Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data

Z Pang, G Zhou, J Ewald, L Chang, O Hacariz… - Nature protocols, 2022 - nature.com
Liquid chromatography coupled with high-resolution mass spectrometry (LC–HRMS) has
become a workhorse in global metabolomics studies with growing applications across …

Identification and prioritization of environmental organic pollutants: from an analytical and toxicological perspective

T Ruan, P Li, H Wang, T Li, G Jiang - Chemical Reviews, 2023 - ACS Publications
Exposure to environmental organic pollutants has triggered significant ecological impacts
and adverse health outcomes, which have been received substantial and increasing …

Integrative analysis of multimodal mass spectrometry data in MZmine 3

R Schmid, S Heuckeroth, A Korf, A Smirnov… - Nature …, 2023 - nature.com
Innovation in mass spectrometry (MS) and the rapidly increasing throughput and sensitivity
of MS instrumentation require adaptations and innovations in data processing tools. Here …

Web-based multi-omics integration using the Analyst software suite

JD Ewald, G Zhou, Y Lu, J Kolic, C Ellis, JD Johnson… - Nature …, 2024 - nature.com
The growing number of multi-omics studies demands clear conceptual workflows coupled
with easy-to-use software tools to facilitate data analysis and interpretation. This protocol …

Directed evolution: methodologies and applications

Y Wang, P Xue, M Cao, T Yu, ST Lane… - Chemical reviews, 2021 - ACS Publications
Directed evolution aims to expedite the natural evolution process of biological molecules
and systems in a test tube through iterative rounds of gene diversifications and library …

Mass spectrometry-based metabolomics in microbiome investigations

A Bauermeister, H Mannochio-Russo… - Nature Reviews …, 2022 - nature.com
Microbiotas are a malleable part of ecosystems, including the human ecosystem.
Microorganisms affect not only the chemistry of their specific niche, such as the human gut …

Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements

NM Shah, HJ Jang, Y Liang, JH Maeng, SC Tzeng… - Nature …, 2023 - nature.com
Cryptic promoters within transposable elements (TEs) can be transcriptionally reactivated in
tumors to create new TE-chimeric transcripts, which can produce immunogenic antigens. We …

Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives

S Shen, C Zhan, C Yang, AR Fernie, J Luo - Molecular plant, 2023 - cell.com
Plants are natural experts in organic synthesis, being able to generate large numbers of
specific metabolites with widely varying structures that help them adapt to variable survival …

The changing metabolic landscape of bile acids–keys to metabolism and immune regulation

I Mohanty, C Allaband, H Mannochio-Russo… - Nature reviews …, 2024 - nature.com
Bile acids regulate nutrient absorption and mitochondrial function, they establish and
maintain gut microbial community composition and mediate inflammation, and they serve as …

Reproducible mass spectrometry data processing and compound annotation in MZmine 3

S Heuckeroth, T Damiani, A Smirnov, O Mokshyna… - Nature protocols, 2024 - nature.com
Untargeted mass spectrometry (MS) experiments produce complex, multidimensional data
that are practically impossible to investigate manually. For this reason, computational …