Method Development In Metabolomics
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Method Development In Metabolomics
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Author : Oliver Alka
language : en
Publisher:
Release Date : 2023
Method Development In Metabolomics written by Oliver Alka and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023 with categories.
The field of metabolomics is concerned with analyzing data from high-throughput experiments. Its objective is the identification, quantification, and elucidation of the function and interaction of small molecules in a biological system. The prevalent methods used in metabolomics are nuclear magnetic resonance spectroscopy and mass spectrometry. A typical mass spectrometry metabolomics analysis workflow is composed of several steps. First, biological samples are measured using liquid chromatography and mass spectrometry. Second, computational mass spectrometry is used to analyze the acquired data. The results are then stored in a human- readable format, statistically post-processed, and visualized. The driving force of the field is the development of new methods on the analytical and computational side to reach the above-mentioned aims. Nonetheless, there are still some major unsolved issues at different stages of the analysis workflow. Controlling the false-discovery rate (FDR) is well established in other fields (i.e., proteomics), but so far, methods are lacking in the field of metabolomics. This seriously limits the confidence in reported identifications and quantifications, and manual assessment is still common practice. In recent years different methods have been established for untargeted approaches. However, in terms of targeted strategies, the lack of robust FDR estimators prevented the field from obtaining highly confident quantifications. Progress in automating the manual process is substantial to advance targeted metabolomics research and allow proper high-throughput analysis. We established an automated, FDR-controlled targeted analysis workflow that enables a robust FDR estimation for the first time, thus improving the comparability of results in the metabolomics field. Another critical aspect of scientific research is representing and sharing analysis results based on the FAIR principles. The FAIR principles stand for findable, accessible, interoperable, and reusable. In 2014, the human-readable file format MzTab was introduced in the proteomics and metabolomics fields to enable the distribution of analysis results in a standardized open format. However, in recent years, the limitations of this format regarding metabolomics data have become apparent. As part of the Proteomics Standard Initiative, we designed the improved standard MzTab-M that focuses on interoperability and reusability and integrated it into our OpenMS software framework. Metabolomics has a massive range of applications and can be used to answer a variety of scientific questions. The field attempts to answer individual data- and objective-related issues by developing new problem-specific post-processing methods, as we show based on an example in the area of food chemistry. In recent years, the production of primary cacao products, such as cacao butter, moved from Europe to the cacao-producing countries. This leads to the challenge of shifting the quality assessment from raw to primary products to uphold the quality standards and control in the European market. To this end, we provided the basis for such a method by using biomarker identification and machine learning. Using a regression method, we were able to assess the shell quantity in a mixture of bean and shell and, with it, the quality of the product.
Analytical Method Development In Liquid Chromatography Mass Spectrometry Based Metabolomics
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Author :
language : en
Publisher:
Release Date : 2021
Analytical Method Development In Liquid Chromatography Mass Spectrometry Based Metabolomics written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with categories.
Method Development For Human Plasma Metabolomics Using Liquid Chromatography Mass Spectrometry
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Author : Xinru Liu
language : en
Publisher:
Release Date : 2007
Method Development For Human Plasma Metabolomics Using Liquid Chromatography Mass Spectrometry written by Xinru Liu and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with Blood plasma categories.
Instrument And Method Development For Targeted And Untargeted Metabolomics
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Author : Mitchell R. Helling
language : en
Publisher:
Release Date : 2019
Instrument And Method Development For Targeted And Untargeted Metabolomics written by Mitchell R. Helling and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019 with Biotechnology categories.
