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Article ; Online: Balancing the Equation: A Natural History of Trimethylamine and Trimethylamine-

Loo, Ruey Leng / Chan, Queenie / Nicholson, Jeremy K / Holmes, Elaine

2022 Volume 21, Issue 3, Page(s) 560–589

Abstract: Trimethylamine (TMA) and ... ...

Abstract	Trimethylamine (TMA) and its
MeSH term(s)	Animals ; Bacteria/metabolism ; Methylamines ; Oxides
Chemical Substances	Methylamines ; Oxides ; trimethyloxamine (FLD0K1SJ1A) ; trimethylamine (LHH7G8O305)
Language	English
Publishing date	2022-02-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00851
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Article ; Online: Unravelling inulin molecules in food sources using a matrix-assisted laser desorption/ionization magnetic resonance mass spectrometry (MALDI-MRMS) pipeline.

Chin, Sung-Tong / Boughton, Berin A / Gay, Melvin C L / Russell, Alyce C / Wang, Yimin / Nambiar, Vimalnath / McHenry, Mark P / Holmes, Elaine / Nicholson, Jeremy K / Loo, Ruey Leng

Food research international (Ottawa, Ont.)

2024 Volume 184, Page(s) 114276

Abstract: Inulin, a polysaccharide characterized by a β-2,1 fructosyl-fructose structure terminating in a glucosyl moiety, is naturally present in plant roots and tubers. Current methods provide average degrees of polymerization (DP) but lack information on the ... ...

Abstract	Inulin, a polysaccharide characterized by a β-2,1 fructosyl-fructose structure terminating in a glucosyl moiety, is naturally present in plant roots and tubers. Current methods provide average degrees of polymerization (DP) but lack information on the distribution and absolute concentration of each DP. To address this limitation, a reproducible (CV < 10 %) high throughput (<2 min/sample) MALDI-MRMS approach capable of characterizing and quantifying inulin molecules in plants using matched-matrix consisting of α-cyano-4-hydroxycinnamic acid butylamine salt (CHCA-BA), chicory inulin-
MeSH term(s)	Inulin ; Helianthus ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Garlic ; Antioxidants ; Biological Products ; Cynara scolymus ; Magnetic Resonance Spectroscopy ; Lasers
Chemical Substances	Inulin (9005-80-5) ; Antioxidants ; Biological Products
Language	English
Publishing date	2024-03-25
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1111695-x
ISSN	1873-7145 ; 0963-9969
ISSN (online)	1873-7145
ISSN	0963-9969
DOI	10.1016/j.foodres.2024.114276
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Article: Balancing the Equation: A Natural History of Trimethylamine and Trimethylamine-N-oxide

Loo, Ruey Leng / Chan, Queenie / Nicholson, Jeremy K. / Holmes, Elaine

Journal of proteome research. 2022 Feb. 10, v. 21, no. 3

2022

Abstract: Trimethylamine (TMA) and its N-oxide (TMAO) are ubiquitous in prokaryote and eukaryote organisms as well as in the environment, reflecting their fundamental importance in evolutionary biology, and their diverse biochemical functions. Both metabolites ... ...

Abstract	Trimethylamine (TMA) and its N-oxide (TMAO) are ubiquitous in prokaryote and eukaryote organisms as well as in the environment, reflecting their fundamental importance in evolutionary biology, and their diverse biochemical functions. Both metabolites have multiple biological roles including cell-signaling. Much attention has focused on the significance of serum and urinary TMAO in cardiovascular disease risk, yet this is only one of the many facets of a deeper TMA–TMAO partnership that reflects the significance of these metabolites in multiple biological processes spanning animals, plants, bacteria, and fungi. We report on analytical methods for measuring TMA and TMAO and attempt to critically synthesize and map the global functions of TMA and TMAO in a systems biology framework.
Keywords	blood serum ; cardiovascular diseases ; equations ; eukaryotic cells ; evolutionary biology ; metabolites ; natural history ; prokaryotic cells ; proteome ; research ; risk ; trimethylamine
Language	English
Dates of publication	2022-0210
Size	p. 560-589.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00851
Database	NAL-Catalogue (AGRICOLA)

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Article: Plasma lipoprotein subclass variation in middle-aged and older adults: Sex-stratified distributions and associations with health status and cardiometabolic risk factors.

