Download or read book New Methods for the Analysis of Noncovalent Biological Complexes and Protein Posttranslational Modifications written by Yonghao Yu and published by . This book was released on 2006 with total page 480 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Analysis of Protein Post Translational Modifications by Mass Spectrometry written by John R. Griffiths and published by John Wiley & Sons. This book was released on 2016-10-12 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covers all major modifications, including phosphorylation, glycosylation, acetylation, ubiquitination, sulfonation and and glycation Discussion of the chemistry behind each modification, along with key methods and references Contributions from some of the leading researchers in the field A valuable reference source for all laboratories undertaking proteomics, mass spectrometry and post-translational modification research

Download or read book Posttranslational Modification of Proteins written by Christoph Kannicht and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: Christoph Kannicht and a panel of highly experienced researchers describe readily reproducible methods for detecting and analyzing the posttranslational modifications of protein, particularly with regard to protein function, proteome research, and the characterization of pharmaceutical proteins.

Download or read book Novel Mass Spectrometry Methods for the Analysis of Covalent and Non covalent Protein Structures and Their Influence on the Functions of Therapeutic Proteins written by Jake Pawlowski and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Biotherapeutics consist of biopolymers (proteins, polysaccharides, DNA, and RNA) that are used to treat a wide range of conditions from cancer to autoimmune disease to enzyme replacement. In recent years biotherapeutics have experience tremendous growth due to advances in technology and our understanding of human biology. They are very important to modern medicine due to their ability to treat diseases which are unable to be treated with small molecule-based drugs. Unlike small molecule drugs which are synthetically produced, biotherapeutics are expressed inside cells. Produced biotherapeutics are not made up of a single homogenous population but instead a population of highly similar variants. The source of these variations are enzymatic and non-enzymatic post-translational modifications. By characterizing these modification, a profile is built that links the in vivo response of a drug to its modifications. The complexity and size of these biopolymers makes their characterization very challenging and demands the development of robust analytical techniques. Mass spectrometry- and liquid chromatography-base methods are an integral part of protein characterization. Mass spectrometry provides accurate mass measurements that are invaluable for confirming the identity of a protein and any modifications. Additionally, mass spectrometry is used to assess a protein's higher order structure. Liquid chromatography is a very powerful tool that allows for different post-translational modified populations of a biotherapeutic sample to separate by their chemical or physical properties. Separated populations can further be characterized to identify and analyze their chemical or structural composition. The presented work utilized a blend of mass spectrometry and liquid chromatography methods to characterize proteins with biotherapeutic potential.

Download or read book Development of Methods for the Analysis of Protein Post translational Modifications written by Min Liu and published by . This book was released on 2014 with total page 23 pages. Available in PDF, EPUB and Kindle. Book excerpt: Analysis of protein posttranslational modifications (PTMs) plays pivotal roles for the understanding of their biological importance. Isoaspartic acid (isoAsp) as the smallest PTM is observed "in vivo" and "in vitro". No mass difference and subtle difference in physiochemical property between isoAsp and Asp pose a great challenging for sensitive detection and ambiguous location of isoAsp site in complex samples. A novel assay of isoAsp by exploiting methylation specificity of protein isoaspartate methyltransferase (PIMT) at isoAsp and subsequent 18O-incorporation during methyl ester hydrolysis is presented for sensitive detection and unambiguous site location of several isoAsp residues in IgG1 ("Anal Chem" 2012, 84, 1056-1062). The method can be applied to biological samples to understand the isoAsp process and identify biomarkers. Ubiquitous protein crosslinks in biological systems and biopharmaceuticals are reported to result in loss of bioactivity and immunogenicity, but their characterization is poor, especially when the crosslink chemistry is undefined, due to their intrinsic structural complexity and a lack of a systematic analytical approach. A comprehensive methodology, XChem-Finder, has been developed to break down the analytical challenge via 18O labeling and mass spectrometry, leading to the discovery of a total of 14 cross-linked thioether peptides in IgG2, including those that have not been previously reported ("Anal Chem" 2013, 85, 5900-5908). Furthermore, a novel Histidine-Histidine (His-His) crosslink in IgG1 was successfully discovered and characterized via our XChem-Finder ("Anal Chem" 2014, 86, 4940-4948). This again demonstrates the broad applicability and utility of our XChem-Finder. The further improvement of XChem-Finder is discussed. The discovery of more novel crosslinks in protein by XChem-Finder will be successful without any doubt.