Bioanalytical chemistry for the measurement of metabolically relevant molecules provides deep insight into the organism under study in the field known as metabolomics. Mass spectrometry based metabolomics methods were developed for the study of the peculiar prokaryote Gemmata obscuriglobus, the thermal tolerance of the bumble bee, Bombus vosnesenskii, and the study of metabolites in soil systems. Investigation of an instrumental platform aimed to improve metabolomic measurements was also conducted. A targeted quantitative metabolomic study of sterol biosynthesis in a unique prokaryotic organism was undertaken. Sterols have traditionally been considered unique to eukaryotic life, with the few prokaryotes found to produce sterols thought to have acquired sterol biosynthesis capability through lateral gene transfer from eukaryotes. Gemmata obscuriglobus (G. obscuriglobus) is a prokaryote that challenges this once clear distinction between eukaryotes and prokaryotes as a bacterium with several interesting eukaryotic characteristics, including sterol biosynthesis, making it a curious specimen for evolutionary study. Quantitative analysis of two sterol isomers, lanosterol and parkeol, and their biosynthetic precursor squalene, revealed evidence of a sterol based negative feedback mechanism, squalene lipotoxicity, and support of sterol essentiality in G. obscuriglobus in this collaborative study. To date, this is the first report of sterol essentiality and of a sterol feedback mechanism in a prokaryote. A mass spectrometry based untargeted metabolomics workflow was developed and implemented to discover biomarkers related to the thermal tolerance differences observed between high latitude and low latitude bumble bees, Bombus vosnesenskii. The head, thorax, and abdomen were sectioned and individually subjected to an untargeted metabolomics analysis to provide an overview of the small molecules throughout the body sections consistently correlated with these groups differing in their thermal tolerance. Our measurements found several sugar alcohol molecules known to be cryo-protectants to be more abundant in all body segments of the higher latitude bees than the low latitude bees, providing novel insight into the thermal tolerance of this bumble bee. Untargeted analysis of complex samples, such as metabolite extracts, requires instrumentation capable of detecting a wide array of compounds over large concentration ranges with minimal bias toward analyte mass and type to accurately portray differences between samples. Chromatographic separation coupled to mass spectrometry has proven itself as a powerful tool for such analyses. The two major instrumental platforms used in metabolomics are liquid chromatography with mass spectrometry (LC-MS) and gas chromatography with mass spectrometry (GC-MS); however, they are not without limitations. The nature of the ionization interface between LC and MS makes it susceptible to ion suppression and poor sensitivity for nonpolar compounds. On the other hand, the gas phase separation of gas chromatography requires analytes to have sufficient volatility and thermal stability, limiting the molecular mass of metabolites than can be analyzed, and requiring chemical derivatization of polar molecules in each sample prior to analysis, providing a potential for the formation of problematic artefacts for some species. It has long been recognized that efficient interfacing of liquid chromatography (LC) to mass spectrometry (MS) via electron ionization (EI) embodies the best attributes of each existing instrumental platform and combines them into one system. An LC-EI-MS system was constructed and evaluated. The distribution and diversity of microbes in the environment is a challenging area of study that has historically been limited to focused geographical locations for targeted investigations. Recent advances in DNA sequencing technologies and data processing have expanded the realm of ecological hypothesis that can be probed, as well as enabling large scale studies aimed at generating new hypotheses. Through collaborative efforts among expert researchers of several different fields, including biology, chemistry, ecology, geology, botany, and bioinformatics, the Microbial Ecology Collaborative (MEC) project at the University of Wyoming aims to study microbes and their effects (consequences) on ecosystems throughout the state of Wyoming. Untargeted metabolomics with mass spectrometry aims to uncover the functional aspects of these microbes in the environment (i.e., what are they doing, eating, etc.). Preliminary soil metabolomics methodology was developed, and data is presented for the differential analysis of metabolites in Wyoming soils.
Metabolomics
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Author :
language : en
Publisher:
Release Date : 2019
Metabolomics written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019 with categories.
Development Of Metabolomics And Lipidomics Workflows For Phosphorylated Metabolites Using Ultra High Performance Liquid Chromatography With Tandem Mass Spectrometry
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Author : Peng Li
language : en
Publisher:
Release Date : 2022
Development Of Metabolomics And Lipidomics Workflows For Phosphorylated Metabolites Using Ultra High Performance Liquid Chromatography With Tandem Mass Spectrometry written by Peng Li and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022 with categories.
