Download or read book Development of Metabolomics and Lipidomics Workflows for Phosphorylated Metabolites Using Ultra high performance Liquid Chromatography with Tandem Mass Spectrometry written by Peng Li and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Processing Metabolomics and Proteomics Data with Open Software written by Robert Winkler and published by Royal Society of Chemistry. This book was released on 2020-03-19 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolomics and proteomics allow deep insights into the chemistry and physiology of biological systems. This book expounds open-source programs, platforms and programming tools for analysing metabolomics and proteomics mass spectrometry data. In contrast to commercial software, open-source software is created by the academic community, which facilitates the direct interaction between users and developers and accelerates the implementation of new concepts and ideas. The first section of the book covers the basics of mass spectrometry, experimental strategies, data operations, the open-source philosophy, metabolomics, proteomics and statistics/ data mining. In the second section, active programmers and users describe available software packages. Included tutorials, datasets and code examples can be used for training and for building custom workflows. Finally, every reader is invited to participate in the open science movement.

Download or read book Metabolic Profiling written by Georgios A. Theodoridis and published by Humana. This book was released on 2019-04-30 with total page 291 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the different approaches and techniques used by researchers to study the recent challenges and developments in metabolic profiling. This book is divided into IV parts. Part I contains chapters that highlight basic concepts, such as experimental design, data treatment, metabolite identification, and harmonization. Part II describes experimental protocols for both targeted and untargeted metabolomics covering the basic analytical technologies: LC-MS, GC-MS, NMR and CE-MS. In addition the protocols describe methods for the study of tissues, feces, blood and other types of biological samples as well as the application of chemical derivatization for GC-MS. Parts III and IV present the use of metabolomics in the study of food, plants and the life sciences, with examples from the quest for the discovery of disease biomarkers, physical exercise omics and metabolic profiling of food, fruit and wine. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and thorough, Metabolic Profiling: Methods and Protocols is a valuable resource for researchers who are interested in expanding their knowledge of this rapidly developing field.

Download or read book Mass Spectrometry Based Lipidomics written by Fong-Fu Hsu and published by Humana. This book was released on 2021-05-29 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume covers conventional MS-based “shotgun lipidomics” by which samples are introduced by infusion or loop injection, as well as LC-MS-based lipidomics, which are becoming increasingly important due to the ever-increasing demand for a complete and precise lipid analysis of the complex and diversified lipids in nature. The volume features protocols applying chemical reactions, the on-line photochemical reactions combined with various MS methods for comprehensive characterization of various lipid classes, and quantification of specific and rare lipids. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Mass Spectrometry-Based Lipidomics: Methods and Protocols serves as an invaluable guide for biochemists and mass spectroscopists who are interested in lipid studies.

Download or read book Chemical Derivatization in Gas Chromatography written by J. Drozd and published by Elsevier. This book was released on 1986-07-01 with total page 247 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical Derivatization in Gas Chromatography

Download or read book Tandem Mass Spectrometry of Lipids written by Robert C Murphy and published by Royal Society of Chemistry. This book was released on 2014-12-02 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: The emerging field of lipidomics has been made possible because of advances in mass spectrometry, and in particular tandem mass spectrometry of lipid ions generated by electrospray ionization. The ability to carry out basic biochemical studies of lipids using electrospray ionization is predicated upon understanding the behaviour of lipid derived ions following collision induced decomposition and mechanisms of product ion formation. During the past 20 years, a wealth of information has been generated about lipid molecules that are now analysed by mass spectrometry, however there is no central source where one can obtain basic information about how these very diverse biomolecules behave following collisional activation. This book brings together, in one volume, this information so that investigators considering using tandem mass spectrometry to structurally characterize lipids or to quantitate their occurrence in a biological matrix, will have a convenient source to review mechanism of decomposition reactions related to the diversity of lipid structures. A separate chapter is devoted to each of seven major lipid classes including fatty acids, eicosanoids and bioactive lipid mediators, fatty acyl esters and amides, glycerol esters, glycerophospholipids, sphingolipids, and steroids. Mechanistic details are provided for understanding the pathways of formation of major product ions and ions used for structural characterization. In most cases specific ancillary information has been critical to understand the pathways, including isotope labeling and high resolution analysis of precursor and product ions. For a few specific examples such data is missing and pathways are proposed as a means to initiate further mass spectral experiments to prove or disprove pathway hypotheses. While this work largely centres on the lipid biochemistry of animal (mammalian) systems, general principles can be taken from the specific examples and applied to lipid biochemistry found in plants, fungi, prokaryotes and archeal organisms.

