Download or read book Use of Liquid Chromatography and Tandem Mass Spectrometry for Identification and Quantification of Proteins and Post Translational Modifications written by Henrik Molina and published by . This book was released on 2006 with total page 160 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 Neuroproteomics written by Oscar Alzate and published by CRC Press. This book was released on 2009-10-26 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this, the post-genomic age, our knowledge of biological systems continues to expand and progress. As the research becomes more focused, so too does the data. Genomic research progresses to proteomics and brings us to a deeper understanding of the behavior and function of protein clusters. And now proteomics gives way to neuroproteomics as we beg

Download or read book Multidimensional Liquid Chromatography Mass Spectrometric Analysis of Selected Post Translationally Modified Peptides written by 全泉 and published by . This book was released on 2017-01-26 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation, "Multidimensional liquid chromatography/mass spectrometric analysis of selected post-translationally modified peptides: from fundamentals to shotgun proteomics" by Quan, Quan, 全泉, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: The continuing evolution of multidimensional liquid chromatography/mass spectrometry (MDLC-MS)-based proteomics is an important element of the developing field of shotgun proteomics for peptide sequencing, protein identification and quantification. The first part of this thesis, Chapter 2, demonstrates the development of a comprehensive automated MDLC platform capable of performing both quantitative proteomics analyses and post-translational modifications analysis-in particular, of protein tyrosine nitration and protein phosphorylation. The current multidimensional reversed-phase (RP) liquid chromatography design was employed with the addition of strong anion exchange (SAX) and cation exchange (SCX) columns. The inclusion of the complementary S(A/C)X column chemistries in the RP-SA(C)X-RP system allowed the retention of deprotonated peptides in the SAX trap column, followed by diversion of non-retained peptides to an online SCX trap column, thereby allowing identification of both anionic and cationic peptides from a single injection event. This MDLC RP-SA(C)X-RP platform provided more extensive protein and proteome coverage, thereby leading to improved protein quantification from analyses of Saccharomyces cerevisiae tryptic digests, a prototypical model proteome, as well as those of various other complex biological samples. Phosphorylated and 3-nitrotyrosyl-containing peptides-two important and biologically relevant post-translational modifications-were efficiently retained in this newly developed platform, in some cases without the need for any pre-enrichment steps. This RP-SA(C)X-RP technology performed well, as judged by the mapped protein inventory from the global collection of endogenous protein tyrosine nitration, the phosphoproteome, and its associated proteomics networks of permanent cerebral ischemia of Macaca fascicularis. The goal of the subsequent study was to gain insight into various aspects of the gas phase radical ion chemistry of phosphorylated peptides; these findings should provide an underlying scientific basis for the development of peptide sequencing strategies, because the general guidelines governing phosphorylated peptide radical cation dissociation remain poorly understood. No previous reports have described the successful generation of radical cationic phosphopeptides under low-energy collision-induced dissociation (CID). Chapters 3 and 4 describe a systematic investigation into the effect of the structures of the metal complexes on the efficient generation of radical phosphopeptide cations. To examine the mechanisms, energetics, and kinetics of these reactions, a combined experimental and computational approach was undertaken to facilitate a greater understanding of their dissociation behavior. Several model phosphopeptide radical cations were synthesized and characterized to formulate the fragmentation rules. The findings suggest that the dissociations of isomeric peptide radical cations can be more efficient than their isomerizations. In a situation similar to the dissociations of analogous even-electron protonated peptides, the losses of H3PO4 from both even- and odd-electron peptide cations are due preferentially to charge-driven mechanisms; the charge-driven loss of H3PO4 is favored as a result of the distonic radical character of the α-radical cation, enhancing the...

