ArticleMetabolites2020
Comparison of Three Untargeted Data Processing Workflows for Evaluating LC-HRMS Metabolomics Data.
Article in Metabolites, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Cultivar to chemotype: characterizing complex botanicals with mass spectrometry metabolomics.Natural product reports · 2026Review
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- A stochastic approach for parameter optimization of feature detection algorithms for non-target screening in mass spectrometry.Analytical and bioanalytical chemistry · 2025Article
- Current Bioinformatics Tools in Precision Oncology.MedComm · 2025Review
- Chloroplastic ascorbate modifies plant metabolism and may act as a metabolite signal regardless of oxidative stress.Plant physiology · 2024Article
- Comparison of reversed-phase, hydrophilic interaction, and porous graphitic carbon chromatography columns for an untargeted toxicometabolomics study in pooled human liver microsomes, rat urine, and rat plasma.Metabolomics : Official journal of the Metabolomic Society · 2024Article
- A Metabolomics-Based Study on the Discriminative Classification Models and Toxicological Mechanism of Estazolam Fatal Intoxication.Metabolites · 2023Article
- In Vitro and In Vivo Toxicometabolomics of the Synthetic Cathinone PCYP Studied by Means of LC-HRMS/MS.Metabolites · 2022Article
- Altered metabolic pathways elucidated via untargeted in vivo toxicometabolomics in rat urine and plasma samples collected after controlled application of a human equivalent amphetamine dose.Archives of toxicology · 2021Article
- Metabolomic Studies for the Evaluation of Toxicity Induced by Environmental Toxicants on Model Organisms.Metabolites · 2021Review
- Phase I In Vitro Metabolic Profiling of the Synthetic Cannabinoid Receptor Agonists CUMYL-THPINACA and ADAMANTYL-THPINACA.Metabolites · 2021Article
- Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics-Standardization, Coverage, and Throughput.Analytical chemistry · 2021Review
- Article
- Chemometric-Guided Approaches for Profiling and Authenticating Botanical Materials.Frontiers in nutrition · 2021Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The evaluation of liquid chromatography high-resolution mass spectrometry (LC-HRMS) raw data is a crucial step in untargeted metabolomics studies to minimize false positive findings. A variety of commercial or open source software solutions are available for such data processing. This study aims to compare three different data processing workflows (Compound Discoverer 3.1, XCMS Online combined with MetaboAnalyst 4.0, and a manually programmed tool using R) to investigate LC-HRMS data of an untargeted metabolomics study. Simple but highly standardized datasets for evaluation were prepared by incubating pHLM (pooled human liver microsomes) with the synthetic cannabinoid A-CHMINACA. LC-HRMS analysis was performed using normal- and reversed-phase chromatography followed by full scan MS in positive and negative mode. MS/MS spectra of significant features were subsequently recorded in a separate run. The outcome of each workflow was evaluated by its number of significant features, peak shape quality, and the results of the multivariate statistics. Compound Discoverer as an all-in-one solution is characterized by its ease of use and seems, therefore, suitable for simple and small metabolomic studies. The two open source solutions allowed extensive customization but particularly, in the case of R, made advanced programming skills necessary. Nevertheless, both provided high flexibility and may be suitable for more complex studies and questions.
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Registered trials
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