Download or read book Proteomics for Biological Discovery written by Timothy D. Veenstra and published by John Wiley & Sons. This book was released on 2006-06-12 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by recognized experts in the study of proteins, Proteomics for Biological Discovery begins by discussing the emergence of proteomics from genome sequencing projects and a summary of potential answers to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are then dealt with in terms of underlying concepts, limitations and future directions. An invaluable source of information, this title also provides a thorough overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, microfabrication, applied proteomics, and bioinformatics relevant to proteomics. Presents a comprehensive and coherent review of the major issues faced in terms of technology development, bioinformatics, strategic approaches, and applications Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Accessible to the novice while providing experienced investigators essential information Proteomics for Biological Discovery is an essential resource for students, postdoctoral fellows, and researchers across all fields of biomedical research, including biochemistry, protein chemistry, molecular genetics, cell/developmental biology, and bioinformatics.

Download or read book Protein Analysis and Purification written by Ian M. Rosenberg and published by Springer Science & Business Media. This book was released on 2013-12-01 with total page 541 pages. Available in PDF, EPUB and Kindle. Book excerpt: How one goes about analyzing proteins is a constantly evolving field that is no longer solely the domain of the protein biochemist. Investi gators from diverse disciplines find themselves with the unanticipated task of identifying and analyzing a protein and studying its physical properties and biochemical interactions. In most cases, the ultimate goal remains understanding the role(s) that the target protein is playing in cellular physiology. It was my intention that this manual would make the initial steps in the discovery process less time consuming and less intimidating. This book is not meant to be read from cover to cover. The expanded Table of Contents and the index should help locate what you are seeking. My aim was to provide practically oriented information that will assist the experimentalist in benchtop problem solving. The appendices are filled with diverse information gleaned from catalogs, handbooks, and manuals that are presented in a distilled fashion designed to save trips to the library and calls to technical service representatives. The user is encouraged to expand on the tables and charts to fit individual experimental situations. This second edition pays homage to the computer explosion and the various genome projects that have revolutionized how benchtop scientific research is performed. Bioinformatics and In silica science are here to stay. However, the second edition still includes recipes for preparing buffers and methods for lysing cells.

Download or read book Co and Post translational Modification of Proteins written by Donald J. Graves and published by Oxford University Press, USA. This book was released on 1994 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work presents the general biological principles--and the chemical and physical concepts-- needed for an understanding of the post- and co-translational modification of proteins, a fundamental topic in the science of protein biochemistry and molecular biology. Examples of the different types of modification reactions (glycosylation, phosphorylation, prenylation, etc.) are presented to illustrate specific points, and the book is intended to serve as a principles-based guide for studying the subject, whether in the classroom or research laboratory. In addition to its value as a timely overview of a broad, vitally important area, the book can be used in advanced courses on signal transduction, enzymology, and protein chemistry, or as a supplementary text for biochemistry or molecular biology.

Download or read book Methods in Protein Sequence Analysis written by K. Imahori and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 307 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Ninth International Conference on Methods in Protein Sequence Analysis was held for the first time in Asia from September 20 to September 24, 1992 in Otsu (a city near Kyoto), Japan. Approximately 400 delegates attended the meeting. Forty papers were presented orally and 147 poster presentations were discussed. Academic sessions were held from early in the morning until late in the evening. We are confident that the Conference was successful in providing up-to-date information about methods in protein sequence analysis to all participants. Moreover, with the knowledge and understanding of the present standard of various methods of analysis that are being used and will be used, we were able to clarify areas that need to be evaluated, to be improved and be explored further. Major topics in the Conference mostly covered areas in the methodology of protein sequence analysis, such as: micropreparation and microsequencing of proteins, mass spectrometry, post-translational modification, prediction and database analysis, and analysis of protein structures of special interests. The evolution of genetic engineering in molecular biology has greatly accelerated the accumulation of knowledge on the amino acid sequence of novel proteins regardless of whether they are expressed or not expressed in living organisms. In the early stage of accumulation of structural information, the amino acid sequence itself is worthy of notice.