Download or read book Ion Mobility Mass Spectrometry written by Giuseppe Paglia and published by Humana. This book was released on 2019-11-15 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on ion mobility-mass spectrometry (IM-MS) and informatics approaches to improve traditional analysis of molecules by providing fundamentals and protocols for exploiting the potential of state-of-the-art IM-MS technology for the most common analytical applications. The chapters have been organized into four parts, each dealing with a particular set of IM-MS applications: 1) metabolomics and lipidomics; 2) proteomics and glycomics; 3) imaging and ambient ionization IM-MS; and 4) bioinformatic solutions for analyzing IM-MS data and deriving CCS values. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Ion Mobility-Mass Spectrometry: Methods and Protocols serves as an ideal resource for scientists delving into the technique's unprecedented analytical advantages, enabling novel qualitative and quantitative applications for the analysis of complex biological samples.

Download or read book Metabolomics From Fundamentals to Clinical Applications written by Alessandra Sussulini and published by Springer. This book was released on 2017-01-28 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive view of metabolomics, from the basic concepts, through sample preparation and analytical methodologies, to data interpretation and applications in medicine. It is the first volume to cover metabolomics clinical applications while also emphasizing analytical and statistical features. Moreover, future trends and perspectives in clinical metabolomics are also presented. For researches already experienced in metabolomics, the book will be useful as an updated definitive reference. For beginners in the field and graduate students, the book will provide detailed information about concepts and experimental aspects in metabolomics, as well as examples and perspectives of applications of this strategy to clinical questions.

Download or read book Periparturient Diseases of Dairy Cows written by Burim N. Ametaj and published by Springer. This book was released on 2017-12-21 with total page 281 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book summarizes the results achieved so far by application of various biological systems (including genomics, transcriptomics, proteomics, and metabolomics) involved in the pathomechanisms and early diagnosis of periparturient diseases as specific biomarkers of disease in cattle. These emerging technologies help to extensively enhance our understanding of the etiology and pathogenesis of periparturient diseases of transition dairy cows. The book includes a chapter dedicated to ‘omics’ sciences and one that discusses the myths established in animal and veterinary sciences in recent decades and emerging, new paradigms. The diseases discussed include metritis, mastitis, laminitis, ketosis, rumen acidosis, periparturient immunosuppression, gastrointestinal microbiota and their involvement in disease, infertility, fatty liver, milk fever, and retained placenta. This book is intended for academics, veterinarians, animal nutritionists, researchers, and graduate students working in the field of ‘omics sciences’ with a special interest in dairy cattle health.

Download or read book Advancements of Mass Spectrometry in Biomedical Research written by Alisa G. Woods and published by Springer. This book was released on 2014-06-20 with total page 601 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the use of mass spectrometry for biomedical applications. Chapters focus on specific therapeutic areas such as oncology, infectious disease and psychiatry. Additional chapters focus on methodology as well as new technologies and instrumentation. This volume provides readers with a comprehensive and informative manual that will allow them to appreciate mass spectrometry and proteomic research but also to initiate and improve their own work. Thus the book acts as a technical guide but also a conceptual guide to the newest information in this exciting field. Mass spectrometry is the central tool used in proteomic research today and is rapidly becoming indispensable to the biomedical scientist. With the completion of the human genome project and the genomic revolution, the proteomic revolution has followed closely behind. Understanding the human proteome has become critical to basic and clinical biomedical research and holds the promise of providing comprehensive understanding of human physiological processes. In addition, proteomics and mass spectrometry are bringing unprecedented biomarker discovery and are helping to personalize medicine.

