The utility of 193 nm ultraviolet photodissociation (UVPD) is evaluated for high-throughput proteomics applications including: analysis of small peptides in a traditional bottom-up proteomics workflow, analysis of heavily modified larger middle down sized peptides, and heavily modified intact proteins in a top-down proteomics workflow. UVPD uses higher energy ultraviolet photons (193 nm, 6.4 eV per photon), which are absorbed by the backbone to activate and dissociate ions effectively. UVPD dissociation is able to generate extensive backbone fragmentation enabling excellent characterization of peptides and proteins compared to traditional methods. Moreover, UVPD is also less hindered by certain experimental variables such as degree of modification, charge state and even ion polarity. These features are easily capitalized on for proteomics applications especially analysis of post translational modifications (PTM's). Characterization of PTM's is of great interest due to their involvement in several important cellular processes including cell signaling, tumorigenesis and gene expression. The studies covered in this work focus on utilizing the unique capabilities of UVPD to: 1.) characterize underrepresented peptides (acidic peptides and phosphopeptides) in the negative polarity including development of software for the analysis of the data generated, 2.) analyze intact proteins which have undergone extensive chemical modification and charge state augmentation, and 3.) precisely characterize histone proteins which are heavily modified due to their central role in gene expression and other transcription related functions.

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.

"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.

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

Comprehensive Foodomics, Three Volume Set offers a definitive collection of over 150 articles that provide researchers with innovative answers to crucial questions relating to food quality, safety and its vital and complex links to our health. Topics covered include transcriptomics, proteomics, metabolomics, genomics, green foodomics, epigenetics and noncoding RNA, food safety, food bioactivity and health, food quality and traceability, data treatment and systems biology. Logically structured into 10 focused sections, each article is authored by world leading scientists who cover the whole breadth of Omics and related technologies, including the latest advances and applications. By bringing all this information together in an easily navigable reference, food scientists and nutritionists in both academia and industry will find it the perfect, modern day compendium for frequent reference. List of sections and Section Editors: Genomics - Olivia McAuliffe, Dept of Food Biosciences, Moorepark, Fermoy, Co. Cork, Ireland Epigenetics & Noncoding RNA - Juan Cui, Department of Computer Science & Engineering, University of Nebraska-Lincoln, Lincoln, NE Transcriptomics - Robert Henry, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia Proteomics - Jens Brockmeyer, Institute of Biochemistry and Technical Biochemistry, University Stuttgart, Germany Metabolomics - Philippe Schmitt-Kopplin, Research Unit Analytical BioGeoChemistry, Neuherberg, Germany Omics data treatment, System Biology and Foodomics - Carlos Leon Canseco, Visiting Professor, Biomedical Engineering, Universidad Carlos III de Madrid Green Foodomics - Elena Ibanez, Foodomics Lab, CIAL, CSIC, Madrid, Spain Food safety and Foodomics - Djuro Josic, Professor Medicine (Research) Warren Alpert Medical School, Brown University, Providence, RI, USA & Sandra Kraljevic Pavelic, University of Rijeka, Department of Biotechnology, Rijeka, Croatia Food Quality, Traceability and Foodomics - Daniel Cozzolino, Centre for Nutrition and Food Sciences, The University of Queensland, Queensland, Australia Food Bioactivity, Health and Foodomics - Miguel Herrero, Department of Bioactivity and Food Analysis, Foodomics Lab, CIAL, CSIC, Madrid, Spain Brings all relevant foodomics information together in one place, offering readers a ‘one-stop,’ comprehensive resource for access to a wealth of information Includes articles written by academics and practitioners from various fields and regions Provides an ideal resource for students, researchers and professionals who need to find relevant information quickly and easily Includes content from high quality authors from across the globe

Explains the role of reactive intermediates in biological systems as well as in environmental remediation With its clear and systematic approach, this book examined the broad range of reactive intermediate that can be generated in biological environments, detailing the fundamental properties of each reactive intermediate. Readers gain a contemporary understanding of how these intermediates react with different compounds, with an emphasis on amino acids, peptides, and proteins. The author not only sets forth the basic chemistry and nature of reactive intermediates, he also demonstrates how the properties of the intermediates presented in the book compare with each other. Oxidation of Amino Acids, Peptides, and Proteins begins with a discussion of radical and non-radical reactive species as well as an exploration of the significance of reactive species in the atmosphere, disinfection processes, and environmental remediation. Next, the book covers such topics as: Thermodynamics of amino acids and reactive species and the effect of metal-ligand binding in oxidation chemistry Kinetics and mechanisms of reactive halogen, oxygen, nitrogen, carbon, sulfur and phosphate species as well as reactive high-valent Cr, Mn, and Fe species Reactivity of the species with molecules of biological and environmental importance Generation of reactive species in the laboratory for kinetics studies Oxidation of amino acids, peptides, and proteins by permanganate, ferryl, and ferrate species Application of reactive species in purifying water and treating wastewater With this book as their guide, readers will be able to assess the overall effects of reactive intermediates in biological environments. Moreover, they’ll learn how to apply this knowledge for successful water purification and wastewater treatment.

Breaking down large biomolecules into fragments in a controlled manner is key to modern biomolecular mass spectrometry. This book is a high-level introduction, as well as a reference work for experienced users, to ECD, ETD, EDD, NETD, UVPD, SID, and other advanced fragmentation methods. It provides a comprehensive overview of their history, mechanisms, instrumentation, and key applications. With contributions from leading experts, this book will act as an authoritative guide to these methods. Aimed at postgraduate and professional researchers, mainly in academia, but also in industry, it can be used as supplementary reading for advanced students on mass spectrometry or analytical (bio)chemistry courses.