Download or read book Protein Sequencing and Identification Using Tandem Mass Spectrometry written by Michael Kinter and published by John Wiley & Sons. This book was released on 2005-04-12 with total page 321 pages. Available in PDF, EPUB and Kindle. Book excerpt: How to design, execute, and interpret experiments for protein sequencing using mass spectrometry The rapid expansion of searchable protein and DNA databases in recent years has triggered an explosive growth in the application of mass spectrometry to protein sequencing. This timely and authoritative book provides professionals and scientists in biotechnology research with complete coverage of procedures for analyzing protein sequences by mass spectrometry, including step-by-step guidelines for sample preparation, analysis, and data interpretation. Michael Kinter and Nicholas Sherman present their own high-quality, laboratory-tested protocols for the analysis of a wide variety of samples, demonstrating how to carry out specific experiments and obtain fast, reliable results with a 99% success rate. Readers will get sufficient experimental detail to apply in their own laboratories, learn about the proper selection and operation of instruments, and gain essential insight into the fundamental principles of mass spectrometry and protein sequencing. Coverage includes: * Peptide fragmentation and interpretation of product ion spectra * Basic polyacrylamide gel electrophoresis * Preparation of protein digests for sequencing experiments * Mass spectrometric analysis using capillary liquid chromatography * Techniques for protein identification by database searches * Characterization of modified peptides using tandem mass spectrometry And much more

Download or read book Identification and Quantification of the Post translational Modifications of Nucleosomal Proteins Using Mass Spectrometry written by Xinzhao Jiang and published by . This book was released on 2006 with total page 454 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Characterization and Identification of Protein Posttranslational Modifications Using Protein Enrichment and Mass Spectrometry written by Liwen Wang and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: This dissertation describes a proteomic workflow for the analysis of protein post-translational modifications (PTMs). The workflow combines the techniques for protein enrichment, multi-dimensional separations, mass spectrometry (MS) and automatic data analysis. The workflow was developed to improve the application of proteomic analysis in the realms of biomarker discovery and experimental therapeutic research. Chapter 2 presents an immunoaffinity chromatography method that was developed to enrich acetylated histones. A self-packed immunoaffinity capillary column was developed using commercial antibodies that could be recycled and used for on-line and off-line enrichment. The acetylated fractions were collected and identified by Matrix Assisted Laser Desorption (MALDI) MS and electrospray ionization (ESI) liquid chromatography tandem mass spectrometry (LC-MS/MS). In chapter 3 an optimized phosphoproteomic analysis workflow based on phosphopeptide enrichment, data-dependant neutral loss mass spectrometry and a novel hierarchical database searching is described. The combination of these approaches improved the confidence of phosphopeptide identifications. Chapter 4 describes the use of phosphoprotein enrichment and a tandem phosphoprotein and phosphopeptide enrichment to improve the identification of phosphoproteins and localization of the phosphorylation sites. Purification of global phosphoproteins from primary CLL B-cells was conducted by use of PhosTag Zn2 enrichment strategy at neutral pH. SDS-PAGE gel was used to separate the purified phosphoprotein fraction and Pro-Q diamond staining was employed to visualize those phosphoprotein bands. Shot-gun proteomic analysis was then performed to identify all the enriched phosphoproteins in the gel. Phosphopeptide enrichment was used in tandem to map phosphorylation sites of the enriched phosphoproteins. Chapter 5 describes the identification of tyrosine phosphoproteins associated with immunotherapy of malignant cells with the small modular immunopharmaceutical targeted against CD37 (CD37-SMIPTM). This drug induces apoptosis and antibody-dependent cellular cytotoxicity (ADCC) in primary Chronic Lymphocyte Leukemia (CLL) cells. Tyrosine phosphorylation of proteins was investigated as an early activation event for the cytotoxicity. Immunoprecipitation was used to purify the phosphotyrosine proteins from treated cell lysate and untreated cell lysate. Detection of modulation of tyrosine phosphorylation and identification of those tyrosine phosphoproteins after treatment by proteomic approaches revealed proteins associated with the signaling pathway activated by immunotherapy. Chapter 6 describes a direct application of the proteomic platform developed in Chapter 3 combined with LC-MS protein profiling. The modulation of histone phosphorylation isoforms induced by various chemotherapy drugs was detected by LC-MS screening. We detected the dephosphorylation of histones H1 and hyperphosphorylation of H2A.X associated with the different drug treatments.

