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Analysis And Identification Of Proteins From Human Cells Using Mass Spectrometry Combined With Liquid Chromatography Electrophoresis And Database Searching
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Book Synopsis Analysis and Identification of Proteins from Human Cells Using Mass Spectrometry Combined with Liquid Chromatography, Electrophoresis, and Database Searching by : Yajuan Chen
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:
Book Synopsis Protein Sequencing and Identification Using Tandem Mass Spectrometry by : Michael Kinter
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
Book Synopsis Coupling Liquid Chromatography to Capillary Zone Electrophoresis Tandem Mass Spectrometry for Deep Top-down Proteomics by : Elijah Neal McCool
Download or read book Coupling Liquid Chromatography to Capillary Zone Electrophoresis Tandem Mass Spectrometry for Deep Top-down Proteomics written by Elijah Neal McCool and published by . This book was released on 2021 with total page 182 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomes are very complex with a large number of unique proteoforms spread across a wide concentration dynamic range. This means that an MS-based platform with highly efficient separation and highly sensitive detection of proteoforms is required. Capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) has been suggested as one such platform. When coupled to offline liquid chromatography-based fractionation, CZE-MS/MS has proven to be invaluable to the TDP community.In Chapter 2, the first optimization of dynamic pH junction-based sample stacking for TDP is provided along with one of the first comparisons of reversed-phase liquid chromatography coupled to mass spectrometry (RPLC-MS) and CZE-MS/MS. Optimization of dynamic pH junction is performed with a standard protein mixture, and this platform was ultimately applied to an Eschericia coli (E. coli) whole cell lysate. This resulted in the largest TDP dataset for single-shot CZE-MS/MS. The comparison of RPLC-MS/MS and CZE-MS/MS also included analysis of an E. coli cell lysate and resulted in high numbers of identifications and highlighted the various pros and cons of each method.In Chapter 3, two dimensional LC fractionation (size exclusion chromatography (SEC) and RPLC) was coupled to CZE-MS/MS for deep TDP of E. coli cells. This study resulted in the largest TDP dataset, at the time, for E. coli, identifying 5700 proteoforms and 850 proteins. We were also able to identify and localize various interesting PTMs and estimate protein abundances using a spectral counting method. From this study it was clear thatour platform was comparable to other RPLC-MS/MS methods for deep TDP in terms of number of proteoform identifications and total instrument time.In Chapter 4, we applied our TDP platform to two isogenic colorectal cancer (CRC) cell lines, SW480 and SW620, from primary and metastatic tumors. Genetic changes have been known for a long time to affect CRC progression but this was the first proteoform-level deep TDP study of CRC metastasis. In total, we identified over 23000 proteoforms and over 2000 proteins, for the largest TDP dataset of any cell type and was a 400% increase in terms of identifications over previous deep TDP studies. We used a special database searching tool to identify single amino acid variants (SAAVs) for the largest dataset of proteoforms containing SAAVs. Quantitative analysis identified 460 proteoforms with significant differences in abundance between SW480 and SW620. Several of these proteoforms were also phosphorylated which could further impact disease progression and outcome for a specific patient phenotype and could serve as biomarkers for deciding how to treat a patient or for drug development.In Chapter 5, both activated ion electron transfer dissociation (AI-ETD) and ultraviolet photodissociation (UVPD) at 213 nm were coupled to CZE for deep TDP of E. coli and zebrafish brain samples, respectively. Optimized CZE-AI-ETD and CZE-UVPD resulted in large numbers of proteoform identifications, and many important modifications were identified and localized using these effective fragmentation techniques. This included N-terminal acetylation, methylation, S-thiolation, disulfide bonds, and lysine succinylation.In Chapter 6, a variety of insights into the future of TDP are provided. This includes important applications for TDP, such as personalized medicine, drug development, embryonic development, and pathogen identification. Also, a few advancements to the TDP workflow that may have increased focus on in the future are mentioned.
Book Synopsis Proteomics Today by : Mahmoud H. Hamdan
Download or read book Proteomics Today written by Mahmoud H. Hamdan and published by John Wiley & Sons. This book was released on 2005-05-13 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: The last few years have seen an unprecedented drive toward theapplication of proteomics to resolving challenging biomedical andbiochemical tasks. Separation techniques combined with modern massspectrometry are playing a central role in this drive. This bookdiscusses the increasingly important role of mass spectrometry inproteomic research, and emphasizes recent advances in the existingtechnology and describes the advantages and pitfalls as well. * Provides a scientifically valid method for analyzing theapproximatey 500,000 proteins that are encoded in the humangenome * Explains the hows and whys of using mass spectrometry inproteomic analysis * Brings together the latest approaches combining separationtechniques and mass spectrometry and their application in proteomeanalysis * Comments on future challenges and how they may be addressed * Includes sections on troubleshooting
Book Synopsis New Methods in Peptide Mapping for the Characterization of Proteins by : William S. Hancock
Download or read book New Methods in Peptide Mapping for the Characterization of Proteins written by William S. Hancock and published by CRC Press. This book was released on 1995-10-23 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text is devoted to the characterization of recombinant DNA-derived proteins by peptide mapping. It describes new technological procedures including capillary electrophoresis, analysis of glycopeptides and the use of electrospray and matrix-assisted laser desorption mass spectrometry. The book presents practical procedures for preparing a protein sample, the enzyme digestion, choice of separation method and procedures for the structural analysis of the separated species. Many figures of peptide maps illustrate typical results. Tables of summary information about digestion, separation conditions, and analyses of important protein samples are also presented.