Over the last decades, system biology and multi-omics have become an emerging field in life science. With the development of analytical instruments, especially the mass spectrometry (MS), MS based metabolomics are widely utilized to understanding the metabolic status. Due to significantly different properties of lipids, lipidomics became more and more an independent research discipline. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the most popular analytical platform in metabolomics and lipidomics. Recent progress in bioinformatical approaches has also facilitated the bottlenecking data processing steps. Although some widely used methods were established for general metabolomics and lipidomics analysis, there are still some challenging analytes like phosphorylated metabolites/lipids, which showed compromised performance. Through highly regulated phosphorylation and dephosphorylation by enzymes, phosphorylated metabolites/lipids regulate many important cellular processes. Despite their importance, the performance of their current analytical methods is not satisfying. Generally, analysis of phosphorylated analytes by LC-MS/MS face the following challenges, including low abundance, low extraction recovery, instability, regioisomers, availability of standards, etc. In order to address these issues, we developed new methods based on phosphate methylation. Accordingly, complete workflows from sample preparation to data processing were developed and validated in biological matrix. In the 1st project, a targeted LC-MS/MS method of fatty acyl-CoAs (acyl-CoAs) with different chain lengths was established. Acyl-CoAs are central metabolic intermediates in numerous biological processes. Due to diverse fatty acyl compositions, acyl-CoAs vary greatly in polarity, which poses great challenges to their chromatographic separation. Currently, short chain acyl-CoAs are separated by HILIC or acidic RP-LC, while medium-, long- and very long-chain acyl-CoAs are analysed in basic RP-LC. Additionally, carryover in LC-MS/MS instrumentation requires extra flushing/cleaning procedures. To address these problems, we developed phosphate methylation strategy for acyl-CoAs. In the sample preparation, mixed-mode SPE was optimized to be compatible with methylation. SRM transitions in MS detection was constructed with fragmentation rule for all methylated acyl-CoAs. Uniformly 13C labelled yeast extract was used as internal standards for accurate quantification. Odd chain and stable isotope labelled analogs were used as surrogate calibrators. The LOQs were between 16.9 nM and 4.2 nM. The method was applied in cultured HeLa cells and human platelets of coronary artery disease patients. The results showed that the established method can be used to profile acyl-CoAs in biological samples. In the 2nd project, an isomer selective LC-MS/MS method of PIPx was developed. PIPx is a family of low abundant phospholipids commonly found in eukaryotic cells. Starting from phosphoinositol (PI), PIPx family consists of three lipid classes (PIP, PIP2, and PIP3) according to phosphorylation degree. There are three distinct regioisomers in each class of PIP and PIP2. As phospholipids, PIPx has two fatty acyl groups at the sn1 and sn2 position of a glycerol backbone. Currently, methods capable of regioisomer separation and fatty acyl coverage are still missing. To develop a comprehensive method, we utilized polysaccharide chiral column with data independent acquisition technique. Stable isotope labelled PIPx were characterized and used as internal standards. The established method was applied to several biological samples, including NIST SRM1950 plasma, Pichia Pastoris, and cultured HeLa cells. The results indicate this method could effectively monitor PIPx profiles in real samples and facilitate our understanding of physiological and pathological conditions. In the 3rd and 4th project, improved LC-MS/MS methods of IPx and SPx were developed. Compared to PIPx and acyl-CoAs, IPx and SPx are more polar and hydrophilic. To apply the phosphate methylation strategy, a new derivatization solvent mixture was developed and optimized. To improve extraction recovery, an extraction kit compromised of TiO2 and centrifuge filter was established. Differential isotope labelling methylation was utilized to generate stable isotope labelled analogs in both projects (internal standards in IPx project, surrogate calibrators in SPx project). Cholesterol-ether bonded RP column was used to separate IPx regioisomers, especially I(1,4,5)P3. Porous graphite carbon column was used to separate SPx in glycolysis pathway. After validation in biological matrix, the methods were applied in different biological samples, including NIST SRM1950 plasma, cultured HeLa cells, and human platelets.