Download or read book Modern Proteomics Sample Preparation Analysis and Practical Applications written by Hamid Mirzaei and published by Springer. This book was released on 2016-12-14 with total page 525 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume serves as a proteomics reference manual, describing experimental design and execution. The book also shows a large number of examples as to what can be achieved using proteomics techniques. As a relatively young area of scientific research, the breadth and depth of the current state of the art in proteomics might not be obvious to all potential users. There are various books and review articles that cover certain aspects of proteomics but they often lack technical details. Subject specific literature also lacks the broad overviews that are needed to design an experiment in which all steps are compatible and coherent. The objective of this book was to create a proteomics manual to provide scientists who are not experts in the field with an overview of: 1. The types of samples can be analyzed by mass spectrometry for proteomics analysis. 2. Ways to convert biological or ecological samples to analytes ready for mass spectral analysis. 3. Ways to reduce the complexity of the proteome to achieve better coverage of the constituent proteins. 4. How various mass spectrometers work and different ways they can be used for proteomics analysis 5. The various platforms that are available for proteomics data analysis 6. The various applications of proteomics technologies in biological and medical sciences This book should appeal to anyone with an interest in proteomics technologies, proteomics related bioinformatics and proteomics data generation and interpretation. With the broad setup and chapters written by experts in the field, there is information that is valuable for students as well as for researchers who are looking for a hands on introduction into the strengths, weaknesses and opportunities of proteomics.

Download or read book Mass Spectrometry Modified Proteins and Glycoconjugates written by A.L. Burlingame and published by Gulf Professional Publishing. This book was released on 2005-12-13 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides comprehensive treatment of tools and proper usage for the identification of proteins, affinity chromatography and studies the complexity of protein machines and assemblages, assignment of the most common protein posttranslational modifications (phosphorylation and glycosylation) and glycolipidomics. *Part 2 of 2 volumes about Mass Spectrometry *Discusses peptide and protein cleanup and preparation requirements for mass spectrometry *Explains protein enzymic and chemical digestion strategies *Includes case studies of protein assemblages and machines

Download or read book Mass Spectrometry Based Chemical Proteomics written by W. Andy Tao and published by John Wiley & Sons. This book was released on 2019-07-10 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: PROVIDES STRATEGIES AND CONCEPTS FOR UNDERSTANDING CHEMICAL PROTEOMICS, AND ANALYZING PROTEIN FUNCTIONS, MODIFICATIONS, AND INTERACTIONS—EMPHASIZING MASS SPECTROMETRY THROUGHOUT Covering mass spectrometry for chemical proteomics, this book helps readers understand analytical strategies behind protein functions, their modifications and interactions, and applications in drug discovery. It provides a basic overview and presents concepts in chemical proteomics through three angles: Strategies, Technical Advances, and Applications. Chapters cover those many technical advances and applications in drug discovery, from target identification to validation and potential treatments. The first section of Mass Spectrometry-Based Chemical Proteomics starts by reviewing basic methods and recent advances in mass spectrometry for proteomics, including shotgun proteomics, quantitative proteomics, and data analyses. The next section covers a variety of techniques and strategies coupling chemical probes to MS-based proteomics to provide functional insights into the proteome. In the last section, it focuses on using chemical strategies to study protein post-translational modifications and high-order structures. Summarizes chemical proteomics, up-to-date concepts, analysis, and target validation Covers fundamentals and strategies, including the profiling of enzyme activities and protein-drug interactions Explains technical advances in the field and describes on shotgun proteomics, quantitative proteomics, and corresponding methods of software and database usage for proteomics Includes a wide variety of applications in drug discovery, from kinase inhibitors and intracellular drug targets to the chemoproteomics analysis of natural products Addresses an important tool in small molecule drug discovery, appealing to both academia and the pharmaceutical industry Mass Spectrometry-Based Chemical Proteomics is an excellent source of information for readers in both academia and industry in a variety of fields, including pharmaceutical sciences, drug discovery, molecular biology, bioinformatics, and analytical sciences.