Download or read book Methods in Protein Sequence Analysis written by Brigitte Wittmann-Liebold and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 608 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Methods in Protein Sequence Analysis - 1988" - contains selected contributions on modern protein- analytical techniques as presented by speakers at the Seventh International Conference on "Methods in Protein Sequence Analysis", held from July 3rd to July 8th, 1988 in Berlin. The book contains information on new methodologies for sensitive amino acid analysis, N- and C-terminal sequence analysis, and protein and peptide purification. In addition recent mass spectrometric approaches are described, as an alter native technique to the common stepwise degradative sequence analysis of polypeptides by the Edman method. The book presents new possibilities in the design of sequencers and sophisticated equipment for the structural analysis of peptides and proteins. It describes practical approaches for the investigation of protein domains and protein complexes, and contains review chapters on the crystallization of cell organelles as well as on recent theoretical aspects of protein folding mechanisms. The nature of protein folding is not yet understood, but further advances in this area would greatly enhance our present knowledge of protein structure and function. Further, the book gives examples of the application of gene technology to protein characterization and to the design of new proteins. This enables new studies on the structure and function of proteins to be made, and opens up efficient approaches to the design of drugs.

Download or read book Dissertation Abstracts International written by and published by . This book was released on 2009 with total page 810 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Development and Application of Mass Spectrometry Methods for Proteomic and Post translational Modification Analysis written by Danqing Wang (Ph.D.) and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are essential biomolecules that perform a wide range of biological functions. Post-translational modifications (PTMs) substantially impact protein structure and function, making their characterization essential for understanding complex biological systems. This dissertation focuses on developing and applying novel mass spectrometry (MS)-based methodologies to address challenges in studying two common and important PTMs: phosphorylation and glycosylation. To this end, new enrichment materials and their corresponding workflows, including Cotton Ti-IMAC, epoxy-ATP-Ti4+ IMAC, and Very Weak Anion Exchange (VWAX) have been introduced for efficient phosphopeptide and glycopeptide enrichment. A strategy combining boronic acid enrichment, high-pH fractionation, and EThcD has been developed for comprehensive O-glycosylation profiling. Additionally, the Boost-DiLeu quantitative approach has been introduced to enhance glycopeptide quantification in size-limited samples, while a periodate oxidation-based SUGAR tag labeling method has been established for high-throughput, intact sialylated glycopeptide-specific quantification. These methods have been applied to study human diseases, such as Alzheimer's Disease, providing insights into dysregulated glycosylation patterns and their potential implications in disease pathogenesis. Overall, this work contributes to advancing MS-based proteomics strategies and broadening our understanding of the roles of PTMs in biological systems and is anticipated to inspire future research endeavors in related fields.

Download or read book Development and Application of Mass Spectrometry Methods for Proteomic and Post translational Modification Analysis written by Danqing Wang (Ph.D.) and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are essential biomolecules that perform a wide range of biological functions. Post-translational modifications (PTMs) substantially impact protein structure and function, making their characterization essential for understanding complex biological systems. This dissertation focuses on developing and applying novel mass spectrometry (MS)-based methodologies to address challenges in studying two common and important PTMs: phosphorylation and glycosylation. To this end, new enrichment materials and their corresponding workflows, including Cotton Ti-IMAC, epoxy-ATP-Ti4+ IMAC, and Very Weak Anion Exchange (VWAX) have been introduced for efficient phosphopeptide and glycopeptide enrichment. A strategy combining boronic acid enrichment, high-pH fractionation, and EThcD has been developed for comprehensive O-glycosylation profiling. Additionally, the Boost-DiLeu quantitative approach has been introduced to enhance glycopeptide quantification in size-limited samples, while a periodate oxidation-based SUGAR tag labeling method has been established for high-throughput, intact sialylated glycopeptide-specific quantification. These methods have been applied to study human diseases, such as Alzheimer's Disease, providing insights into dysregulated glycosylation patterns and their potential implications in disease pathogenesis. Overall, this work contributes to advancing MS-based proteomics strategies and broadening our understanding of the roles of PTMs in biological systems and is anticipated to inspire future research endeavors in related fields.

