A heuristic method for determining CO2 efficiency in transportation planning

Background CO2 emissions are generally considered the most important indicator to determine the global warming effects. Their evaluation in the case of a transportation infrastructure is generally not easy and could be achieved through a separate balance

Towards a comprehensive characterisation of the human internal chemical exposome: Challenges and perspectives

The holistic characterisation of the human internal chemical exposome using high-resolution mass spectrometry (HRMS) would be a step forward to investigate the environmental AE tiology of chronic diseases with an unprecedented precision. HRMS-based methods are currently operational to reproducibly profile thousands of endogenous metabolites as well as externally-derived chemicals and their biotransformation products in a large number of biological samples from human cohorts. These approaches provide a solid ground for the discovery of unrecognised biomarkers of exposure and metabolic effects associated with many chronic diseases. Nevertheless, some limitations remain and have to be overcome so that chemical exposomics can provide unbiased detection of chemical exposures affecting disease susceptibility in epidemiological studies. Some of these limitations include (i) the lack of versatility of analytical techniques to capture the wide diversity of chemicals; (ii) the lack of analytical sensitivity that prevents the detection of exogenous (and endogenous) chemicals occurring at (ultra) trace levels from restricted sample amounts, and (iii) the lack of automation of the annotation/identification process. In this article, we discuss a number of technological and methodological limitations hindering applications of HRMS-based methods and propose initial steps to push towards a more comprehensive characterisation of the internal chemical exposome. We also discuss other challenges including the need for harmonisation and the difficulty inherent in assessing the dynamic nature of the internal chemical exposome, as well as the need for establishing a strong international collaboration, high level networking, and sustainable research infrastructure. A great amount of research, technological development and innovative bio-informatics tools are still needed to profile and characterise the "invisible" (not profiled), "hidden" (not detected) and "dark" (not annotated) components of the internal chemical exposome and concerted efforts across numerous research fields are paramount

Utilisation de la métabolomique pour l'étude de l'encéphalopathie hépatique et développement de nouvelles approches pour l'acquisition de données par spectrométrie de masse

Untargeted metabolomics aims at studying the whole metabolite content of biological media. This allows to assess phenotypic changes in these samples. In the frame of this work, a cohort of patients suffering from hepatic encephalopathy (HE) was studied using metabolomics, in association with lipidomics and glycomics. HE is a disease still poorly understood, but with high medical and social impact. This work, performed on cerebrospinal fluid and blood samples, demonstrates that HE is associated to an alteration of energy metabolism. Then, considering the limitations of metabolomics raised in our first study, we aim at developing new analytical chemistry methods for metabolomics. We demonstrate that the use of new instrument such as Orbitrap Fusion, which can reach very high resolution, gives acces to isotopic fine structure of metabolites, thus facilitating their identification. Furthermore, the study of ion fragmentation from MS² spectra enabled to better understand the involved mechanisms and should help for interpreting MS² spectra obtained from unknown metabolites. Finally, we showed that improvements achieved with the Orbitrap Fusion instrument in terms of data acquisition speed enables the implementation of new acquisition modes based on multi events MS and MS² acquisition, such as data dependent or data idependant acquisitions. All these improvements in the field of metabolomics should rapidly be applicable to medical cohort analyses.La métabolomique non ciblée est une approche visant à caractériser le contenu métabolique d’un échantillon biologique. Cela permet d’évaluer les changements phénotypiques ayant lieux en son sein. Au cours de cette thèse, une cohorte de patients souffrant d’encéphalopathie hépatique (EH) a été étudiée en métabolomique, en association avec de la lipidomique et de la glycomique. L’EH est une maladie dont les mécanismes sont encore mal compris mais avec un impact important médicale et sociétal. Ces travaux ont montré que l’EH est associée à une altération du métabolisme énergétique observable dans le sang et dans le liquide céphalorachidien. A la suite de cette étude et face aux limites mises en exergue, la suite de ces travaux a visé à développer de nouvelles approches analytiques en métabolomique. Nous ainsi avons montré que l’utilisation de nouveaux instruments de type Orbitrap-Fusion, permettant d’atteindre de très hautes résolutions, donne accès à la structure isotopique fine des métabolites ce qui facilite leur l’identification. L’étude de la fragmentation MS² des ions a permis de mieux comprendre des mécanismes mis en jeu, améliorant l'interprétation des spectres. Enfin, nous avons montré que les améliorations apportées aux instruments, notamment en termes de vitesse d’acquisition, permettaient d’envisager la mise en place de nouveaux modes d’acquisition basés sur l’acquisition multi-événements de spectres MS et MS². Ces améliorations proposées devraient rapidement être utilisables et applicables à l'étude métabolomique de nouvelles cohortes médicales

