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States.
Timothy J GarrettDepartment of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida 32610, United States.ORCID 0000-0003-1623-009X
William R HoganDepartment of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida 32611, United States.ORCID 0000-0002-9881-1017
Dominick J LemasDepartment of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida 32611, United States.

Funding

Using social networks to map and evaluate team science across CTSA hubsUL1TR001427 · NCATS · UNIVERSITY OF FLORIDA · PI MITCHELL, DUANE A. · 2015 to 2024
$37.2M
Human milk metabolomics and microbe-host interactions associated with pediatric obesityK01DK115632 · NIDDK · UNIVERSITY OF FLORIDA · PI LEMAS, DOMINICK JOSEPH · 2019 to 2023
$831k
NCATS NIH HHS UL1 TR001427NIDDK NIH HHS K01 DK115632
6 · The paper itself

Abstract

Reproducibility in untargeted metabolomics data processing remains a significant challenge due to software limitations and the complex series of steps required. To address these issues, we developed Nextflow4MS-DIAL, a reproducible workflow for liquid chromatography-mass spectrometry (LC-MS) metabolomics data processing, validated with publicly available data from MetaboLights (MTBLS733). Nextflow4MS-DIAL automates LC-MS data processing to minimize human errors from manual data handling. The workflow supports software containerization, ensuring computational reproducibility and enabling collaborative research. Nextflow4MS-DIAL is compatible with any Unix-like system and supports multiple job schedulers, offering flexibility and ease of use. The Nextflow4MS-DIAL workflow is available under the permissive MIT license: https://github.com/Nextflow4Metabolomics/nextflow4ms-dial.

Indexed as

Mass SpectrometryMetabolomicsSoftwareChromatography, LiquidHumansLiquid Chromatography-Mass SpectrometryReproducibility of ResultsWorkflowLC-MSMetabolomicsNextflowReproducibilityWorkflow

Identifiers

PMID39755959
PMCPMC12711355

What OpenQuestion holds

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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.