Download or read book Advancement of Photodissociation Mass Spectrometry Methods for the Analysis of Protein Post translational Modifications written by Michelle Renee Robinson and published by . This book was released on 2016 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: Post-translational modifications (PTMs) are important for regulating protein structure and function. Despite significant progress for PTM analysis using liquid chromatography tandem mass spectrometry (LC-MS/MS), opportunities for new method development remain. The research presented in this dissertation promotes 193 nm ultraviolet photodissociation (UVPD) as an alternative activation technique for PTM analysis with specific utility for phosphorylated and sulfated peptides. A novel de novo sequencing method with applications for unbiased PTM discovery was developed utilizing Lys-N proteolysis, N-terminal imidazolinylation, and UVPD to direct fragmentation for the formation of N-terminal ions. The N-terminal a, b, and c ions generated by UVPD were differentiated from one another by characteristic mass shifts. Sets of triplet peaks were used to distinguish N-terminal ions from confounding C-terminal ions and improve the accuracy of de novo sequencing. UVPD was evaluated for the analysis of phosphopeptide cations and anions. Negative mode analysis was advantageous for the detection of casein peptides in high phosphorylation states, while positive mode proved more robust for global phosphoproteomic analysis of HeLa and HCC70 cell lysates. Compared to collisional activation, the depth of coverage was lower using UVPD yet more extensive fragmentation and improved phosphate retention on products ions was achieved. Phosphorylation mapping by LC-UVPD-MS was carried out in the C-terminal domain (CTD) of RNA polymerase II as a function of kinase treatment, ERK2 or TFIIH, and organism, yeast or fruit fly. Single phosphorylations on Ser2 or Ser5 in the consensus heptad, YSPTSPS, were observed across all experimental conditions. Analysis of the non-consensus fruit fly CTD revealed the significance of Tyr1 and Pro residues in the +1 position relative to Ser for phosphorylation to occur. For sulfated peptides, negative mode UVPD yielded a and x ions that largely retained the labile sulfate modification, facilitating peptide sequencing and PTM localization. With appropriate MS/MS tools established, the next step towards global sulfoproteomics was the development of enrichment methods. Weak anion exchange (WAX) was applied for this purpose. Following carbamylation to neutralize primary amines which otherwise repel the anion exchanger; improved WAX retention was observed for sulfopeptides relative to a complex mixture of unmodified bovine serum albumin peptides.

