High-resolution mass spectrometry for human exposomics: Expanding chemical space coverage

Y Lai, JP Koelmel, DI Walker, EJ Price… - Environmental …, 2024 - ACS Publications
In the modern “omics” era, measurement of the human exposome is a critical missing link
between genetic drivers and disease outcomes. High-resolution mass spectrometry …

Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools

NF de Jonge, K Mildau, D Meijer, JJR Louwen… - Metabolomics, 2022 - Springer
Background Untargeted metabolomics approaches based on mass spectrometry obtain
comprehensive profiles of complex biological samples. However, on average only 10% of …

Deep learning-assisted spectrum–structure correlation: state-of-the-art and perspectives

XY Lu, HP Wu, H Ma, H Li, J Li, YT Liu, ZY Pan… - Analytical …, 2024 - ACS Publications
Spectrum–structure correlation is playing an increasingly crucial role in spectral analysis
and has undergone significant development in recent decades. With the advancement of …

[HTML][HTML] Machine learning applications in precision medicine: overcoming challenges and unlocking potential

H Nilius, S Tsouka, M Nagler, M Masoodi - TrAC Trends in Analytical …, 2024 - Elsevier
Precision medicine, utilizing genomic and phenotypic data, aims to tailor treatments for
individual patients. However, successful implementation into clinical practice is challenging …

IDSL_MINT: a deep learning framework to predict molecular fingerprints from mass spectra

SF Baygi, DK Barupal - Journal of Cheminformatics, 2024 - Springer
The majority of tandem mass spectrometry (MS/MS) spectra in untargeted metabolomics and
exposomics studies lack any annotation. Our deep learning framework, Integrated Data …

Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights N-acylnornicotine innovations

D Elser, D Pflieger, C Villette, B Moegle, L Miesch… - Science …, 2023 - science.org
Specialized metabolite (SM) diversification is a core process to plants' adaptation to diverse
ecological niches. Here, we implemented a computational mass spectrometry–based …

Metabolome-guided genome mining of RiPP natural products

MM Zdouc, JJJ van der Hooft, MH Medema - Trends in Pharmacological …, 2023 - cell.com
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a
chemically diverse class of metabolites. Many RiPPs show potent biological activities that …

[PDF][PDF] Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome …

JL Baker - FEMS Microbiology Reviews, 2023 - academic.oup.com
The oral microbiota has an enormous impact on human health, with oral dysbiosis now
linked to many oral and systemic diseases. Recent advancements in sequencing, mass …

MAW: the reproducible M etabolome A nnotation W orkflow for untargeted tandem mass spectrometry

M Zulfiqar, L Gadelha, C Steinbeck, M Sorokina… - Journal of …, 2023 - Springer
Map** the chemical space of compounds to chemical structures remains a challenge in
metabolomics. Despite the advancements in untargeted liquid chromatography-mass …

Machine learning-assisted identification of environmental pollutants by liquid chromatography coupled with high-resolution mass spectrometry

H Wang, L Zhong, W Su, T Ruan, G Jiang - TrAC Trends in Analytical …, 2024 - Elsevier
Chemical exposure can be linked with various adverse effects, but the causal association is
still poorly understood. To meet the challenge, non-target screening (NTS) based on liquid …