Download or read book Analysis and Identification of Proteins from Human Cells Using Mass Spectrometry Combined with Liquid Chromatography Electrophoresis and Database Searching written by Yajuan Chen and published by . This book was released on 1999 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Method Development and Application of Mass Spectrometry for Better Understanding of Disease Mechanisms and Diagnosis written by Yuan Liu (Ph.D.) and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry is a very powerful tool for identifying and quantifying biomolecules of interest, including metabolites, drug compounds, proteins, and post-translational modifications of (PTMs) of proteins. In mass spectrometry (MS)-based analytical techniques, liquid-chromatography coupled with tandem mass spectrometry (LC-MS/MS) is widely used for biomolecule analysis, including relative and absolute quantification of metabolites, proteins and PTMs. Data dependent acquisition (DDA) and data-independent acquisition (DIA) are two main methods for quantification of biomolecules in LC-MS/MS. By integrating isotopic and/or isobaric tags labeling, the DDA method enables precise absolute quantification and high-throughput analysis of biomolecules, facilitating biomarker discovery and elucidation of disease mechanisms. In contrast, DIA has garnered significant interest due to its exceptional reproducibility and depth in identifying and quantifying biomolecules. In this dissertation work, I apply these isotopic/isobaric tag labeling and label-free strategies to investigate potential biomarkers in the serum of Alzheimer's disease (AD) and colorectal cancer (CRC). Additionally, I explore the crosstalk between pancreatic stellate cells and pancreatic cancer cells using multi-faceted MS approaches.In addition to LC-MS/MS, mass spectrometry imaging (MSI) offers unparalleled insights into the spatial distribution of biomolecules across organs, tissues, and cell cultures, further enhancing our understanding of biological systems. We develop a tagging method to enhance the identification, quantification, and visualization of amine-containing metabolites by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Furthermore, I optimize a workflow for rapid sample preparation and high throughput MSI of biomolecule distribution in a widely used three-dimensional cell culture system - spheroids. In summary, the integration of various mass spectrometry techniques and method development discussed in this dissertation demonstrates that combining different mass spectrometry approaches can provide a more comprehensive molecular picture of the complex biological system, ultimately enhancing our understanding of disease mechanisms and advancing diagnosis and treatment options.

Download or read book Ultra Performance Liquid Chromatography Mass Spectrometry written by Mu Naushad and published by CRC Press. This book was released on 2014-03-18 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a unique collection of up-to-date UPLC-MS/MS (ultra performance liquid chromatography-tandem mass spectrometric) methods for the separation and quantitative determination of pesticides, capsaicinoids, heterocyclic amines, aflatoxin, perfluorochemicals, acrylamide, procyanidins and alkaloids, lactose content, phenolic compounds, vitamins, and aroma and flavor compounds in a wide variety of foods and food products. With contributions by experts in interdisciplinary fields, this reference offers practical information for readers in research and development, production, and routing analysis of foods and food products.

Download or read book The Use of 2D LC MS MS in Disease Characterization and Global Proteomics written by Jeffrey Clark Joyner and published by . This book was released on 2006 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Proteins occupy more than 50% of the dry weight of the average human cell. The proteins present in a given cell at a given time reflect the function and specialization of that cell. In addition to the specialization of cells within the body leading to various normal protein states, protein 'sub-states' can be induced by various conditions such as infections or cancer [9,21]. These disease-induced protein sub-states result in both qualitative and quantitative differences in both ribosomal production of proteins and posttranslational modification of proteins [2]. Each disease-induced sub-state therefore has its own protein profile or signature. For diseases such as cancer, which can easily progress undetected and whose manifestations have grave consequences, statistical comparisons of a patient's protein profile with many cancer-state protein profiles can be made for early detection. Two-dimensional-liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) holds much promise in the analysis of such diseaseinduced protein profiles. 2D-LC-MS/MS uses two means of separation prior to online mass analysis, whereas one-dimensional (1D) methods use only one means of separation. The increased separation of a 2D system allows for much more complete mass analysis of proteins and results in the identification and characterization of many more proteins and modifications than with a 1D system [15]. By comparing patients' protein profiles with a comprehensive proteomic database, 2D-LC-MS/MS could serve as the critical step in an efficient early-detection method for diseases such as cancer. Before protein profiles can be accurately compared and linked with diseases, a standardized technique must be used, and mechanisms that account for experimental variations must be implemented. The 2DLC- MS/MS technique proposed here is both very useful and can be standardized easily.