Application of metabolomics for the study of hepatic encephalopathy and development of new data acquisition protocols in mass spectrometry

La métabolomique non ciblée est une approche visant à caractériser le contenu métabolique d’un échantillon biologique. Cela permet d’évaluer les changements phénotypiques ayant lieux en son sein. Au cours de cette thèse, une cohorte de patients souffrant d’encéphalopathie hépatique (EH) a été étudiée en métabolomique, en association avec de la lipidomique et de la glycomique. L’EH est une maladie dont les mécanismes sont encore mal compris mais avec un impact important médicale et sociétal. Ces travaux ont montré que l’EH est associée à une altération du métabolisme énergétique observable dans le sang et dans le liquide céphalorachidien. A la suite de cette étude et face aux limites mises en exergue, la suite de ces travaux a visé à développer de nouvelles approches analytiques en métabolomique. Nous ainsi avons montré que l’utilisation de nouveaux instruments de type Orbitrap-Fusion, permettant d’atteindre de très hautes résolutions, donne accès à la structure isotopique fine des métabolites ce qui facilite leur l’identification. L’étude de la fragmentation MS² des ions a permis de mieux comprendre des mécanismes mis en jeu, améliorant l'interprétation des spectres. Enfin, nous avons montré que les améliorations apportées aux instruments, notamment en termes de vitesse d’acquisition, permettaient d’envisager la mise en place de nouveaux modes d’acquisition basés sur l’acquisition multi-événements de spectres MS et MS². Ces améliorations proposées devraient rapidement être utilisables et applicables à l'étude métabolomique de nouvelles cohortes médicales.Untargeted metabolomics aims at studying the whole metabolite content of biological media. This allows to assess phenotypic changes in these samples. In the frame of this work, a cohort of patients suffering from hepatic encephalopathy (HE) was studied using metabolomics, in association with lipidomics and glycomics. HE is a disease still poorly understood, but with high medical and social impact. This work, performed on cerebrospinal fluid and blood samples, demonstrates that HE is associated to an alteration of energy metabolism. Then, considering the limitations of metabolomics raised in our first study, we aim at developing new analytical chemistry methods for metabolomics. We demonstrate that the use of new instrument such as Orbitrap Fusion, which can reach very high resolution, gives acces to isotopic fine structure of metabolites, thus facilitating their identification. Furthermore, the study of ion fragmentation from MS² spectra enabled to better understand the involved mechanisms and should help for interpreting MS² spectra obtained from unknown metabolites. Finally, we showed that improvements achieved with the Orbitrap Fusion instrument in terms of data acquisition speed enables the implementation of new acquisition modes based on multi events MS and MS² acquisition, such as data dependent or data idependant acquisitions. All these improvements in the field of metabolomics should rapidly be applicable to medical cohort analyses

Etude expérimentale du métabolisme du coumatétralyl chez le rat (implications dans les mécanismes de résistance aux anticoagulants)

LYON1-BU Santé (693882101) / SudocTOULOUSE-EN Vétérinaire (315552301) / SudocNANTES-Ecole Nat.Vétérinaire (441092302) / SudocSudocFranceF

Investigation of space charge effects and ion trapping capacity on direct introduction ultra‐high‐resolution mass spectrometry workflows for metabolomics

