Establishment of a New Workflow for the Assessment of Isotopologue Distribution Measurements by Mass Spectrometry

International audienc

Development of reference methods for lipid profile biomarqueurs : application to quality controle in clinical chemistry

En biologie clinique, il est indispensable de disposer de mesures fiables et comparables dans le temps et entre les laboratoires afin de permettre un dépistage et un suivi appropriés des patients. Pour cela, il est indispensable d’établir leur traçabilité métrologique aux unités du système international notamment par des méthodes de référence primaires ou des matériaux de référence certifiés (MRC) d’ordre supérieur. Ces travaux de thèse ont consisté à développer et valider des méthodes de référence pour le cholestérol total, les triglycérides, le HDL-cholestérol et le LDL-cholestérol. Leur valeur ajoutée par rapport à une valeur consensuelle a été démontrée lors d’évaluations externes de la qualité. Elles ont également permis de certifier un MRC qui pourra être utilisé pour le contrôle qualité et/ou l’étalonnage des méthodes de routine. Nous avons montré que le MRC était commutable pour la plupart des méthodes de routine pour les différents biomarqueurs, ce qui a permis de l’utiliser pour évaluer leur justesse. Les méthodes de routine avaient généralement tendance à sous-estimer la concentration en triglycérides (en particulier aux valeurs basses) et à surestimer nettement la concentration de cholestérol total et de LDL-cholestérol (en particulier aux concentrations proches du seuil de décision clinique), ce qui se traduit par une augmentation du nombre de faux-positifs (patients traités à tort). Une approche de correction de non commutabilité a également été proposée afin de permettre l’utilisation de matériaux non commutables pour évaluer la justesse. Pour conclure, ces travaux ont démontré l’importance de disposer de méthodes de référence ainsi que de MRC commutablesReliable measurements in medical biology are essential for early screening and appropriate follow-up of patients. Ensuring metrological traceability of clinical measurements to higher order reference methods or certified reference materials enables to obtain comparable results over time and between different laboratories that could use different methods to quantify the same biomarker.In this study, reference methods were developed and validated for lipid profile biomarkers (total cholesterol, triglycerides, HDL-C, and LDL-C). Their value added in proficiency testing schemes was demonstrated against consensus mean. They were also used to characterize a certified reference material (CRM) that may be used both as quality control and/or calibrator of field methods. The CRM was shown to be commutable for most field methods and lipid profile biomarkers, which proved it was suitable to assess trueness. Results of our multicenter study showed that field methods tend to underestimate triglycerides (particularly at low concentrations) and overestimate total cholesterol and LDL-C (especially around the clinical threshold), resulting in false positives and significant patient misclassifications. An approach of non-commutanility correction was also presented to allow trueness assessment with non-commutable samples. In conclusion, this work highlights the importance of using reference methods and also commutable CRM to rigorously assess accuracy of field methods used in clinical laboratorie

Développement de méthodes de référence pour les biomarqueurs du bilan lipidique : application au contrôle qualité en biologie clinique

Reliable measurements in medical biology are essential for early screening and appropriate follow-up of patients. Ensuring metrological traceability of clinical measurements to higher order reference methods or certified reference materials enables to obtain comparable results over time and between different laboratories that could use different methods to quantify the same biomarker.In this study, reference methods were developed and validated for lipid profile biomarkers (total cholesterol, triglycerides, HDL-C, and LDL-C). Their value added in proficiency testing schemes was demonstrated against consensus mean. They were also used to characterize a certified reference material (CRM) that may be used both as quality control and/or calibrator of field methods. The CRM was shown to be commutable for most field methods and lipid profile biomarkers, which proved it was suitable to assess trueness. Results of our multicenter study showed that field methods tend to underestimate triglycerides (particularly at low concentrations) and overestimate total cholesterol and LDL-C (especially around the clinical threshold), resulting in false positives and significant patient misclassifications. An approach of non-commutanility correction was also presented to allow trueness assessment with non-commutable samples. In conclusion, this work highlights the importance of using reference methods and also commutable CRM to rigorously assess accuracy of field methods used in clinical laboratoriesEn biologie clinique, il est indispensable de disposer de mesures fiables et comparables dans le temps et entre les laboratoires afin de permettre un dépistage et un suivi appropriés des patients. Pour cela, il est indispensable d’établir leur traçabilité métrologique aux unités du système international notamment par des méthodes de référence primaires ou des matériaux de référence certifiés (MRC) d’ordre supérieur. Ces travaux de thèse ont consisté à développer et valider des méthodes de référence pour le cholestérol total, les triglycérides, le HDL-cholestérol et le LDL-cholestérol. Leur valeur ajoutée par rapport à une valeur consensuelle a été démontrée lors d’évaluations externes de la qualité. Elles ont également permis de certifier un MRC qui pourra être utilisé pour le contrôle qualité et/ou l’étalonnage des méthodes de routine. Nous avons montré que le MRC était commutable pour la plupart des méthodes de routine pour les différents biomarqueurs, ce qui a permis de l’utiliser pour évaluer leur justesse. Les méthodes de routine avaient généralement tendance à sous-estimer la concentration en triglycérides (en particulier aux valeurs basses) et à surestimer nettement la concentration de cholestérol total et de LDL-cholestérol (en particulier aux concentrations proches du seuil de décision clinique), ce qui se traduit par une augmentation du nombre de faux-positifs (patients traités à tort). Une approche de correction de non commutabilité a également été proposée afin de permettre l’utilisation de matériaux non commutables pour évaluer la justesse. Pour conclure, ces travaux ont démontré l’importance de disposer de méthodes de référence ainsi que de MRC commutable

