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

The Special Issue “Plant Proteomics 3.0” was conceived in an attempt to address the recent advancements in as well as limitations of current proteomic techniques and their diverse applications to attain new insights into plant molecular responses to various biotic and abiotic stressors and the molecular bases of other processes. Proteomics’ focus is also related to translational purposes, including food traceability and allergen detection. In addition, bioinformatic techniques are needed for more confident identification, quantitation, data analysis and networking, especially with non-model or orphan plants, including medicinal and meditational plants as well as forest tree species. This Special Issue contains 23 articles, including four reviews and 19 original papers.

This book explores the mechanism of alkali-metal ion/molecule association reaction, surveys the instrumental basis to study its kinetic, and describes the instrumentation to the measurement of alkali-metal ion affinities. The applications of the ion complexation mechanism in the condensed phase in reaction to direct analysis MS are also covered. Other topics include mechanism and reaction rate, experimental and theoretical ion affinities, applications of ion attachment reactions (IAR) to mass spectrometry such as alkali ion CIMS, ion attachment MS and cationization mass spectrometry of ESI, FAB, FD, LD, MALDI and SIMS and topics of IAR-based direct analysis mass spectrometry.

This book highlights current approaches and future trends in the use of mass spectrometry to characterize protein therapies. As one of the most frequently utilized analytical techniques in pharmaceutical research and development, mass spectrometry has been widely used in the characterization of protein therapeutics due to its analytical sensitivity, selectivity, and specificity. This book begins with an overview of mass spectrometry techniques as related to the analysis of protein therapeutics, structural identification strategies, quantitative approaches, followed by studies involving characterization of process related protein drug impurities/degradants, metabolites, higher order structures of protein therapeutics. Both general practitioners in pharmaceutical research and specialists in analytical sciences will benefit from this book that details step-by-step approaches and new strategies to solve challenging problems related to protein therapeutics research and development.

Written by an experienced and well-published individual, this unique reference source takes a forward-looking approach. It describes the concepts and practice of protein phosphorylation analysis by tandem mass spectrometry and related techniques. These include purification, enrichment, database searching, other software tools, synthesis, phosphatase treatment, phospho-specific staining methods, isoelectric focusing and element mass spectrometry. The book then goes on to cover the fragmentation behaviour of phosphopeptides in tandem MS (pos+neg ions) and the implementation of the particular features into an analytical strategy. The book ends with a summary and discussion of useful internet and software tools currently available.

Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry Detailed resource presenting the capabilities of MALDI mass spectrometry (MS) to industrially and environmentally significant areas in the biosciences Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry fulfills a need to bring the key analytical technique of MALDI mass spectrometric analysis into routine practice by specialists and non-specialists, and technicians. It informs and educates established researchers on the development of techniques as applied to industrially significant areas within the biosciences. Throughout the text, the reader is presented with recognized and emerging techniques of this powerful and continually advancing field of analytical science to key areas of importance. While many scientific papers are reporting new applications of MS-based analysis in specific foci, this book is unique in that it draws together an incredibly diverse range of applications that are pushing the boundaries of MS across the broad field of biosciences. Contributed to by recognized experts in the field of MALDI MS who have been key players in promoting the advancement and dissemination of authoritative information in this field, Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry covers sample topics such as: Oil microbiology, marine and freshwater ecosystems, agricultural and food microbiology, and industrial waste microbiology Bioremediation and landfill sites microbiology, microbiology of inhospitable sites (e.g. Arctic and Antarctic, and alkaline and acidic sites, and hot temperatures) Veterinary, poultry and animals, viral applications of MS, and antibiotic resistance using tandem MS methods Recent developments which are set to transform the use of MS from its success in clinical microbiology to a wide range of commercial and environmental uses Bridging the gap between measurement and key applications, this text is an ideal resource for industrial and environmental analytical scientists, including technologists in the food industry, pharmaceuticals, and agriculture, as well as biomedical scientists, researchers, clinicians and academics and scientists in bio-resource centers.

To date, processing of high-throughput Mass Spectrometry (MS) data is accomplished using serial algorithms. Developing new methods to process MS data is an active area of research but there is no single strategy that focuses on scalability of MS based methods. Mass spectrometry is a diverse and versatile technology for high-throughput functional characterization of proteins, small molecules and metabolites in complex biological mixtures. In the recent years the technology has rapidly evolved and is now capable of generating increasingly large (multiple tera-bytes per experiment) and complex (multiple species/microbiome/high-dimensional) data sets. This rapid advance in MS instrumentation must be matched by equally fast and rapid evolution of scalable methods developed for analysis of these complex data sets. Ideally, the new methods should leverage the rich heterogeneous computational resources available in a ubiquitous fashion in the form of multicore, manycore, CPU-GPU, CPU-FPGA, and IntelPhi architectures. The absence of these high-performance computing algorithms now hinders scientific advancements for mass spectrometry research. In this book we illustrate the need for high-performance computing algorithms for MS based proteomics, and proteogenomics and showcase our progress in developing these high-performance algorithms.

The aim of this book is to provide the researcher with important sample preparation strategies in a wide variety of analyte molecules, specimens, methods, and biological applications requiring mass spectrometric analysis as a detection end-point. In this volume we have compiled the contributions from several laboratories which are employing mass spectrometry for biological analysis. With the latest inventions and introduction of highly sophisticated mass spectrometry equipment sample preparation becomes an extremely important bottleneck of biomedical analysis. We have a goal of giving the reader several successful examples of sample preparation, development and optimization, leading to the success in analytical steps and proper conclusions made at the end of the day. This book is structured as a compilation of contributed chapters ranging from protocols to research articles and reviews. The main philosophy of this volume is that sample preparation methods have to be optimized and validated for every project, for every sample type and for every downstream analytical technique.

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.

This book offers a balanced mixture of practice-oriented information and theoretical background as well as numerous references, clear illustrations, and useful data tables. Problems and solutions are accessible via a special website. This new edition has been completely revised and extended; it now includes three new chapters on tandem mass spectrometry, interfaces for sampling at atmospheric pressure, and inorganic mass spectrometry.