The maternal serum metabolome by multisegment injection-capillary electrophoresis-mass spectrometry: a high-throughput platform and standardized data workflow for large-scale epidemiological studies

Shanmuganathan, Meera; Kroezen, Zachary; Gill, Biban; Souza, Russell J. de; Teo, Koon; Atkinson, Stephanie A.; Subbarao, Padmaja; Desai, Dipika; Anand, Sonia S.; Britz‐McKibbin, Philip

doi:10.1038/s41596-020-00475-0

Cited by 39 publications

(50 citation statements)

References 65 publications

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“…In this case, duplicate analysis of each serum filtrate diluted in a distinctive pattern (1:2, 1:1, 2:1) together with a pooled QC sample were acquired in random sequence as shown for alanine and lactic acid in Figure 1A . Data pre-processing in MSI-CE-MS combined both targeted analysis of known serum metabolites, as well as a nontargeted screening strategy to authenticate unknown metabolites from a pooled serum sample as described elsewhere ( Shanmuganathan et al, 2021 ). All serum metabolites were annotated based on their characteristic accurate mass: relative migration time ( m/z :RMT) under positive (p) or negative (n) ion mode detection after rejecting spurious signals, background ions and dataset redundancy ( Saoi et al, 2020 ).…”

Section: Resultsmentioning

confidence: 99%

“…CE-MS based methods have not been widely used within the metabolomics community due to longstanding concerns regarding migration time variability and long-term robustness. However, these technical obstacles can be overcome with implementation of standardized protocols in large-scale metabolomic studies ( Harada et al, 2018 ; Shanmuganathan et al, 2021 ). These protocols have been recently implemented in international ring trials to demonstrate cross-laboratory comparability ( Drouin et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

“…BGE and sheath liquid were degassed before use by sonication for 10 min. Data normalization for peak integration used 20 μM 4-chlorotyrosine (Cl-Tyr) and naphthalene monosulfonic acid (NMS) as internal standards for positive and negative ion mode, respectively with the exception of glucose (total hexose) that used 13 C 6 -glucose as it co-migrates with the electroosmotic flow ( Shanmuganathan et al, 2021 ). A recovery standard, 3-fluorophenylalanine (F-Phe) was added to all serum samples prior to ultrafiltration to monitor for technical precision using control charts.…”

Section: Methodsmentioning

confidence: 99%

“…Yet, separations in LC-MS are generally constrained by lower throughput and complicated data pre-processing when performing non-targeted metabolite profiling (i.e., time alignment, peak picking), where a major fraction of molecular features comprise compounds with unknown chemical structures ( da Silva et al, 2015 ). Alternatively, multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS) offers a multiplexed separation platform for metabolomics ( Kuehnbaum et al, 2013 ) with higher sample throughput, improved quality control, and lower sample volume requirements ( Nori de Macedo et al, 2017 ) Furthermore, customized serial injection configurations accelerate biomarker discovery using novel data workflows to encode mass spectral information temporally within a separation ( DiBattista et al, 2017 ) while providing robust inter-batch adjustment in large-scale metabolomic studies ( Shanmuganathan et al, 2021 ). Although there have been several cross-platform metabolomic analysis involving NMR and LC-MS ( Nevedomskaya et al, 2011 ; Psychogios et al, 2011 ; Bruno et al, 2018 ; Bhatia et al, 2019 ), to the best of our knowledge no study to date has explored the potential benefits of combining CE-MS with NMR methodologies in metabolomics ( Marshall and Powers, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

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A Cross-Platform Metabolomics Comparison Identifies Serum Metabolite Signatures of Liver Fibrosis Progression in Chronic Hepatitis C Patients

Shanmuganathan

Sarfaraz

Kroezen

et al. 2021

Front. Mol. Biosci.