Download or read book LC MS MS in Proteomics written by Pedro R. Cutillas and published by Humana Press. This book was released on 2011-04-06 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the development of new quantitative strategies and powerful bioinformatics tools to cope with the analysis of the large amounts of data generated in proteomics experiments, liquid chromatography with tandem mass spectrometry (LC-MS/MS) is making possible the analysis of proteins on a global scale, meaning that proteomics can now start competing with cDNA microarrays for the analysis of whole genomes. In LC-MS/MS in Proteomics: Methods and Applications, experts in the field provide protocols and up-to-date reviews of the applications of LC-MS/MS, with a particular focus on MS-based methods of protein and peptide quantification and the analysis of post-translational modifications. Beginning with overviews of the use of LC-M/MS in protein analysis, the book continues with topics such as protocols for the analysis of post-translational modifications, with particular focus on phosphorylation and glycosylation, popular techniques for quantitative proteomics, such as multiple reaction monitoring, metabolic labelling, and chemical tagging, biomarker discovery in biological fluids, as well as novel applications of LC-MS/MS. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective subjects, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, LC-MS/MS in Proteomics: Methods and Applications presents the techniques and concepts necessary in order to aid proteomic practitioners in the application of LC-MS/MS to essentially any biological problem.

Download or read book Methodologies for Metabolomics written by Norbert W. Lutz and published by Cambridge University Press. This book was released on 2013-01-21 with total page 641 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolomics, the global characterisation of the small molecule complement involved in metabolism, has evolved into a powerful suite of approaches for understanding the global physiological and pathological processes occurring in biological organisms. The diversity of metabolites, the wide range of metabolic pathways and their divergent biological contexts require a range of methodological strategies and techniques. Methodologies for Metabolomics provides a comprehensive description of the newest methodological approaches in metabolomic research. The most important technologies used to identify and quantify metabolites, including nuclear magnetic resonance and mass spectrometry, are highlighted. The integration of these techniques with classical biological methods is also addressed. Furthermore, the book presents statistical and chemometric methods for evaluation of the resultant data. The broad spectrum of topics includes a vast variety of organisms, samples and diseases, ranging from in vivo metabolomics in humans and animals to in vitro analysis of tissue samples, cultured cells and biofluids.

Download or read book Cancer Metabolomics written by Shen Hu and published by Springer Nature. This book was released on 2021-04-01 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cancer metabolomics is a rapidly evolving field that aims for a comprehensive dissection of the metabolic phenotypes and functional network of metabolites in human cancers. State of the art metabolomics tools have been developed and applied to studying cancer metabolism and developing metabolic targets for improved diagnosis, prognosis and therapeutic treatment of human cancers. Chapters are written by subject experts in the field of cancer metabolomics with cross-disciplinary contributions. Coverage includes advanced metabolomics technologies and methodologies, including chemical isotope labelling liquid chromatography - mass spectrometry, capillary ion chromatography - mass spectrometry, 2-D gas chromatography – mass spectrometry, capillary electrophoresis – mass spectrometry, nuclear magnetic resonance spectroscopy, shotgun lipidomics, tracer-based metabolomics, microbial metabolomics, mass spectrometry imaging for single cell metabolomics and functional metabolomics. In addition, the book highlights new discoveries in cancer metabolism such as hypoxia inducible factor pathway, isocitrate dehydrogenase 1 mutation and oncometabolites. Finally, contributors focus on the translational applications of metabolomics in human cancers such as glioma, head and neck cancer, and gastric cancer. This new volume will be a unique reference source for cancer researchers and promote applications of metabolomics in understanding cancer metabolism.

Download or read book Differential Ion Mobility Spectrometry written by Alexandre A. Shvartsburg and published by CRC Press. This book was released on 2008-12-24 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the last decade, scientific and engineering interests have been shifting from conventional ion mobility spectrometry (IMS) to field asymmetric waveform ion mobility spectrometry (FAIMS). Differential Ion Mobility Spectrometry: Nonlinear Ion Transport and Fundamentals of FAIMS explores this new analytical technology that separates and characterizes ions by the difference between their mobility in gases at high and low electric fields. It also covers the novel topics of higher-order differential IMS and IMS with alignment of dipole direction. The book relates the fundamentals of FAIMS and other nonlinear IMS methods to the physics of gas-phase ion transport. It begins with the basics of ion diffusion and mobility in gases, covering the main attributes of conventional IMS that are relevant to all IMS approaches. Building on this foundation, the author reviews diverse high-field transport phenomena that underlie differential IMS. He discusses the conceptual implementation and first-principles optimization of FAIMS as a filtering technique, emphasizing the dependence of FAIMS performance metrics on instrumental parameters and properties of ion species. He also explores ion reactions in FAIMS caused by field heating and the effects of inhomogeneous electric field in curved FAIMS gaps. Written by an accomplished scientist in the field, this state-of-the-art book supplies the foundation to understand the new technology of nonlinear IMS methods.