Book Synopsis Proteome Research: Mass Spectrometry by : Peter James
Download or read book Proteome Research: Mass Spectrometry written by Peter James and published by Springer Science & Business Media. This book was released on 2000-10-26 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in large scale DNA sequencing technology have made it possible to sequence the entire genome of an organism. Attention is now turning to the analysis of the product of the genome, the proteome, which is the set of proteins being expressed by a cell. Mass spectrometry is the method of choice for the rapid large-scale identification of these proteomes and their modifications. This is the first book to extensively cover the applications of mass spectrometry to proteome research.
Book Synopsis Protein and Peptide Analysis by LC-MS by : Thomas Letzel
Download or read book Protein and Peptide Analysis by LC-MS written by Thomas Letzel and published by Royal Society of Chemistry. This book was released on 2011-07-22 with total page 195 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the first example in presenting LC-MS strategies for the analysis of peptides and proteins with detailed information and hints about the needs and problems described from experts on-the-job. The best advantage is -for sure- the practical insight of experienced analysts into their novel protein analysis techniques. Readers starting in 'Proteomics' should be able to repeat each experiment with own equipment and own protein samples, like clean-up, direct protein analysis, after (online) digest, with modifications and others. Furthermore, the reader will learn more about strategies in protein analysis, like quantitative analysis, industrial standards, functional analysis and more.
Book Synopsis Protein Analysis using Mass Spectrometry by : Mike S. Lee
Download or read book Protein Analysis using Mass Spectrometry written by Mike S. Lee and published by John Wiley & Sons. This book was released on 2017-05-26 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents Practical Applications of Mass Spectrometry for Protein Analysis and Covers Their Impact on Accelerating Drug Discovery and Development Covers both qualitative and quantitative aspects of Mass Spectrometry protein analysis in drug discovery Principles, Instrumentation, Technologies topics include MS of peptides, proteins, and ADCs , instrumentation in protein analysis, nanospray technology in MS protein analysis, and automation in MS protein analysis Details emerging areas from drug monitoring to patient care such as Identification and validation of biomarkers for cancer, targeted MS approaches for biomarker validation, biomarker discovery, and regulatory perspectives Brings together the most current advances in the mass spectrometry technology and related method in protein analysis
Book Synopsis Protein Analysis and Purification by : Ian M. Rosenberg
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 2006-12-22 with total page 541 pages. Available in PDF, EPUB and Kindle. Book excerpt: How one goes about analyzing proteins is a constantly evolving ?eld that is no longer solely the domain of the protein biochemist. Inves- gators from diverse disciplines ?nd 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 ?lled 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 ?t individual experimental situations. This second edition pays homage to the computer explosion and the various genome projects that have revolutionized how benchtop scienti?c research is performed. Bioinformatics and In silico science are here to stay. However, the second edition still includes recipes for preparing buffers and methods for lysing cells.
Book Synopsis The Expanding Role of Mass Spectrometry in Biotechnology by : Gary Siuzdak
Download or read book The Expanding Role of Mass Spectrometry in Biotechnology written by Gary Siuzdak and published by . This book was released on 2006 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covers the basic concepts in mass spectrometry as well as advanced topics including protein identification/protein structural analysis, carbohydrate and oligonucleotide analysis. Topics also include pharmacokinetics, high throughput screening, and the recent development of mass spectrometry in clinical diagnosis.
Book Synopsis Microcharacterization of Proteins by : Roland Kellner
Download or read book Microcharacterization of Proteins written by Roland Kellner and published by John Wiley & Sons. This book was released on 2008-09-26 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomics - the analysis of the whole set of proteins and their functions in a cell - is based on the revolutionary developments which have been achieved in protein analysis during the last years. The number of finished genome projects is growing and in parallel there is a dramatically increasing need to identify the products of revealed genes. Acting on a micro level modern protein chemistry increases our understanding of biological events by elucidating the relevant structure-function relationships. The second edition of the successful title Microcharacterization of Proteins presents a current overview of modern protein analysis: From sample preparation to sequence analysis, mass spectrometry and bioinformatics it informs about the tools needed in protein research. This makes the book indispensable for everyone involved in proteomics!