International audienceAbstract Ultra‐high‐resolution mass spectrometry, in the absence of chromatography, is finding its place for direct analyses of highly complex mixtures, such as those encountered during untargeted metabolomics screening. Advances, however, have been tempered by difficulties such as uneven signal suppression experienced during electrospray ionization. Moreover, ultra‐high‐resolution mass spectrometers that use Orbitrap and ICR analyzers both suffer from limited ion trapping capacities, owing principally to space‐charge effects. This study has evaluated and contrasted the above two types of Fourier transform mass spectrometers for their abilities to detect and identify by accurate mass measurement, small molecule metabolites present in complex mixtures. For these direct introduction studies, the Orbitrap Fusion showed a major advantage in terms of speed of analysis, enabling detection of 218 of 440 molecules (<2 ppm error, 500 000 resolution at m / z 200) present in a complex mixture in 5 min. This approach is the most viable for high‐throughput workflows, such as those used in investigations involving very large cohorts of metabolomics samples. From the same mixture, 183 unique molecules were observed by FT‐ICR in the broadband mode, but this number was raised to 235 when “selected ion monitoring‐stitching” (SIM‐stitching) was employed (<0.1 ppm error, 7 T magnet with dynamic harmonization cell, 1.8 million resolution at m / z 200, both cases). SIM‐stitching FT‐ICR thus offered the most complete detection, which may be of paramount importance in situations where it is essential to obtain the most complete metabolic profile possible. This added completeness, however, came at the cost of a more lengthy analysis time (120 min including manual treatment). Compared to the data presented here, future automation of processing, plus the use of absorption mode detection, segmented ion detection (stepwise detection of smaller width m / z sections), and higher magnetic field strengths, can substantially reduce FT‐ICR acquisition times

Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: Where do we stand?

National audienceTypical mass spectrometry (MS) based untargeted metabolomics protocols are tedious as well as time and sample-consuming. In particular, they often rely on "full-scan-only" analyses using liquid chromatography (LC) coupled to high resolution mass spectrometry (HRMS) from which metabolites of interest are first highlighted, and then tentatively identified by using targeted MS/MS experiments. However, this situation is evolving with the emergence of integrated HRMS based-data acquisition protocols able to perform multi-event acquisitions. Most of these protocols, referring to as data dependent and data independent acquisition (DDA and DIA, respectively), have been initially developed for proteomic applications and have recently demonstrated their applicability to biomedical studies. In this context, the aim of this article is to take stock of the progress made in the field of DDA- and DIA-based protocols, and evaluate their ability to change conventional metabolomic and lipidomic data acquisition workflows, through a review of HRMS instrumentation, DDA and DIA workflows, and also associated informatics tools

Comparative Evaluation of Data Dependent and Data Independent Acquisition Workflows Implemented on an Orbitrap Fusion for Untargeted Metabolomics

International audienceConstant improvements to the Orbitrap mass analyzer, such as acquisition speed, resolution, dynamic range and sensitivity have strengthened its value for the large-scale identification and quantification of metabolites in complex biological matrices. Here, we report the development and optimization of Data Dependent Acquisition (DDA) and Sequential Window Acquisition of all THeoretical fragment ions (SWATH-type) Data Independent Acquisition (DIA) workflows on a high-field Orbitrap FusionTM TribridTM instrument for the robust identification and quantification of metabolites in human plasma. By using a set of 47 exogenous and 72 endogenous molecules, we compared the efficiency and complementarity of both approaches. We exploited the versatility of this mass spectrometer to collect meaningful MS/MS spectra at both high- and low-mass resolution and various low-energy collision-induced dissociation conditions under optimized DDA conditions. We also observed that complex and composite DIA-MS/MS spectra can be efficiently exploited to identify metabolites in plasma thanks to a reference tandem spectral library made from authentic standards while also providing a valuable data resource for further identification of unknown metabolites. Finally, we found that adding multi-event MS/MS acquisition did not degrade the ability to use survey MS scans from DDA and DIA workflows for the reliable absolute quantification of metabolites down to 0.05 ng/mL in human plasma