Download or read book Biomarkers for Endometriosis written by Thomas D'Hooghe and published by Springer. This book was released on 2017-09-22 with total page 271 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of the diagnostic performance of non- or semi-invasive tests for endometriosis in peripheral blood, endometrium, saliva, peritoneal fluid and urine. The value of existing and emerging systems biology technologies for biomarker development is addressed in several chapters on genetics, microarrays, proteomics and metabolomics. Although tests with high sensitivity and acceptable specificity have been developed, sometimes validated in independent populations and seem promising, more research is needed to translate these data into clinical benefit for patients and coordinate efforts internationally to standarize analysis, reports and operating procedures. The gold standard to diagnose endometriosis is currently through laparoscopic inspection with histological confirmation, a surgical procedure with rare but significant potential risks for the patients. A non-invasive test for endometriosis would be critical for the early detection of endometriosis of symptomatic women with pelvic pain and/or subfertility with normal ultrasound. This would include nearly all cases of minimal-mild endometriosis, some cases of moderate-severe endometriosis without a clearly visible ovarian endometrioma and cases with pelvic adhesions and/or other pelvic pathology, who might benefit from surgery to improve pelvic pain and/or subfertility. Such a test would also be useful in symptomatic women with ultrasound imaging suspicious for endometriosis, since it may be difficult to differentiate an ovarian endometrioma from other ovarian cysts and since the quality of ultrasound imaging is highly variable worldwide.

Download or read book Charged Aerosol Detection for Liquid Chromatography and Related Separation Techniques written by Paul H. Gamache and published by John Wiley & Sons. This book was released on 2017-05-30 with total page 548 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first book devoted exclusively to a highly popular, relatively new detection technique Charged Aerosol Detection for Liquid Chromatography and Related Separation Techniques presents a comprehensive review of CAD theory, describes its advantages and limitations, and offers extremely well-informed recommendations for its practical use. Using numerous real-world examples based on contributors’ professional experiences, it provides priceless insights into the actual and potential applications of CAD across a wide range of industries. Charged aerosol detection can be combined with a variety of separation techniques and in numerous configurations. While it has been widely adapted for an array of industrial and research applications with great success, it is still a relatively new technique, and its fundamental performance characteristics are not yet fully understood. This book is intended as a tool for scientists seeking to identify the most effective and efficient uses of charged aerosol detection for a given application. Moving naturally from basic to advanced topics, the author relates fundamental principles, practical uses, and applications across a range of industrial settings, including pharmaceuticals, petrochemicals, biotech, and more. Offers timely, authoritative coverage of the theory, experimental techniques, and end-user applications of charged aerosol detection Includes contributions from experts from various fields of applications who explore CAD’s advantages over traditional HPLC techniques, as well its limitations Provides a current theoretical and practical understanding of CAD, derived from authorities on aerosol technology and separation sciences Features numerous real-world examples that help relate fundamental properties and general operational variables of CAD to its performance in a variety of conditions Charged Aerosol Detection for Liquid Chromatography and Related Separation Techniques is a valuable resource for scientists who use chromatographic techniques in academic research and across an array of industrial settings, including the biopharmaceutical, biotechnology, biofuel, chemical, environmental, and food and beverage industries, among others.

Download or read book Metabolism and Metabolomics of Liver in Health and Disease written by Walter Wahli and published by . This book was released on 2021 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: Women and men have probably never been concerned as much by their health as during this COVID-19 pandemic. In this context, lifestyle habits continue to be promoted as allies for daily prevention against diseases. This is valid also for metabolic diseases, among which many affect the liver and are risk factors for aggravating the disease course of COVID-19. In fact, liver diseases are currently a major global health problem. There is a huge range of liver diseases and non-alcoholic fatty liver disease (NAFLD) is the most common chronic hepatic condition, which in some patients progresses to cirrhosis and liver cancer. Currently, substantial efforts are being made to better understand NAFLD, especially, because there is no U.S. Food and Drug Administration (FDA)-approved pharmacological therapy. To explore this disease, metabolomics is the most recently developed omics technology after genomics, transcriptomics, and proteomics. Metabolomics is the large-scale analysis of molecules, known as metabolites that are intermediate or end products of metabolism found within cells, tissues, and biofluids. This technology has a very high potential to identify biomarker candidates for the future development of new therapeutics. The book features articles that address metabolomics technology and its use to document different liver functions and dysfunctions, with a major focus on NAFLD.