Evidence map›Paper›PMID 41292869›Full record

ArticlebioRxiv : the preprint server for biology2025

Simulating Tandem Mass Spectra for Small Molecules using a General-Purpose Large-Language Model.

Tuan Nguyen, Dinesh Barupal

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

2 authors.

Tuan NguyenIntegrated Data Science Laboratory for Metabolomics and Exposomics, Department of Environmental Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
Dinesh BarupalIntegrated Data Science Laboratory for Metabolomics and Exposomics, Department of Environmental Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.ORCID 0000-0002-9954-8628

Funding

Conduits: Mount Sinai Health System Translational Science HubUL1TR004419 · NCATS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Rosalind J Wright · 2022 to 2026
$46.4M
The Mount Sinai Transdisciplinary Center on Early Environmental ExposuresP30ES023515 · NIEHS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Robert O Wright · 2014 to 2026
$21.3M
Exposome Correlation and Interpretation Database (ECID)U24ES035386 · NIEHS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Dinesh Barupal, SUSAN L TEITELBAUM · 2023 to 2026
$3.3M
Perfluoroalkyl substances and incident type 2 diabetes in a US population: A metabolome-genome investigationR01ES033688 · NIEHS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Damaskini Valvi · 2022 to 2026
$3.2M
Mapping the blood cancer exposome for environmental risk profiles of mature B-cell neoplasmsR01ES032831 · NIEHS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Douglas Ian Walker · 2022 to 2026
$2.3M
Metal Mixtures, MicroRNAs and Metabolomics in Extracellular Vesicles, and Early-life Programming of Childhood Sleep Patterns: A Longitudinal StudyR01ES035478 · NIEHS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Dinesh Barupal, Allison Kupsco · 2024 to 2026
$2.1M
GeoSpace - GeoSpatial Knowledgebase for ExposomicsR24ES036917 · NIEHS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Dinesh Barupal, Itai Kloog · 2025 to 2026
$1.1M
NCATS NIH HHS UL1 TR004419NIEHS NIH HHS P30 ES023515NIEHS NIH HHS R01 ES032831NIEHS NIH HHS R01 ES033688NIEHS NIH HHS R01 ES035478NIEHS NIH HHS R24 ES036917NIEHS NIH HHS U24 ES035386
6 · The paper itself

Abstract

We show a practical application of the Google Gemini large-language-model for simulating tandem mass spectra for compounds from the Blood Exposome Database. This approach bypasses the need for domain-specific model training, suggesting that the chemical fragmentation knowledge could be latently encoded within the Gemini model. General-purpose LLMs represent a useful and accessible tool for expanding

Identifiers

PMID41292869
PMCPMC12642542

What OpenQuestion holds

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LicenceCC BY-NC
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.