Download or read book Quantitative Characterization of Proteins and Post translational Modifications in Complex Proteomes Using High resolution Mass Spectrometry based Proteomics written by Zhou Li (Researcher in biological systems) and published by . This book was released on 2014 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry-based proteomics is focused on identifying the entire suite of proteins and their post-translational modifications (PTMs) in a cell, organism, or community. In particular, quantitative proteomics measures abundance changes of thousands of proteins among multiple samples and provides network-level insight into how biological systems respond to environmental perturbations. Various quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling. This dissertation starts with systematic comparison of these three methods, and shows that isobaric chemical labeling provides accurate, precise, and reproducible quantification for thousands of proteins. Based on these results, we applied this approach to characterizing the proteome of Arabidopsis seedlings treated with Strigolactones (SLs), a new class of plant hormones that modulate various developmental processes. Our study reveals that SLs regulate the expression of a range of proteins that have not been assigned to SL pathways, which provides novel targets for follow-up genetic and biochemical characterization of SL signaling. The same approach was also used to measure how elevated temperature impacts the physiology of individual microbial groups in an acid mine drainage (AMD) microbial community, and shows that related organisms differed in their abundance and functional responses to temperature. Elevated temperature repressed carbon fixation by two Leptospirillum genotypes, whereas carbon fixation was significantly up-regulated at higher temperature by a third member of this genus. Further, we developed a new proteomic approach that harnessed high-resolution mass spectrometry and supercomputing for direct identification and quantification of a broad range of PTMs from an AMD microbial community. We find that PTMs are extraordinarily diverse between different growth stages and highly divergent between closely related bacteria. The findings of this study motivate further investigation of the role of PTMs in the ecology and evolution of microbial communities. Finally, a computational approach has been developed to improve the sensitivity of phosphopeptide identification. Overall, the research presented in the dissertation not only reveals biological insights with existing quantitative proteomics methods, but also develops novel methodologies that open up new avenues in studying PTMs of proteins (e.g. PTM cross-talk).

Download or read book Proteomics Sample Preparation written by Jörg von Hagen and published by John Wiley & Sons. This book was released on 2011-08-24 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: This long-awaited first guide to sample preparation for proteomics studies overcomes a major bottleneck in this fast growing technique within the molecular life sciences. By addressing the topic from three different angles -- sample, method and aim of the study -- this practical reference has something for every proteomics researcher. Following an introduction to the field, the book looks at sample preparation for specific techniques and applications and finishes with a section on the preparation of sample types. For each method described, a summary of the pros and cons is given, as well as step-by-step protocols adaptable to any specific proteome analysis task.

Download or read book Advancing Quantitative Proteomics and Protein Post translational Modification Analyses by Multi dimensional Mass Spectrometric Approaches written by Zihui Li and published by . This book was released on 2021 with total page 620 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are important molecules that are involved in numerous critical biological processes. Consequently, understanding the functional roles and dysregulation of proteins constitutes a vital task in both basic and clinical research. However, it is very challenging to define the full complement of proteins due to their large degree of variations, especially considering that many proteins can undergo numerous post-translational modifications (PTMs) which dramatically affect protein conformations and functions. Recently, mass spectrometry (MS) has evolved as a powerful tool to characterize proteins and their PTMs benefiting from its high speed, sensitivity and the ability to monitor thousands of analytes simultaneously.This dissertation is devoted to the development and application of various MS-based strategies to facilitate the detection of proteins and their PTMs qualitatively and quantitatively. A portion of this dissertation describes the investigation of proteome-wide alterations with the development and maturation of human pancreas using custom-developed isobaric tags. This study focuses on the extracellular matrix proteins and provides information on the localization changes of selected proteins in islet or acinar compartments as well. The normal baseline data across the lifespan of human pancreas will become a valuable resource and benefit future studies into the pancreatic pathologies. Switching gear to protein PTMs, this dissertation documents the design and development of a novel biotin thiol tag to greatly improve the in-depth profiling of two important PTMs, citrullination and homocitrullination, from complex biological samples. The utility of the approach is demonstrated by providing the first tissue-specific citrullination and homocitrullination atlas in mice. The first high-throughput quantitative analysis pipeline of protein citrullination is subsequently developed by the integration with isobaric labeling strategy. We also further improve the protein citrullination detection by using a combination of various digestion and fragmentation techniques. Citrullination alteration during the progression of Alzheimer's disease is further explored using human cerebrospinal fluid to shed light on the disease pathogenesis. This dissertation also highlights the application of a novel sub-atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry platform for the in situ imaging of N-glycans. Spatial distribution of N-glycans in ovarian cancer tissue section may indicate potential association of this modification with tumor progression. Collectively, we expect the biological insights and technological advancements presented in this work will lead to improved understanding of microenvironment in both healthy and disease conditions, and the new knowledge gained from these studies will inspire and benefit future research effort in related fields.