Développement de méthodes de référence pour les biomarqueurs du bilan lipidique (application au contrôle qualité en biologie clinique)

En biologie clinique, il est indispensable de disposer de mesures fiables et comparables dans le temps et entre les laboratoires afin de permettre un dépistage et un suivi appropriés des patients. Pour cela, il est indispensable d établir leur traçabilité métrologique aux unités du système international notamment par des méthodes de référence primaires ou des matériaux de référence certifiés (MRC) d ordre supérieur. Ces travaux de thèse ont consisté à développer et valider des méthodes de référence pour le cholestérol total, les triglycérides, le HDL-cholestérol et le LDL-cholestérol. Leur valeur ajoutée par rapport à une valeur consensuelle a été démontrée lors d évaluations externes de la qualité. Elles ont également permis de certifier un MRC qui pourra être utilisé pour le contrôle qualité et/ou l étalonnage des méthodes de routine. Nous avons montré que le MRC était commutable pour la plupart des méthodes de routine pour les différents biomarqueurs, ce qui a permis de l utiliser pour évaluer leur justesse. Les méthodes de routine avaient généralement tendance à sous-estimer la concentration en triglycérides (en particulier aux valeurs basses) et à surestimer nettement la concentration de cholestérol total et de LDL-cholestérol (en particulier aux concentrations proches du seuil de décision clinique), ce qui se traduit par une augmentation du nombre de faux-positifs (patients traités à tort). Une approche de correction de non commutabilité a également été proposée afin de permettre l utilisation de matériaux non commutables pour évaluer la justesse. Pour conclure, ces travaux ont démontré l importance de disposer de méthodes de référence ainsi que de MRC commutablesReliable measurements in medical biology are essential for early screening and appropriate follow-up of patients. Ensuring metrological traceability of clinical measurements to higher order reference methods or certified reference materials enables to obtain comparable results over time and between different laboratories that could use different methods to quantify the same biomarker.In this study, reference methods were developed and validated for lipid profile biomarkers (total cholesterol, triglycerides, HDL-C, and LDL-C). Their value added in proficiency testing schemes was demonstrated against consensus mean. They were also used to characterize a certified reference material (CRM) that may be used both as quality control and/or calibrator of field methods. The CRM was shown to be commutable for most field methods and lipid profile biomarkers, which proved it was suitable to assess trueness. Results of our multicenter study showed that field methods tend to underestimate triglycerides (particularly at low concentrations) and overestimate total cholesterol and LDL-C (especially around the clinical threshold), resulting in false positives and significant patient misclassifications. An approach of non-commutanility correction was also presented to allow trueness assessment with non-commutable samples. In conclusion, this work highlights the importance of using reference methods and also commutable CRM to rigorously assess accuracy of field methods used in clinical laboratoriesDIJON-BU Doc.électronique (212319901) / SudocSudocFranceF

(15)N-NMR-based approach for amino acids-based (13)C-metabolic flux analysis of metabolism

NMR analysis of the isotope incorporation in amino acids can be used to derive information about the topology and operation of cellular metabolism. Although traditionally performed by (1)H and/or (13)C NMR, we present here novel experiments that exploit the (15)N nucleus to derive the same information with increased efficiency. Combined with a novel Hα-(13)CO experiment, we increase the coverage of the isotopic space that can be probed by obtaining the complete distribution of isotopic species for the first two carbons of amino acids in cellular biomass hydrolysates. Our approach was evaluated using as reference material a biologically produced sample containing (15)N-labeled metabolites with fully predictable (13)C-labeling patterns. Results show excellent agreement between measured and expected isotopomer abundances for the different NMR experiments, with an accuracy and precision within 1%. We also demonstrate how these experiments can give detailed information about metabolic fluxes depending on the expression level of a critical enzyme. Hence, exploiting the (15)N labeling of a cellular sample accelerates subsequent analysis of the hydrolyzed biomass and increases the coverage of isotopomers that can be quantified, making it a promising tool to increase the throughput and the resolution of (13)C-fluxomics studies

