Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950–Metabolites in Frozen Human Plasma

Journal of Lipid Research, Journal Year: 2017, Volume and Issue: 58(12), P. 2275 - 2288

Published: Oct. 7, 2017

As the lipidomics field continues to advance, self-evaluation within community is critical. Here, we performed an interlaboratory comparison exercise for using Standard Reference Material (SRM) 1950-Metabolites in Frozen Human Plasma, a commercially available reference material. The study comprised 31 diverse laboratories, with each laboratory different workflow. A total of 1,527 unique lipids were measured across all laboratories and consensus location estimates associated uncertainties determined 339 these at sum composition level by five or more participating laboratories. These evaluated detected SRM 1950 serve as community-wide benchmarks intra- quality control method validation. analyses nonstandardized laboratory-independent workflows. locations also compared previous examination LIPID MAPS consortium. While central theme was provide values help harmonize lipids, lipid mediators, precursor measurements community, it initiated stimulate discussion regarding areas need improvement.

Language: Английский

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LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data

BMC Bioinformatics, Journal Year: 2017, Volume and Issue: 18(1)

Published: July 10, 2017

Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to great potential as candidates for elucidating biomarkers pathway perturbations associated with disease. Methods expanding coverage of the lipidome increase likelihood biomarker discovery could lead more comprehensive understanding disease etiology. We introduce LipidMatch, an R-based tool lipid identification liquid chromatography tandem mass spectrometry workflows. LipidMatch currently has over 250,000 species spanning 56 types contained in silico fragmentation libraries. Unique libraries, compared other open source software, include oxidized lipids, bile acids, sphingosines, previously uncharacterized adducts, including ammoniated cardiolipins. uses rule-based identification. For each type, user can select which fragments must be observed Rule-based allows correct annotation based on observed, unlike typical solely spectral similarity scores, where over-reporting structural details that not conferred by data is common. Another unique feature ranking identifications a given sum fragment intensities. candidate, intensities experimental exact matches expected summed. The greatest summed intensity using this algorithm were comparable software annotations, MS-DIAL Greazy. example, features from all 3 92% fatty acyl constituents corroborated at least one positive mode 98% negative ion mode. users annotate across wide range high resolution experiments, imaging direct infusion experiments employing chromatography. leverages most extensive libraries freely available software. When integrated into larger lipidomics workflow, may probability finding lipid-based determining etiology covering greater portion does over-report biologically relevant identified molecules.

Language: Английский

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Lipidomics from sample preparation to data analysis: a primer

Analytical and Bioanalytical Chemistry, Journal Year: 2019, Volume and Issue: 412(10), P. 2191 - 2209

Published: Dec. 10, 2019

Abstract Lipids are amongst the most important organic compounds in living organisms, where they serve as building blocks for cellular membranes well energy storage and signaling molecules. Lipidomics is science of large-scale determination individual lipid species, underlying analytical technology that used to identify quantify lipidome generally mass spectrometry (MS). This review article provides an overview crucial steps MS-based lipidomics workflows, including sample preparation, either liquid–liquid or solid-phase extraction, derivatization, chromatography, ion-mobility spectrometry, MS, data processing by various software packages. The associated concepts discussed from a technical perspective terms their application. Furthermore, this sheds light on recent advances field its current limitations. Particular emphasis placed quality assurance adequate reporting; some common pitfalls discussed, along with how circumvent them.

Language: Английский

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Analytical Challenges and Recent Advances in Mass Spectrometry Based Lipidomics

Analytical Chemistry, Journal Year: 2017, Volume and Issue: 90(1), P. 374 - 397

Published: Nov. 22, 2017

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTAnalytical Challenges and Recent Advances in Mass Spectrometry Based LipidomicsYepy H. Rustam† Gavin E. Reid*†‡§View Author Information† Department of Biochemistry Molecular Biology, University Melbourne, Parkville, Victoria 3010, Australia‡ School Chemistry, Australia§ Bio21 Science Biotechnology Institute, Australia*E-mail: [email protected]Cite this: Anal. Chem. 2018, 90, 1, 374–397Publication Date (Web):November 22, 2017Publication History Published online8 December 2017Published inissue 2 January 2018https://pubs.acs.org/doi/10.1021/acs.analchem.7b04836https://doi.org/10.1021/acs.analchem.7b04836review-articleACS PublicationsCopyright © 2017 American Chemical SocietyRequest reuse permissionsArticle Views6605Altmetric-Citations223LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum full text article downloads since November 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 by 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:Ionization,Ions,Lipidomics,Lipids,Mass spectrometry Get e-Alerts