Download or read book Development of a Novel Liquid Chromatography Based Tool to Study Post translational Modifications written by and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: There are many tools available for the study of post-translational modifications. The majority of these tools is specific towards the individual modification and involves separation of modified proteins from non-modified ones. The drawback of using a modification specific method is that there is a lack of flexibility in its usage for other modifications. The goal of these studies was to investigate the possibility of obtaining a similar separation effect by fractionating post-translationally modified proteins based on the physical properties of proteins. The post-translational modification chosen to be the basis of this study was the O-GlcNAc modification. Using the C2C12 mouse myoblast cell line, it was determined that the optimal conditions for producing lysates containing increased yields of O-GlcNAc modified proteins was to treat differentiated C2C12 cells with 10nM insulin, 12g/L glucose and 2mM of the O-GlcNAcase inhibitor Streptozotocin for 24 hours. Using the optimized lysis buffer, it was shown that protein separation by surface charge using standard anion exchange separation did not provide enough resolution or material to obtain any identifications of modified proteins. However, when a chromatofocusing method which separates proteins on the basis of their isoelectric points was used, a separation scheme with larger capacity and higher resolution was possible. Using this separation method followed by gel electrophoresis of individual fractions, proteins which are potentially O-GlcNAc modified were identified by mass spectrometry. It was evident from the number of protein bands observed per fraction on the Coomassie stained gels and the number of proteins identified per protein band by mass spectrometry that further reduction in sample complexity was required to assist in the positive identification of O-GlcNAc modified proteins. Among the identified proteins, 32 percent were metabolic proteins, 21 percent were protein processing proteins, 16 percent were s.

Download or read book Proteome Informatics written by Conrad Bessant and published by Royal Society of Chemistry. This book was released on 2016-11-15 with total page 429 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of proteomics has developed rapidly over the past decade nurturing the need for a detailed introduction to the various informatics topics that underpin the main liquid chromatography tandem mass spectrometry (LC-MS/MS) protocols used for protein identification and quantitation. Proteins are a key component of any biological system, and monitoring proteins using LC-MS/MS proteomics is becoming commonplace in a wide range of biological research areas. However, many researchers treat proteomics software tools as a black box, drawing conclusions from the output of such tools without considering the nuances and limitations of the algorithms on which such software is based. This book seeks to address this situation by bringing together world experts to provide clear explanations of the key algorithms, workflows and analysis frameworks, so that users of proteomics data can be confident that they are using appropriate tools in suitable ways.

Download or read book Proteome Characterization and Proteomics written by Timothy D. Veenstra and published by Academic Press. This book was released on 2003-10-01 with total page 445 pages. Available in PDF, EPUB and Kindle. Book excerpt: The content of this volume is designed to reach a wide audience, including those involved with relevant technologies such as electrophoresis and mass spectrometry, to those interested in how proteomics can benefit research. A wide range of techniques are discussed, each specifically designed to address different needs in proteomic analysis. The concluding chapter discusses the important issue related to handling large amounts of data accumulated in proteomic studies. Discusses proteomics in the postgenomic age Includes various strategies for quantitative proteomics Covers the role of MS in structural functional proteomics and proteomics in drug discovery and bioinformatics