An approach to overtopping assessment for a resilient railway at Dawlish, UK

Following regular disruptions to the Southwest rail network, especially during the storm events of 2014, Arup was appointed by Network Rail (NR) to complete a feasibility review, optioneering and single option development for the Dawlish railway section from Colonnade to Coastguards (C2C) including Dawlish Station and Dawlish Water River basin. The objective of the project was to assess resilience options to wave overtopping, determine feasibility of each option and analyse their respective advantages to select the most appropriate option. The criteria included resilience performance, sustainability, buildability, programme, adaptation and whole life cost. This paper focuses on wave overtopping as a key driver of the design process with important lessons learned from a large physical modelling campaign. A staged approach was developed; it involved development of specific criteria for the assessment of the wave overtopping performance; analytical estimations of overtopping performance based on Eurotop, 2018; testing in a 2D physical model to assess the sensitivity to varying seawall configurations; testing of the initial scheme in a 3D physical model; design optimisation in the 3D physical model; tests of the existing/’do nothing’ in 2D or 3Dto highlight the benefits of the proposed scheme; development of an adaptive design

Mechanistic study of competitive releases of H2O, NH3 and CO2 from deprotonated aspartic and glutamic acids: Role of conformation

The aims of this study were to highlight the impact of minor structural differences (e.g. an aminoacid side chain enlargement by one methylene group), on ion dissociation under collision-induced dissociation conditions, and to determine the underlying chemical mechanisms. Therefore, we compared fragmentations of deprotonated aspartic and glutamic acids generated in negative electrospray ionization. Energy-resolved mass spectrometry breakdown curves were recorded and MS3 experiments performed on an Orbitrap Fusion for high-resolution and high-mass accuracy measurements. Activated fragmentations were performed using both the resonant and non-resonant excitation modes (i.e., CID and HCD, respectively) in order to get complementary information on the competitive and consecutive dissociative pathways. These experiments showed a specific loss of ammonia from the activated aspartate but not from the activated glutamate. We mainly focused on this specific observed loss from aspartate. Two different mechanisms based on intramolecular reactions (similar to those occurring in organic chemistry) were proposed, such as intramolecular elimination (i.e. Ei-like) and nucleophilic substitution (i.e. SNi-like) reactions, respectively, yielding anions as fumarate and α lactone from a particular conformation with the lowest steric hindrance (i.e. with antiperiplanar carboxyl groups). The detected deaminated aspartate anion can then release CO2 as observed in the MS3 experimental spectra. However, quantum calculations did not indicate the formation of such a deaminated aspartate product ion without loss of carbon dioxide. Actually, calculations displayed the double neutral (NH3+CO2) loss as a concomitant pathway (from a particular conformation) with relative high activation energy instead of a consecutive process. This disagreement is apparent since the concomitant pathway may be changed into consecutive dissociations according to the collision energy i.e., at higher collision energy and at lower excitation conditions, respectively. The latter takes place by stabilization of the deaminated aspartate solvated with two residual molecules of water (present in the collision cell). This desolvated anion formed is an α lactone substituted by a methylene carboxylate group. The vibrational excitation acquired by [(D−H)−NH3]−during its isolation is enough to allow its prompt decarboxylation with a barrier lower than 8.4 kJ/mol. In addition, study of glutamic acid-like diastereomers constituted by a cyclopropane, hindering any side chain rotation, confirms the impact of the three-dimensional geometry on fragmentation pathways. A significant specific loss of water is only observed for one of these diastereomers. Other experiments, such as stable isotope labeling, need to be performed to elucidate all the observed losses from activated aspartate and glutamate anions. These first mechanistic interpretations enhance understanding of this dissociative pathway and underline the necessity of studying fragmentation of a large number of various compounds to implement properly new algorithms for de novo elucidation of unknown metabolites