Metabolomics In Practice
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Author : Michael Lämmerhofer
language : en
Publisher: John Wiley & Sons
Release Date : 2013-02-14
Metabolomics In Practice written by Michael Lämmerhofer and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-02-14 with Science categories.
Unlike other handbooks in this emerging field, this guide focuses on the challenges and critical parameters in running a metabolomics study, including such often-neglected issues as sample preparation, choice of separation and detection method, recording and evaluating data as well as method validation. By systematically covering the entire workflow, from sample preparation to data processing, the insight and advice offered here helps to clear the hurdles in setting up and running a successful analysis, resulting in high-quality data from every experiment. Based on more than a decade of practical experience in developing, optimizing and validating metabolomics approaches as a routine technology in the academic and industrial research laboratory, the lessons taught here are highly relevant for all systems-level approaches, whether in systems biology, biotechnology, toxicology or pharmaceutical sciences. From the Contents: * Sampling and Sample Preparation in Microbial Metabolomics * Tandem Mass Spectrometry Hyphenated with HPLC and UHPLC for Targeted Metabolomics * GC-MS, LC-MS, CE-MS and Ultrahigh Resolution MS (FTICR-MS) in Metabolomics * NMR-based metabolomics analysis * Potential of Microfluidics and Single Cell Analysis in Metabolomics * Data Processing in Metabolomics * Validation and Measurement Uncertainty in Metabolomic Studies * Metabolomics and its Role in the Study of Mammalian Systems and in Plant Sciences * Metabolomics in Biotechnology and Nutritional Metabolomics and more.
Metabolomics
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Author : Vijay Soni
language : en
Publisher: Springer Nature
Release Date : 2023-10-24
Metabolomics written by Vijay Soni and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-10-24 with Science categories.
This book Introduces the extensive applications of metabolomics from all possible areas of research and development so that not only an undergraduate can understand the advancement of metabolomics, but an entrepreneur can harness the knowledge to address possible problems to make a perfect tool to address their research question. Topics covered include the role of metabolomics in the development of agriculture, plant pathology, and their applications; the generalized application of the metabolomics and use of related technologies in various sectors of industries; and the future of metabolomics and upcoming related technologies that can fill the gap between different -omics and their applications for the betterment of humankind. This is an ideal book for university professors, researchers, and advanced-level scientists who are exploring different avenues in metabolomics. Availability of this concise information in one place will aid scientists by expanding their arsenal of techniques and can be helpful to bring more collaborations and to identify the expert at the global level.
Metabolomics Based Method Development For Biomarker Identification
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Author : Ivana Blaženović
language : en
Publisher:
Release Date : 2017
Metabolomics Based Method Development For Biomarker Identification written by Ivana Blaženović and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.
Advancing Mass Spectrometry Based Metabolomics And Proteomics
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Author : Ling Hao
language : en
Publisher:
Release Date : 2017
Advancing Mass Spectrometry Based Metabolomics And Proteomics written by Ling Hao and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.
Quantitative analysis of endogenous biomolecules offers a wealth of clues to understand cell biology and disease mechanisms. Mass spectrometry (MS) has become a foremost technology for the study of biomolecules and their dynamic alterations involved in disease processes. This dissertation is devoted to the development of novel and improved MS-based metabolomic and proteomic methodologies and the application to human disease studies. Specifically, both label-free and stable isotope labeling strategies have been developed for the analysis of metabolites, peptides, and proteins in various biological systems. Label-free methods provide straightforward measurements of biomolecules and are combined with advanced bioinformatics tools for biomarker discovery. Stable isotope labeling, particularly custom DiLeu, iDiLeu, and mdDiLeu tags, offers high-throughput and accurate quantification of biomolecules. Novel online software platform has also been developed for automated omics data analysis. The advancements of analytical methodologies in this work have been mainly achieved on standard flow liquid chromatography (LC)-MS, nanoflow LC-MS, and capillary electrophoresis (CE)-MS platforms. Comprehensive metabolomic and proteomic studies have been successfully applied to disease biomarker discovery for human Preclinical Alzheimer's Disease and Lower Urinary Tract Symptoms in human and mouse models.