Comprehensive investigation of pathway enrichment methods for functional interpretation of LC–MS global metabolomics data

Y Lu, Z Pang, J Xia - Briefings in Bioinformatics, 2023 - academic.oup.com
Background: Global or untargeted metabolomics is widely used to comprehensively
investigate metabolic profiles under various pathophysiological conditions such as …

[HTML][HTML] Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data

A Marco-Ramell, M Palau-Rodriguez, A Alay… - BMC …, 2018 - Springer
Background Bioinformatic tools for the enrichment of 'omics' datasets facilitate interpretation
and understanding of data. To date few are suitable for metabolomics datasets. The main …

[HTML][HTML] Advantages and pitfalls of mass spectrometry based metabolome profiling in systems biology

I Aretz, D Meierhofer - International journal of molecular sciences, 2016 - mdpi.com
Mass spectrometry-based metabolome profiling became the method of choice in systems
biology approaches and aims to enhance biological understanding of complex biological …

[HTML][HTML] MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data

A Kaever, M Landesfeind, K Feussner, A Mosblech… - Metabolomics, 2015 - Springer
A central aim in the evaluation of non-targeted metabolomics data is the detection of
intensity patterns that differ between experimental conditions as well as the identification of …

MMEASE: online meta-analysis of metabolomic data by enhanced metabolite annotation, marker selection and enrichment analysis

Q Yang, B Li, S Chen, J Tang, Y Li, Y Li, S Zhang… - Journal of …, 2021 - Elsevier
Large-scale and long-term metabolomic studies have attracted widespread attention in the
biomedical studies yet remain challenging despite recent technique progresses. In …

[HTML][HTML] 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 …

Advanced analytical and informatic strategies for metabolite annotation in untargeted metabolomics

Y Cai, Z Zhou, ZJ Zhu - TrAC Trends in Analytical Chemistry, 2023 - Elsevier
Liquid chromatography–mass spectrometry (LC–MS)-based untargeted metabolomics is
constantly challenged by large-scale and unambiguous metabolite annotation in complex …

Enhancing metabolome coverage in data-dependent LC–MS/MS analysis through an integrated feature extraction strategy

Y Hu, B Cai, T Huan - Analytical chemistry, 2019 - ACS Publications
In untargeted metabolomics, conventional data preprocessing software (eg, XCMS, MZmine
2, MS-DIAL) are used extensively due to their high efficiency in metabolic feature extraction …

[HTML][HTML] Bioinformatics: the next frontier of metabolomics

CH Johnson, J Ivanisevic, HP Benton… - Analytical …, 2015 - ACS Publications
Bioinformatic tools are required to carry out essential functions such as statistical analyses
and database functionalities. Now, they are also needed for one of the most difficult tasks …

Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets

M Brown, DC Wedge, R Goodacre, DB Kell… - …, 2011 - academic.oup.com
Motivation: The study of metabolites (metabolomics) is increasingly being applied to
investigate microbial, plant, environmental and mammalian systems. One of the limiting …