Search results for "Targeted metabolomics"
showing 10 items of 11 documents
The Combined Effects of Ethylene and MeJA on Metabolic Profiling of Phenolic Compounds in Catharanthus roseus Revealed by Metabolomics Analysis
2016
Phenolic compounds belong to a class of secondary metabolites and are implicated in a wide range of responsive mechanisms in plants triggered by both biotic and abiotic elicitors. In this study, we approached the combinational effects of ethylene and MeJA (methyl jasmonate) on phenolic compounds profiles and gene expressions in the medicinal plant Catharanthus roseus. In virtue of a widely non-targeted metabolomics method, we identified a total of 34 kinds of phenolic compounds in the leaves, composed by 7 C6C1-, 11 C6C3-, and 16 C6C3C6 compounds. In addition, 7 kinds of intermediates critical for the biosynthesis of phenolic compounds and alkaloids were identified and discussed with phenol…
MetProc: Separating Measurement Artifacts from True Metabolites in an Untargeted Metabolomics Experiment
2019
High-throughput metabolomics using liquid chromatography and mass spectrometry (LC/MS) provides a useful method to identify biomarkers of disease and explore biological systems. However, the majority of metabolic features detected from untargeted metabolomics experiments have unknown ion signatures, making it critical that data should be thoroughly quality controlled to avoid analyzing false signals. Here, we present a postalignment method relying on intermittent pooled study samples to separate genuine metabolic features from potential measurement artifacts. We apply the method to lipid metabolite data from the PREDIMED (PREvención con DIeta MEDi-terránea) study to demonstrate clear remova…
Monitoring of system conditioning after blank injections in untargeted UPLC-MS metabolomic analysis
2019
AbstractUltra-performance liquid chromatography – mass spectrometry (UPLC-MS) is widely used for untargeted metabolomics in biomedical research. To optimize the quality and precision of UPLC-MS metabolomic analysis, evaluation of blank samples for the elimination of background features is required. Although blanks are usually run either at the beginning or at the end of a sequence of samples, a systematic analysis of their effect of the instrument performance has not been properly documented. Using the analysis of two common bio-fluids (plasma and urine), we describe how the injection of blank samples within a sequence of samples may affect both the chromatographic and MS detection performa…
genuMet: distinguish genuine untargeted metabolic features without quality control samples
2019
AbstractMotivationLarge-scale untargeted metabolomics experiments lead to detection of thousands of novel metabolic features as well as false positive artifacts. With the incorporation of pooled QC samples and corresponding bioinformatics algorithms, those measurement artifacts can be well quality controlled. However, it is impracticable for all the studies to apply such experimental design.ResultsWe introduce a post-alignment quality control method called genuMet, which is solely based on injection order of biological samples to identify potential false metabolic features. In terms of the missing pattern of metabolic signals, genuMet can reach over 95% true negative rate and 85% true posit…
Perturbation of metabolic pathways mediates the association of air pollutants with asthma and cardiovascular diseases.
2018
Background: Epidemiologic evidence indicates common risk factors, including air pollution exposure, for respiratory and cardiovascular diseases, suggesting the involvement of common altered molecular pathways. Objectives: The goal was to find intermediate metabolites or metabolic pathways that could be associated with both air pollutants and health outcomes (“meeting-in-the-middle”), thus shedding light on mechanisms and reinforcing causality. Methods: We applied a statistical approach named ‘meet-in-the-middle’ to untargeted metabolomics in two independent case-control studies nested in cohorts on adult-onset asthma (AOA) and cardio-cerebrovascular diseases (CCVD). We compared the results …
Targeted Metabolomics Analyses Reveal Specific Metabolic Alterations in High-Grade Prostate Cancer Patients
2020
Prostate cancer (PCa) is a hormone-dependent tumor characterized by an extremely heterogeneous prognosis. Despite recent advances in partially uncovering some of the biological processes involved in its progression, there is still an urgent need for identifying more accurate and specific prognostic procedures to differentiate between disease stages. In this context, targeted approaches, focused on mapping dysregulated metabolic pathways, could play a critical role in identifying the mechanisms driving tumorigenesis and metastasis. In this study, a targeted analysis of the nuclear magnetic resonance-based metabolomic profile of PCa patients with different tumor grades, guided by transcriptom…
Untargeted Metabolomics Investigation on Selenite Reduction to Elemental Selenium by Bacillus mycoides SeITE01
2021
Bacillus mycoides SeITE01 is an environmental isolate that transforms the oxyanion selenite (SeO32−) into the less bioavailable elemental selenium (Se0) forming biogenic selenium nanoparticles (Bio-SeNPs). In the present study, the reduction of sodium selenite (Na2SeO3) by SeITE01 strain and the effect of SeO32− exposure on the bacterial cells was examined through untargeted metabolomics. A time-course approach was used to monitor both cell pellet and cell free spent medium (referred as intracellular and extracellular, respectively) metabolites in SeITE01 cells treated or not with SeO32−. The results show substantial biochemical changes in SeITE01 cells when exposed to SeO32−. The initial u…
Untargeted metabolomics of fresh and heat treatment Tiger nut ( Cyperus esculentus L. ) milks reveals further insight into food quality and nutrition
2017
Tiger nut (Cyperus esculentus L.) is a crop traditionally grown in Valencia Region (Spain) and other temperate and tropical regions in the world, where its tubers are commonly consumed as tiger nut milk (horchata). Because of their nutritive potential and original taste, these products are beginning to spread internationally and, as consequence, analytical procedures to assess nutritional profiles, quality control issues are acquiring increasing relevance. The main objective of this study was to use an advance analytical method and chemometrics tools to determine if the ultra-high temperature (UHT) treatment necessary to extend the shelf life of tiger nut milk would affect the profile of nu…
High precision mass measurements for wine metabolomics
2014
An overview of the critical steps for the non-targeted Ultra-High Performance Liquid Chromatography coupled with Quadrupole Time-of-Flight Mass Spectrometry (UPLC-Q-ToF-MS) analysis of wine chemistry is given, ranging from the study design, data preprocessing and statistical analyses, to markers identification. UPLC-Q-ToF-MS data was enhanced by the alignment of exact mass data from FTICR-MS, and marker peaks were identified using UPLC-Q-ToF-MS(2). In combination with multivariate statistical tools and the annotation of peaks with metabolites from relevant databases, this analytical process provides a fine description of the chemical complexity of wines, as exemplified in the case of red (P…
Can we Trust Untargeted Metabolomics: Results of the Metabo-ring Initiative, a Large-scale Multi-instruments Inter-laboratoire Study
2013
This work was presented at the 6th Journée Scientifique du Réseau Français de Métabolomique et Fluxomique, Nantes, May 2012 and at the 8th International Conference of the Metabolomics Society, Washington, June 2012This work was presented at the 6th Journée Scientifique du Réseau Français de Métabolomique et Fluxomique, Nantes, May 2012 and at the 8th International Conference of the Metabolomics Society, Washington, June 2012; The metabo-ring initiative brought together five nuclear magnetic resonance instruments (NMR) and 11different mass spectrometers with the objective of assessing the reliability of untargeted metabolomics approaches in obtaining comparable metabolomics profiles. This wa…