MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 49(W1), P. W388 - W396

Published: April 28, 2021

Since its first release over a decade ago, the MetaboAnalyst web-based platform has become widely used for comprehensive metabolomics data analysis and interpretation. Here we introduce version 5.0, aiming to narrow gap from raw functional insights global based on high-resolution mass spectrometry (HRMS). Three modules have been developed help achieve this goal, including: (i) LC-MS Spectra Processing module which offers an easy-to-use pipeline that can perform automated parameter optimization resumable significantly lower barriers LC-MS1 spectra processing; (ii) Functional Analysis expands previous MS Peaks Pathways allow users intuitively select any peak groups of interest evaluate their enrichment potential functions as defined by metabolic pathways metabolite sets; (iii) Meta-Analysis combine multiple datasets obtained under complementary conditions or similar studies arrive at insights. There are many other new including weighted joint-pathway analysis, data-driven network batch effect correction, merging technical replicates, improved compound name matching, etc. The web interface, graphics underlying codebase also refactored improve performance user experience. At end session, now easily switch compatible more streamlined analysis. 5.0 is freely available https://www.metaboanalyst.ca.

Language: Английский

---

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

Metabolites, Journal Year: 2018, Volume and Issue: 8(2), P. 31 - 31

Published: May 10, 2018

The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the unknown compounds. Only by elucidating metabolites first is it possible biologically interpret complex systems, map compounds pathways create reliable predictive metabolic models for translational clinical research. These strategies include construction quality tandem spectral databases such as coalition MassBank repositories investigations MS/MS matching confidence. present silico fragmentation tools MS-FINDER, CFM-ID, MetFrag, ChemDistiller CSI:FingerID can annotate from existing structure have been used CASMI (critical assessment molecule identification) contests. Furthermore, use retention time liquid chromatography utility collision cross-section modelling ion mobility experiments covered. Workflows published examples successfully annotated included.

Language: Английский

---

Metabolomics in cancer research and emerging applications in clinical oncology

CA A Cancer Journal for Clinicians, Journal Year: 2021, Volume and Issue: 71(4), P. 333 - 358

Published: May 13, 2021

Abstract Cancer has myriad effects on metabolism that include both rewiring of intracellular to enable cancer cells proliferate inappropriately and adapt the tumor microenvironment, changes in normal tissue metabolism. With recognition fluorodeoxyglucose‐positron emission tomography imaging is an important tool for management many cancers, other metabolites biological samples have been spotlight diagnosis, monitoring, therapy. Metabolomics global analysis small molecule like ‐omics technologies can provide critical information about state are otherwise not apparent. Here, authors review how therapies interact with at cellular systemic levels. An overview metabolomics provided a focus currently available they applied clinical translational research setting. The also discuss could be further leveraged future improve patients cancer.

Language: Английский

---

Review of recent developments in GC–MS approaches to metabolomics-based research

Metabolomics, Journal Year: 2018, Volume and Issue: 14(11)

Published: Nov. 1, 2018

Language: Английский

---

Cardiovascular Metabolomics

Circulation Research, Journal Year: 2018, Volume and Issue: 122(9), P. 1238 - 1258

Published: April 26, 2018

Disturbances in cardiac metabolism underlie most cardiovascular diseases. Metabolomics, one of the newer omics technologies, has emerged as a powerful tool for defining changes both global and cardiac-specific that occur across spectrum disease states. Findings from metabolomics studies have contributed to better understanding metabolic heart failure ischemic identified new biomarkers. As technologies advance, field continues evolve rapidly. In this review, we will discuss current state including consideration various platforms elements study design; emerging utility stable isotopes flux studies; use understand specific diseases, with an emphasis on recent advances field.