IsoCor: isotope correction for high-resolution MS labeling experiments

International audienceMass spectrometry (MS) is widely used for isotopic studies of metabolism and other (bio)chemical processes. Quantitative applications in systems and synthetic biology require to correct the raw MS data for the contribution of naturally occurring isotopes. Several tools are available to correct low-resolution MS data, and recent developments made substantial improvements by introducing resolution-dependent correction methods, hence opening the way to the correction of high-resolution MS (HRMS) data. Nevertheless, current HRMS correction methods partly fail to determine which isotopic species are resolved from the tracer isotopologues and should thus be corrected. We present an updated version of our isotope correction software (IsoCor) with a novel correction algorithm which ensures to accurately exploit any chemical species with any isotopic tracer, at any MS resolution. IsoCor v2 also includes a novel graphical user interface for intuitive use by end-users and a command-line interface to streamline integration into existing pipelines

Sink/Source Balance of Leaves Influences Amino Acid Pools and Their Associated Metabolic Fluxes in Winter Oilseed Rape (Brassica napus L.)

International audienceNitrogen remobilization processes from source to sink tissues in plants are determinant for seed yield and their implementation results in a complete reorganization of the primary metabolism during sink/source transition. Here, we decided to characterize the impact of the sink/source balance on amino acid metabolism in the leaves of winter oilseed rape grown at the vegetative stage. We combined a quantitative metabolomics approach with an instationary N-15-labeling experiment by using [N-15](L)-glycine as a metabolic probe on leaf ranks with a gradual increase in their source status. We showed that the acquisition of the source status by leaves was specifically accompanied by a decrease in asparagine, glutamine, proline and S-methyl-l-cysteine sulphoxide contents and an increase in valine and threonine contents. Dynamic analysis of N-15 enrichment and concentration of amino acids revealed gradual changes in the dynamics of amino acid metabolism with respect to the sink/source status of leaf ranks. Notably, nitrogen assimilation into valine, threonine and proline were all decreased in source leaves compared to sink leaves. Overall, our results suggested a reduction in de novo amino acid biosynthesis during sink/source transition at the vegetative stage

¹⁵N‑NMR-Based Approach for Amino Acids-Based ¹³C‑Metabolic Flux Analysis of Metabolism

NMR analysis of the isotope incorporation in amino acids can be used to derive information about the topology and operation of cellular metabolism. Although traditionally performed by ¹H and/or ¹³C NMR, we present here novel experiments that exploit the ¹⁵N nucleus to derive the same information with increased efficiency. Combined with a novel Hα-¹³CO experiment, we increase the coverage of the isotopic space that can be probed by obtaining the complete distribution of isotopic species for the first two carbons of amino acids in cellular biomass hydrolysates. Our approach was evaluated using as reference material a biologically produced sample containing ¹⁵N-labeled metabolites with fully predictable ¹³C-labeling patterns. Results show excellent agreement between measured and expected isotopomer abundances for the different NMR experiments, with an accuracy and precision within 1%. We also demonstrate how these experiments can give detailed information about metabolic fluxes depending on the expression level of a critical enzyme. Hence, exploiting the ¹⁵N labeling of a cellular sample accelerates subsequent analysis of the hydrolyzed biomass and increases the coverage of isotopomers that can be quantified, making it a promising tool to increase the throughput and the resolution of ¹³C-fluxomics studies

Methodology for the Validation of Isotopic Analyses by Mass Spectrometry in Stable-Isotope Labeling Experiments

Stable-isotope labeling experiments (ILEs) are widely used to investigate the topology and operation of metabolic networks. The quality of isotopic data collected in ILEs is of utmost importance to ensure reliable biological interpretations, but current evaluation approaches are limited due to a lack of suitable reference material and relevant evaluation criteria. In this work, we present a complete methodology to evaluate mass spectrometry (MS) methods used for quantitative isotopic studies of metabolic systems. This methodology, based on a biological sample containing metabolites with controlled labeling patterns, exploits different quality metrics specific to isotopic analyses (accuracy and precision of isotopologue masses, abundances, and mass shifts and isotopic working range). We applied this methodology to evaluate a novel LC-MS method for the analysis of amino acids, which was tested on high resolution (Orbitrap operating in full scan mode) and low resolution (triple quadrupole operating in multiple reaction monitoring mode) mass spectrometers. Results show excellent accuracy and precision over a large working range and revealed matrix-specific as well as mode-specific characteristics. The proposed methodology can identify reliable (and unreliable) isotopic data in an easy and straightforward way and efficiently supports the identification of sources of systematic biases as well as of the main factors that influence the overall accuracy and precision of measurements. This approach is generic and can be used to validate isotopic analyses on different matrices, analytical platforms, labeled elements, or classes of metabolites. It is expected to strengthen the reliability of isotopic measurements and thereby the biological value of ILEs