Masuda, Reika / Wist, Julien / Lodge, Samantha / Kimhofer, Torben / Hunter, Michael / Hui, Jennie / Beilby, John P / Burnett, John R / Dwivedi, Girish / Schlaich, Markus P / Bong, Sze-How / Loo, Ruey Leng / Holmes, Elaine / Nicholson, Jeremy K / Yeap, Bu B

Journal of clinical lipidology

2023 Volume 17, Issue 5, Page(s) 677–687

Abstract: Background: Circulating lipids and lipoproteins mediate cardiovascular risk, however routine plasma lipid biochemistry provides limited information on pro-atherogenic remnant particles.: Objective: We analysed plasma lipoprotein subclasses including ... ...

Abstract	Background: Circulating lipids and lipoproteins mediate cardiovascular risk, however routine plasma lipid biochemistry provides limited information on pro-atherogenic remnant particles. Objective: We analysed plasma lipoprotein subclasses including very low-density and intermediate-density lipoprotein (VLDL and IDL); and assessed their associations with health and cardiometabolic risk. Methods: From 1,976 community-dwelling adults aged 45-67 years, 114/1071 women (10.6%) and 153/905 men (16.9%) were categorised as very healthy. Fasting plasma lipoprotein profiles comprising 112 parameters were measured using Results: HDL cholesterol was higher, and IDL and VLDL cholesterol and triglycerides lower, in very healthy women compared to other women, and women compared to men. IDL and VLDL cholesterol and triglyceride were lower in very healthy men compared to other men. HDL cholesterol and apolipoprotein (apo) A-I were inversely, and IDL and VLDL cholesterol, apoB-100, and apoB-100/apoA-I ratio directly associated with body mass index (BMI) in women and men. In women, LDL, IDL and VLDL cholesterol increased with age. Women with diabetes and cardiovascular disease had higher cholesterol, triglycerides, phospholipids and free cholesterol across IDL and VLDL fractions, with similar trends for men with diabetes. Conclusion: Lipoprotein subclasses and density fractions, and their lipid and apolipoprotein constituents, are differentially distributed by sex, health status and BMI. Very healthy women and men are distinguished by favorable lipoprotein profiles, particularly lower concentrations of VLDL and IDL, providing reference intervals for comparison with general populations and adults with cardiometabolic risk factors.
MeSH term(s)	Male ; Middle Aged ; Humans ; Female ; Aged ; Apolipoprotein B-100 ; Cholesterol, VLDL ; Cholesterol, HDL ; Cardiometabolic Risk Factors ; Lipoproteins ; Lipoproteins, VLDL ; Cholesterol ; Triglycerides ; Diabetes Mellitus ; Health Status
Chemical Substances	Apolipoprotein B-100 ; Cholesterol, VLDL ; Cholesterol, HDL ; Lipoproteins ; Lipoproteins, VLDL ; Cholesterol (97C5T2UQ7J) ; Triglycerides
Language	English
Publishing date	2023-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2365061-8
ISSN	1876-4789 ; 1933-2874
ISSN (online)	1876-4789
ISSN	1933-2874
DOI	10.1016/j.jacl.2023.06.004
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Article ; Online: Targeted lipidomics coupled with machine learning for authenticating the provenance of chicken eggs.

Chin, Sung-Tong / Hoerlendsberger, Gerhard / Wong, Kok Wai / Li, Sirui / Bong, Sze How / Whiley, Luke / Wist, Julien / Masuda, Reika / Greeff, Johan / Holmes, Elaine / Nicholson, Jeremy K / Loo, Ruey Leng

Food chemistry

2022 Volume 410, Page(s) 135366

Abstract: Free-range eggs are ethically desirable but as with all high-value commercial products, the establishment of provenance can be problematic. Here, we compared a simple one-step isopropanol method to a two-step methyl-tert-butyl ether method for extracting ...

Abstract	Free-range eggs are ethically desirable but as with all high-value commercial products, the establishment of provenance can be problematic. Here, we compared a simple one-step isopropanol method to a two-step methyl-tert-butyl ether method for extracting lipid species in chicken egg yolks before liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The isopropanol method extracted 937 lipid species from 20 major lipid subclasses with high reproducibility (CV < 30 %). Machine learning techniques could differentiate conventional cage, barn, and free-range eggs using an external test dataset with an accuracy of 0.94, 0.82, and 0.82, respectively. Lipid species that differentiated cage eggs were predominantly phosphocholines and phosphoethanolamines whilst the free-range egg lipidomes were dominated by acylglycerides with up to three fatty acids. The lipid profiles were found to be characteristic of the cage, barns, and free-range eggs. The lipidomic analysis together with the statistical modeling approach thus provides an efficient tool for verifying the provenance of conventional chicken eggs.
MeSH term(s)	Animals ; Chromatography, Liquid/methods ; Lipidomics ; Chickens ; Tandem Mass Spectrometry/methods ; 2-Propanol ; Reproducibility of Results ; Eggs/analysis ; Lipids ; Chromatography, High Pressure Liquid/methods
Chemical Substances	2-Propanol (ND2M416302) ; Lipids
Language	English
Publishing date	2022-12-30
Publishing country	England
Document type	Journal Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2022.135366
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Article ; Online: Integrative Molecular Structure Elucidation and Construction of an Extended Metabolic Pathway Associated with an Ancient Innate Immune Response in COVID-19 Patients.