Book Synopsis Protein and Peptide Mass Spectrometry in Drug Discovery by : Michael L. Gross
Download or read book Protein and Peptide Mass Spectrometry in Drug Discovery written by Michael L. Gross and published by John Wiley & Sons. This book was released on 2011-09-26 with total page 484 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book that highlights mass spectrometry and its application in characterizing proteins and peptides in drug discovery An instrumental analytical method for quantifying the mass and characterization of various samples from small molecules to large proteins, mass spectrometry (MS) has become one of the most widely used techniques for studying proteins and peptides over the last decade. Bringing together the work of experts in academia and industry, Protein and Peptide Mass Spectrometry in Drug Discovery highlights current analytical approaches, industry practices, and modern strategies for the characterization of both peptides and proteins in drug discovery. Illustrating the critical role MS technology plays in characterizing target proteins and protein products, the methods used, ion mobility, and the use of microwave radiation to speed proteolysis, the book also covers important emerging applications for neuroproteomics and antigenic peptides. Placing an emphasis on the pharmaceutical industry, the book stresses practice and applications, presenting real-world examples covering the most recent advances in mass spectrometry, and providing an invaluable resource for pharmaceutical scientists in industry and academia, analytical and bioanalytical chemists, and researchers in protein science and proteomics.
Book Synopsis Protein Structure Analysis by : Roza Maria Kamp
Download or read book Protein Structure Analysis written by Roza Maria Kamp and published by Springer Science & Business Media. This book was released on 1997 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Protein Structure Analysis - Preparation and Characterization" is a compilation of practical approaches to the structural analysis of proteins and peptides. Here, about 20 authors describe and comment on techniques for sensitive protein purification and analysis. These methods are used worldwide in biochemical and biotechnical research currently being carried out in pharmaceu tical and biomedical laboratories or protein sequencing facilities. The chapters have been written by scientists with extensive ex perience in these fields, and the practical parts are well documen ted so that the reader should be able to easily reproduce the described techniques. The methods compiled in this book were demonstrated in student courses and in the EMBO Practical Course on "Microsequence Analysis of Proteins" held in Berlin September 10-15, 1995. The topics also derived from a FEBS Workshop, held in Halkidiki, Thessaloniki, Greece, in April, 1995. Most of the authors participated in these courses as lecturers and tutors and made these courses extremely lively and successful. Since polypeptides greatly vary depending on their specific structure and function, strategies for their structural analysis must for the most part be adapted to each individual protein. Therefore, advantages and limitations of the experimen tal approaches are discussed here critically, so that the reader becomes familiar with problems that might be encountered.
Book Synopsis LC-MS/MS in Proteomics by : Pedro R. Cutillas
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.
Book Synopsis Characterization and Identification of Protein Posttranslational Modifications Using Protein Enrichment and Mass Spectrometry by : Liwen Wang
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.
Book Synopsis Mass Spectrometry of Proteins and Peptides by : John R. Chapman
Download or read book Mass Spectrometry of Proteins and Peptides written by John R. Chapman and published by Springer Science & Business Media. This book was released on 2008-02-05 with total page 539 pages. Available in PDF, EPUB and Kindle. Book excerpt: Little more than three years down the line and I am already writing the Preface to a second volume to follow Protein and Peptide Analysis by Mass . What has happened in between these times to make this second venture worthwhile? New types of mass spectrometric instrumentation have appeared so that new techniques have become possible and existing techniques have become much more feasible. More particularly, however, the newer ionization te- niques, introduced for the analysis of high molecular weight materials, have now been thoroughly used and studied. As a result, there has been an en- mous improvement in the associated sample handling technology so that these methods are now routinely applied to much smaller sample amounts as well as to more intractable samples. Again, this particular community of mass spectrometry users has both increased in number and diversified. And, riding this wave of acceptance, leaders in the field have set their sights on more complex problems: molecular interaction, ion structures, quantitation, and kinetics are just a few of the newer areas reported in Mass Spectrometry of Proteins and Peptides. As with the first volume, one purpose of this collection, Mass Spectr- etry of Proteins and Peptides, is to show the reader what can be done by the application of mass spectrometry, and perhaps even to encourage the reader to venture down new paths.
Book Synopsis Quantitative Proteomics by Mass Spectrometry by : Salvatore Sechi
Download or read book Quantitative Proteomics by Mass Spectrometry written by Salvatore Sechi and published by Springer Science & Business Media. This book was released on 2008-02-05 with total page 223 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a compendium of cutting-edge protocols for quantitative proteomics, and presents the most significant methods used in the field today. The focus on mass spectrometry (MS) is integral. Attention is given to state-of-the-art techniques for the characterization of the phosphoproteome and tandem MS for detection of inborn errors of metabolism. This volume is an indispensable resource in the search for novel biomarkers.