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Metabolomics offers new insights into disease mechanisms that is enhanced when adopting orthogonal instrumental platforms to expand metabolome coverage, while also reducing false discoveries by independent replication. Herein, we report the first inter-method comparison when using multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS) and nuclear magnetic resonance (NMR) spectroscopy for characterizing the serum metabolome of patients with liver fibrosis in chronic hepatitis C virus (HCV) infection (n = 20) and non-HCV controls (n = 14). In this study, 60 and 30 serum metabolites were detected frequently (>75%) with good technical precision (median CV < 10%) from serum filtrate samples (n = 34) when using standardized protocols for MSI-CE-MS and NMR, respectively. Also, 20 serum metabolite concentrations were consistently measured by both methods over a 500-fold concentration range with an overall mean bias of 9.5% (n = 660). Multivariate and univariate statistical analyses independently confirmed that serum choline and histidine were consistently elevated (p < 0.05) in HCV patients with late-stage (F2-F4) as compared to early-stage (F0-F1) liver fibrosis. Overall, the ratio of serum choline to uric acid provided optimal differentiation of liver disease severity (AUC = 0.848, p = 0.00766) using a receiver operating characteristic curve, which was positively correlated with liver stiffness measurements by ultrasound imaging (r = 0.606, p = 0.0047). Moreover, serum 5-oxo-proline concentrations were higher in HCV patients as compared to non-HCV controls (F = 4.29, p = 0.0240) after adjustment for covariates (age, sex, BMI), indicative of elevated oxidative stress from glutathione depletion with the onset and progression of liver fibrosis. Both instrumental techniques enable rapid yet reliable quantification of serum metabolites in large-scale metabolomic studies with good overlap for biomarker replication. Advantages of MSI-CE-MS include greater metabolome coverage, lower operating costs, and smaller sample volume requirements, whereas NMR offers a robust platform supported by automated spectral and data processing software.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Cross-Platform Metabolomics Comparison Identifies Serum Metabolite Signatures of Liver Fibrosis Progression in Chronic Hepatitis C Patients

Shanmuganathan

Sarfaraz

Kroezen

et al. 2021

Front. Mol. Biosci.

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“…Frozen serum samples (START (n=72), CHILD (n=82)) were thawed on ice and an aliquot of 50 µL was transferred into a 0.5 mL centrifuge tubes for sample dilution (a 4-fold) with internal/recovery standards followed by ultrafiltration (3 kDa) to remove protein (i.e., serum filtrate) as described previously [53]. In addition, a pooled quality control (QC) was prepared by combining an equal aliquot of serum samples from START maternal cohort (n=300) that was used to assess technical precision (This was the first cohort to be analyzed in the lab).…”

Section: Methodsmentioning

confidence: 99%

Effects of Diet on the Microbiome and Serum Metabolome of South Asian Infants at 1 Year

Cy¹,

Shanmuganathan²,

Sm³

et al. 2021

Preprint

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Diet is known to affect the gut microbiome and metabolome composition in adults, but this has not been fully explored in infants. Dietary patterns from 1 year-old infants (n=182) from the South Asian Birth Cohort (START) study were compared to gut microbiome alpha and beta diversity and to taxa abundance differences. Diet – serum metabolite associations were identified using multivariate analysis (partial least squares-discriminant analysis, PLS-DA) and univariate analysis (T-Test). Dietary biomarkers identified from START were also examined in a separate cohort of white Caucasian infants (CHILD Cohort Study, n=82). Lastly, the association of diet with gut microbiome and serum biomarkers, considering maternal, perinatal and infant characteristics was investigated using multivariate forward stepwise regression. A dietary pattern characterized by breastfeeding, supplemented by formula and dairy was the strongest predictor of the gut microbiome that also differentiated the serum metabolome of infants. The formula and dairy dietary pattern was associated with a panel of circulating metabolites in both cohorts, including: S-methylcysteine, branched-chain/aromatic amino acids, lysine, dimethylglycine, and methionine. Breastfeeding status, the prominent feature of the dietary pattern, was also associated with a sub-set of serum metabolites in both cohorts. In START, this diet pattern was associated with the metabolites tryptophan betaine, 2-hydroxybutyric acid, tyrosine, phenylalanine, and trimethyl-N-oxide. In the CHILD Cohort Study(CHILD), breastfeeding status was associated with the metabolites aminooctanoic acid, 3-hydroxybutyric acid, and methyl-proline. The results of our study suggest that breastfeeding has the largest effect on the composition of the gut microbiome and the serum metabolome at 1 year, even when solid food diet and other covariates are considered.

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Utility and Advances of Capillary Electrophoresis–Mass Spectrometry for Metabolomics

Zhang¹,

Ramautar²

2022

Capillary Electrophoresis‐Mass Spectrometry for Proteomics and Metabolomics

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The maternal serum metabolome by multisegment injection-capillary electrophoresis-mass spectrometry: a high-throughput platform and standardized data workflow for large-scale epidemiological studies

Cited by 39 publications

References 65 publications

A Cross-Platform Metabolomics Comparison Identifies Serum Metabolite Signatures of Liver Fibrosis Progression in Chronic Hepatitis C Patients

A Cross-Platform Metabolomics Comparison Identifies Serum Metabolite Signatures of Liver Fibrosis Progression in Chronic Hepatitis C Patients

Effects of Diet on the Microbiome and Serum Metabolome of South Asian Infants at 1 Year

Utility and Advances of Capillary Electrophoresis–Mass Spectrometry for Metabolomics

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