Language: Английский

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A metabolome atlas of the aging mouse brain

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Oct. 15, 2021

Abstract The mammalian brain relies on neurochemistry to fulfill its functions. Yet, the complexity of metabolome and changes during diseases or aging remain poorly understood. Here, we generate a atlas wildtype mouse from 10 anatomical regions spanning adolescence old age. We combine data three assays structurally annotate 1,547 metabolites. Almost all metabolites significantly differ between age groups, but not by sex. A shift in sphingolipid patterns related myelin remodeling is accompanied large other metabolic pathways. Functionally (brain stem, cerebrum cerebellum) are also metabolically similar. In cerebrum, correlations markedly weaken adulthood, whereas at age, cross-region correlation reflect decreased segregation. show that can be mapped existing gene protein atlases. publicly available ( https://mouse.atlas.metabolomics.us/ ) serves as foundation dataset for future metabolomic studies.

Language: Английский

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The underappreciated diversity of bile acid modifications

Cell, Journal Year: 2024, Volume and Issue: 187(7), P. 1801 - 1818.e20

Published: March 1, 2024

The repertoire of modifications to bile acids and related steroidal lipids by host microbial metabolism remains incompletely characterized. To address this knowledge gap, we created a reusable resource tandem mass spectrometry (MS/MS) spectra filtering 1.2 billion publicly available MS/MS for bile-acid-selective ion patterns. Thousands are distributed throughout animal human bodies as well cultures. We employed library identify polyamine amidates, prevalent in carnivores. They present humans, their levels alter with diet change from Mediterranean typical American diet. This work highlights the existence many more acid than previously recognized value leveraging public large-scale untargeted metabolomics data discover metabolites. availability modification-centric will inform future studies investigating roles health disease.

Language: Английский

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Sensitization of cancer cells to ferroptosis coincident with cell cycle arrest

Cell chemical biology, Journal Year: 2023, Volume and Issue: 31(2), P. 234 - 248.e13

Published: Nov. 13, 2023

Language: Английский

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Selenium reduction of ubiquinone via SQOR suppresses ferroptosis

Nature Metabolism, Journal Year: 2024, Volume and Issue: 6(2), P. 343 - 358

Published: Feb. 13, 2024

Language: Английский

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High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage

Environmental Science & Technology, Journal Year: 2024, Volume and Issue: 58(29), P. 12784 - 12822

Published: July 10, 2024

In the modern "omics" era, measurement of human exposome is a critical missing link between genetic drivers and disease outcomes. High-resolution mass spectrometry (HRMS), routinely used in proteomics metabolomics, has emerged as leading technology to broadly profile chemical exposure agents related biomolecules for accurate measurement, high sensitivity, rapid data acquisition, increased resolution space. Non-targeted approaches are increasingly accessible, supporting shift from conventional hypothesis-driven, quantitation-centric targeted analyses toward data-driven, hypothesis-generating exposome-wide profiling. However, HRMS-based exposomics encounters unique challenges. New analytical computational infrastructures needed expand analysis coverage through streamlined, scalable, harmonized workflows pipelines that permit longitudinal tracking, retrospective validation, multi-omics integration meaningful health-oriented inferences. this article, we survey literature on state-of-the-art technologies, review current informatic pipelines, provide an up-to-date reference exposomic chemists, toxicologists, epidemiologists, care providers, stakeholders health sciences medicine. We propose efforts benchmark fit-for-purpose platforms expanding space, including gas/liquid chromatography-HRMS (GC-HRMS LC-HRMS), discuss opportunities, challenges, strategies advance burgeoning field exposome.

Language: Английский

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FSP1-mediated lipid droplet quality control prevents neutral lipid peroxidation and ferroptosis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 6, 2025

ABSTRACT Lipid droplets (LDs) are organelles that store and supply lipids based on cellular needs. While mechanisms preventing oxidative damage to membrane phospholipids established, the vulnerability of LD neutral peroxidation protective unknown. Here, we identify LD-localized Ferroptosis Suppressor Protein 1 (FSP1) as a critical regulator prevents lipid by recycling coenzyme Q10 (CoQ10) its lipophilic antioxidant form. Lipidomics reveal FSP1 loss leads accumulation oxidized triacylglycerols cholesteryl esters, biochemical reconstitution with CoQ10 NADH suppresses triacylglycerol in vitro . Notably, polyunsaturated fatty acid (PUFA)-rich enhance cancer cell sensitivity inducing PUFA-rich LDs triggers LD-initiated ferroptosis when activity is impaired. These findings uncover first quality control pathway, wherein maintains integrity prevent buildup induction ferroptosis.

Language: Английский

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