Sala, Samuele / Nitschke, Philipp / Masuda, Reika / Gray, Nicola / Lawler, Nathan G / Wood, James M / Buckler, Joshua N / Berezhnoy, Georgy / Bolaños, Jose / Boughton, Berin A / Lonati, Caterina / Rössler, Titus / Singh, Yogesh / Wilson, Ian D / Lodge, Samantha / Morillon, Aude-Claire / Loo, Ruey Leng / Hall, Drew / Whiley, Luke /

Evans, Gary B / Grove, Tyler L / Almo, Steven C / Harris, Lawrence D / Holmes, Elaine / Merle, Uta / Trautwein, Christoph / Nicholson, Jeremy K / Wist, Julien

Journal of proteome research

2024 Volume 23, Issue 3, Page(s) 956–970

Abstract: We present compelling evidence for the existence of an extended innate viperin-dependent pathway, which provides crucial evidence for an adaptive response to viral agents, such as SARS-CoV-2. We show the in vivo biosynthesis of a family of novel ... ...

Abstract	We present compelling evidence for the existence of an extended innate viperin-dependent pathway, which provides crucial evidence for an adaptive response to viral agents, such as SARS-CoV-2. We show the in vivo biosynthesis of a family of novel endogenous cytosine metabolites with potential antiviral activities. Two-dimensional nuclear magnetic resonance (NMR) spectroscopy revealed a characteristic spin-system motif, indicating the presence of an extended panel of urinary metabolites during the acute viral replication phase. Mass spectrometry additionally enabled the characterization and quantification of the most abundant serum metabolites, showing the potential diagnostic value of the compounds for viral infections. In total, we unveiled ten nucleoside (cytosine- and uracil-based) analogue structures, eight of which were previously unknown in humans
MeSH term(s)	Humans ; COVID-19 ; Molecular Structure ; SARS-CoV-2 ; Immunity, Innate ; Cytosine ; Metabolic Networks and Pathways ; Antiviral Agents
Chemical Substances	Cytosine (8J337D1HZY) ; Antiviral Agents
Language	English
Publishing date	2024-02-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00654
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Article ; Online: Correction to "Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection".

Kimhofer, Torben / Lodge, Samantha / Whiley, Luke / Gray, Nicola / Loo, Ruey Leng / Lawler, Nathan G / Nitschke, Philipp / Bong, Sze-How / Morrison, David L / Begum, Sofina / Richards, Toby / Yeap, Bu B / Smith, Chris / Smith, Kenneth G C / Holmes, Elaine / Nicholson, Jeremy K

Journal of proteome research

2021 Volume 20, Issue 6, Page(s) 3400

Language	English
Publishing date	2021-05-05
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00273
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Article ; Online: Low Volume in Vitro Diagnostic Proton NMR Spectroscopy of Human Blood Plasma for Lipoprotein and Metabolite Analysis: Application to SARS-CoV-2 Biomarkers.

Lodge, Samantha / Nitschke, Philipp / Loo, Ruey Leng / Kimhofer, Torben / Bong, Sze-How / Richards, Toby / Begum, Sofina / Spraul, Manfred / Schaefer, Hartmut / Lindon, John C / Holmes, Elaine / Nicholson, Jeremy K

Journal of proteome research

2021 Volume 20, Issue 2, Page(s) 1415–1423

Abstract: The utility of low sample volume in vitro diagnostic (IVDr) proton nuclear magnetic resonance ( ...

Abstract	The utility of low sample volume in vitro diagnostic (IVDr) proton nuclear magnetic resonance (
MeSH term(s)	Adult ; Aged ; Biomarkers/blood ; Biomarkers/metabolism ; COVID-19/blood ; COVID-19/diagnosis ; COVID-19/virology ; Female ; Humans ; Lipoproteins/blood ; Lipoproteins/metabolism ; Male ; Metabolomics/methods ; Middle Aged ; Protein Interaction Maps ; Proteomics/methods ; Proton Magnetic Resonance Spectroscopy/methods ; SARS-CoV-2/metabolism ; SARS-CoV-2/physiology
Chemical Substances	Biomarkers ; Lipoproteins
Language	English
Publishing date	2021-01-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.0c00815
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Article: Demographic, Health and Lifestyle Factors Associated with the Metabolome in Older Women.

