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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Collision cross section compendium to annotate and predict multi-omic compound identities

Chemical Science, Journal Year: 2018, Volume and Issue: 10(4), P. 983 - 993

Published: Nov. 27, 2018

The Unified Compendium is an online interactive tool that utilizes ion mobility collision cross sections to annotate biochemical molecules.

Language: Английский

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Trapped ion mobility spectrometry and PASEF enable in-depth lipidomics from minimal sample amounts

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Jan. 16, 2020

Abstract A comprehensive characterization of the lipidome from limited starting material remains very challenging. Here we report a high-sensitivity lipidomics workflow based on nanoflow liquid chromatography and trapped ion mobility spectrometry (TIMS). Taking advantage parallel accumulation–serial fragmentation (PASEF), fragment average 15 precursors in each 100 ms TIMS scans, while maintaining full resolution co-eluting isomers. The acquisition speed over Hz allows us to obtain MS/MS spectra vast majority isotope patterns. Analyzing 1 µL human plasma, PASEF increases number identified lipids more than three times standard TIMS-MS/MS, achieving attomole sensitivity. Building high intra- inter-laboratory precision accuracy collisional cross sections (CCS), compile 1856 lipid CCS values liver cancer cells. Our study establishes analysis paves way for sensitive, mobility-enhanced four dimensions.

Language: Английский

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Large-scale lipid analysis with C=C location and sn-position isomer resolving power

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Jan. 17, 2020

Lipids play a pivotal role in biological processes and lipid analysis by mass spectrometry (MS) has significantly advanced lipidomic studies. While the structure specificity of proves to be critical for studying functions lipids, current mainstream methods large-scale can only identify classes fatty acyl chains, leaving C=C location sn-position unidentified. In this study, combining photochemistry tandem MS we develop simple but effective workflow enable near-complete characterization with powerful capability identifying location(s) sn-position(s) simultaneously. Quantitation isomers at multiple levels is achieved different subtypes human breast cancer cells are successfully discriminated. Remarkably, lung tissues distinguished from adjacent normal using quantitative results both isomers.

Language: Английский

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Chemical Discovery in the Era of Metabolomics

Journal of the American Chemical Society, Journal Year: 2020, Volume and Issue: 142(20), P. 9097 - 9105

Published: April 10, 2020

Untargeted metabolomics aims to quantify the complete set of metabolites within a biological system, most commonly by liquid chromatography/mass spectrometry (LC/MS). Since nearly inception field, compound identification has been widely recognized as rate-limiting step experimental workflow. In spite exponential increases in size metabolomic databases, which now contain MS/MS spectra for over half million reference compounds, chemical structures still cannot be confidently assigned many signals typical LC/MS dataset. The purpose this Perspective is consider why rates continue low untargeted metabolomics. One rationalization that naturally occurring detected are true "novel" compounds have yet incorporated into databases. An alternative possibility, however, research data do not provide database matches because informatic artifacts, contaminants, and signal redundancies. Increasing evidence suggests that, at least some sample types, unidentifiable result from latter rather than new originating specimen being measured. implications these observations on discovery discussed.

Language: Английский

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Brain lipidomics: From functional landscape to clinical significance

Science Advances, Journal Year: 2022, Volume and Issue: 8(37)

Published: Sept. 16, 2022

Lipids are crucial components of cellular function owing to their role in membrane formation, intercellular signaling, energy storage, and homeostasis maintenance. In the brain, lipid dysregulations have been associated with etiology progression neurodegeneration other neurological pathologies. Hence, brain lipids emerging as important potential targets for early diagnosis prognosis diseases. This review aims highlight significance usefulness lipidomics diagnosing treating We explored alterations diseases, paying attention organ-specific characteristics functions lipids. As recent advances would impossible without analytical techniques, we provide up-to-date information on mass spectrometric approaches integrative analysis omic approaches. Last, present applications combined artificial intelligence techniques interdisciplinary collaborative research diseases clinical heterogeneities.

Language: Английский

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Ion mobility mass spectrometry in the omics era: Challenges and opportunities for metabolomics and lipidomics

Mass Spectrometry Reviews, Journal Year: 2021, Volume and Issue: 41(5), P. 722 - 765

Published: Feb. 1, 2021

Abstract Researchers worldwide are taking advantage of novel, commercially available, technologies, such as ion mobility mass spectrometry (IM‐MS), for metabolomics and lipidomics applications in a variety fields including life, biomedical, food sciences. IM‐MS provides three main technical advantages over traditional LC‐MS workflows. Firstly, addition to mass, allows collision cross‐section values be measured metabolites lipids, physicochemical identifier related the chemical shape an analyte that increases confidence identification. Second, peak capacity signal‐to‐noise, improving fingerprinting well quantification, better defining spatial localization lipids biological samples. Third, can coupled with various fragmentation modes, adding new tools improve structural characterization molecular annotation. Here, we review state‐of‐the‐art technologies approaches utilized support assess challenges opportunities this growing field.

Language: Английский

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Mass Spectrometry-Based Techniques to Elucidate the Sugar Code

Chemical Reviews, Journal Year: 2021, Volume and Issue: 122(8), P. 7840 - 7908

Published: Sept. 7, 2021

Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about “sugar code” biological roles these molecules. The reason glycobiology lags behind its counterparts dealing with acids proteins lies complexity carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only configuration a single stereocenter, combined vast possibilities connect monosaccharide units, lead an immense variety isomers, poses formidable challenge conventional mass spectrometry. In recent years, however, combination innovative ion activation methods, commercialization mobility–mass spectrometry, progress gas-phase spectroscopy, advances computational chemistry have led revolution spectrometry-based glycan analysis. present review focuses on above techniques expanded traditional glycomics toolkit provided spectacular insight into structure fascinating biomolecules. To emphasize specific challenges associated them, major classes mammalian discussed separate sections. By doing so, we aim put spotlight most important element glycobiology: themselves.

Language: Английский

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Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section

Chemical Reviews, Journal Year: 2023, Volume and Issue: 123(6), P. 2902 - 2949

Published: Feb. 24, 2023

The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field structural biology over past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, all three these can be used discern information. While charge are determined in (MS), it is addition that enables separation isomeric isobaric ions direct elucidation which reaped huge benefits for biology. In this review, where we focus on analysis proteins their complexes, outline typical features an experiment from preparation samples, creation ions, different spectrometers. We describe interpretation data terms protein conformation how compared other sources use computational tools. benefit coupling activation via collisions gas or surfaces photons photoactivation detailed reference recent examples. And finally, afforded by experiments when study conformationally dynamic intrinsically disordered proteins.

Language: Английский

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Single-cell lipidomics enabled by dual-polarity ionization and ion mobility-mass spectrometry imaging

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 25, 2023

Single-cell (SC) analysis provides unique insight into individual cell dynamics and cell-to-cell heterogeneity. Here, we utilize trapped ion mobility separation coupled with dual-polarity ionization mass spectrometry imaging (MSI) to enable high-throughput in situ profiling of the SC lipidome. Multimodal imaging, which dual-polarity-mode MSI is used perform serial data acquisition runs on cells, significantly enhanced lipidome coverage. High-spatial resolution SC-MSI identifies both inter- intracellular lipid heterogeneity; this heterogeneity further explicated by Uniform Manifold Approximation Projection machine learning-driven classifications. We characterize alteration response stearoyl-CoA desaturase 1 inhibition and, additionally, identify cell-layer specific distribution patterns mouse cerebellar cortex. This integrated multimodal technology enables high-resolution spatial mapping intercellular heterogeneity, remodeling induced pharmacological intervention, region-specific diversity within tissue.

Language: Английский

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