Language: Английский

---

Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics

Analytical Chemistry, Journal Year: 2018, Volume and Issue: 91(1), P. 704 - 742

Published: Nov. 19, 2018

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTAccelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, Silico Databases, ChemometricsJean-Luc Wolfender*Jean-Luc WolfenderSchool Pharmaceutical Sciences, EPGL, University Geneva, Lausanne, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland*E-mail: [email protected]. Phone: 41-22 379-3385.More by Jean-Luc WolfenderView Biographyhttp://orcid.org/0000-0002-0125-952X, Jean-Marc NuzillardJean-Marc NuzillardInstitut de Chimie Moléculaire Reims, UMR CNRS 7312, Université Reims Champagne Ardenne, 51687 Cedex 2, FranceMore NuzillardView Biographyhttp://orcid.org/0000-0002-5120-2556, Justin J. van der HooftJustin HooftBioinformatics Group, Wageningen University, 6708 PB, The NetherlandsMore HooftView Biographyhttp://orcid.org/0000-0002-9340-5511, Jean-Hugues RenaultJean-Hugues RenaultInstitut RenaultView Biography, Samuel BertrandSamuel BertrandGroupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Nantes, 44035 FranceThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, BertrandView Biographyhttp://orcid.org/0000-0002-5934-7012Cite this: Anal. Chem. 2019, 91, 1, 704–742Publication Date (Web):November 19, 2018Publication History Published online19 November 2018Published inissue 2 January 2019https://pubs.acs.org/doi/10.1021/acs.analchem.8b05112https://doi.org/10.1021/acs.analchem.8b05112review-articleACS PublicationsCopyright © 2018 American Chemical SocietyRequest reuse permissionsArticle Views7046Altmetric-Citations159LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum full text article downloads since 2008 (both PDF HTML) across all institutions individuals. These metrics regularly updated to reflect usage leading up last few days.Citations number other articles citing this article, calculated Crossref daily. Find more information about citation counts.The Altmetric Attention Score is a quantitative measure attention that research has received online. Clicking on donut icon will load page at altmetric.com with additional details score social media presence for given article. how calculated. Share Add toView InAdd Full Text ReferenceAdd Description ExportRISCitationCitation abstractCitation referencesMore Options onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Mass spectrometry,Metabolism,Metabolomics,Molecules,Nuclear magnetic resonance spectroscopy Get e-Alerts

Language: Английский

---

Metabolomics: A Way Forward for Crop Improvement

Metabolites, Journal Year: 2019, Volume and Issue: 9(12), P. 303 - 303

Published: Dec. 14, 2019

Metabolomics is an emerging branch of “omics” and it involves identification quantification metabolites chemical footprints cellular regulatory processes in different biological species. The metabolome the total metabolite pool organism, which can be measured to characterize genetic or environmental variations. plays a significant role exploring environment–gene interactions, mutant characterization, phenotyping, biomarkers, drug discovery. promising approach decipher various metabolic networks that are linked with biotic abiotic stress tolerance plants. In this context, metabolomics-assisted breeding enables efficient screening for yield crops at level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance (HPLC), direct flow injection (DFI) mass spectrometry, have sped up profiling. Presently, integrating post-genomics tools has enabled dissection phenotypic association crop This review provides insight into state-of-the-art plant improvement. Here, we describe workflow research focusing on elucidation mechanisms Furthermore, potential improvement its future applications speed also discussed. Mention been made possible bottlenecks prospects metabolomics.

Language: Английский

---

From correlation to causation: analysis of metabolomics data using systems biology approaches

Metabolomics, Journal Year: 2018, Volume and Issue: 14(4)

Published: Feb. 27, 2018

Metabolomics is a well-established tool in systems biology, especially the top–down approach. experiments often results discovery studies that provide intriguing biological hypotheses but rarely offer mechanistic explanation of such findings. In this light, interpretation metabolomics data can be boosted by deploying biology approaches. This review aims to an overview approaches are relevant and discuss some successful applications these methods. We most recent tools field metabolomics, as network inference analysis, metabolic modelling pathways analysis. ample applied address problems. The characteristics application discussed also comparative manner. Systems biology-enhanced analysis insights into molecular mechanisms originating observed profiles enhance scientific impact studies.

Language: Английский

---

Suspect and non-targeted screening of chemicals of emerging concern for human biomonitoring, environmental health studies and support to risk assessment: From promises to challenges and harmonisation issues

Environment International, Journal Year: 2020, Volume and Issue: 139, P. 105545 - 105545

Published: April 29, 2020

Large-scale suspect and non-targeted screening approaches based on high-resolution mass spectrometry (HRMS) are today available for chemical profiling holistic characterisation of biological samples. These advanced techniques allow the simultaneous detection a large number features, including markers human exposure. Such interest biomonitoring, environmental health studies support to risk assessment. Furthermore, these have promising capability detect chemicals emerging concern (CECs), document extent exposure, generate new research hypotheses provide early warning policy. Whilst growing importance in environment food safety areas, respectively, CECs remain poorly addressed field biomonitoring. This shortfall is due several scientific methodological reasons, global lack harmonisation. In this context, main aim paper present an overview basic principles, promises challenges applied samples as specific introduce major specificities compared other fields. Focused liquid chromatography coupled HRMS-based data acquisition methods, addresses all steps analytical workflows. Beyond general picture, activities carried out topic within particular framework European Human Biomonitoring initiative (project HBM4EU, 2017–2021) described, with emphasis harmonisation measures.

Language: Английский

---

New software tools, databases, and resources in metabolomics: updates from 2020

Metabolomics, Journal Year: 2021, Volume and Issue: 17(5)

Published: May 1, 2021

Language: Английский

---