Navarro, Sandi L / Nagana Gowda, G A / Bettcher, Lisa F / Pepin, Robert / Nguyen, Natalie / Ellenberger, Mathew / Zheng, Cheng / Tinker, Lesley F / Prentice, Ross L / Huang, Ying / Yang, Tao / Tabung, Fred K / Chan, Queenie / Loo, Ruey Leng / Liu, Simin / Wactawski-Wende, Jean / Lampe, Johanna W / Neuhouser, Marian L / Raftery, Daniel

Metabolites

2023 Volume 13, Issue 4

Abstract: Demographic and clinical factors influence the metabolome. The discovery and validation of disease biomarkers are often challenged by potential confounding effects from such factors. To address this challenge, we investigated the magnitude of the ... ...

Abstract	Demographic and clinical factors influence the metabolome. The discovery and validation of disease biomarkers are often challenged by potential confounding effects from such factors. To address this challenge, we investigated the magnitude of the correlation between serum and urine metabolites and demographic and clinical parameters in a well-characterized observational cohort of 444 post-menopausal women participating in the Women's Health Initiative (WHI). Using LC-MS and lipidomics, we measured 157 aqueous metabolites and 756 lipid species across 13 lipid classes in serum, along with 195 metabolites detected by GC-MS and NMR in urine and evaluated their correlations with 29 potential disease risk factors, including demographic, dietary and lifestyle factors, and medication use. After controlling for multiple testing (FDR < 0.01), we found that log-transformed metabolites were mainly associated with age, BMI, alcohol intake, race, sample storage time (urine only), and dietary supplement use. Statistically significant correlations were in the absolute range of 0.2-0.6, with the majority falling below 0.4. Incorporation of important potential confounding factors in metabolite and disease association analyses may lead to improved statistical power as well as reduced false discovery rates in a variety of data analysis settings.
Language	English
Publishing date	2023-04-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo13040514
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Article ; Online: A feasibility study of metabolic phenotyping of dried blood spot specimens in rural Chinese women exposed to household air pollution.

Loo, Ruey Leng / Lu, Qinwei / Carter, Ellison M / Liu, Si / Clark, Sierra / Wang, Yulan / Baumgartner, Jill / Tang, Huiru / Chan, Queenie

Journal of exposure science & environmental epidemiology

2020 Volume 31, Issue 2, Page(s) 328–344

Abstract: Background: Exposure-response studies and policy evaluations of household air pollution (HAP) are limited by current methods of exposure assessment which are expensive and burdensome to participants.: Methods: We collected 152 dried blood spot (DBS) ... ...

Abstract	Background: Exposure-response studies and policy evaluations of household air pollution (HAP) are limited by current methods of exposure assessment which are expensive and burdensome to participants. Methods: We collected 152 dried blood spot (DBS) specimens during the heating and non-heating seasons from 53 women who regularly used biomass-burning stoves for cooking and heating. Participants were enrolled in a longitudinal study in China. Untargeted metabolic phenotyping of DBS were generated using ultra-high performance liquid chromatography coupled with mass spectrometry to exemplify measurement precision and assessment for feasibility to detect exposure to HAP, evaluated by season (high pollution vs. low pollution) and measured personal exposure to fine particulate matter <2.5 μm diameters (PM Results: Metabolites e.g., amino acids, acyl-carnitines, lyso-phosphorylcholines, sphinganine, and choline were detected in the DBS specimens. Our approach is capable of detecting the differences in personal exposure to HAP whilst showing high analytical reproducibility, coefficient of variance (CV) <15%, meeting the U.S. Food and Drug Administration criteria. Conclusions: Our results provide a proof of principle that high-resolution metabolic phenotypic data can be generated using a simple DBS extraction method thus suitable for exposure studies in remote, low-resource settings where the collection of serum and plasma is logistically challenging or infeasible. The analytical run time (19 min/specimen) is similar to most global phenotyping methods and therefore suitable for large-scale application.
MeSH term(s)	Air Pollutants/analysis ; Air Pollution/analysis ; Air Pollution, Indoor/analysis ; China ; Cooking ; Environmental Exposure/analysis ; Feasibility Studies ; Female ; Humans ; Longitudinal Studies ; Particulate Matter/analysis ; Reproducibility of Results ; Rural Population
Chemical Substances	Air Pollutants ; Particulate Matter
Language	English
Publishing date	2020-07-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2218551-3
ISSN	1559-064X ; 1559-0631
ISSN (online)	1559-064X
ISSN	1559-0631
DOI	10.1038/s41370-020-0252-0
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