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Köp båda 2 för 2615 krThis book introduces the reader to all the key concepts and technologies needed to begin developing their own bioinformatics tools. The new edition includes more bioinformatics-specific content and a new chapter on good software engineering practi...
This is a timely book for the proteomics researcher in guiding decision trees involved in the informatics pipelines of this rapidly developing field. The book does an excellent job in focusing on that part of the informatics discipline, both at the user interface and behind the scenes algorithms, that is of great importance to developing innovative and effective methods for protein interrogation. -- Taufika Islam Williams * Analytical and Bioanalytical Chemistry * Books topic: Proteomics, the comprehensive interrogation of proteins expressed by a living system, has enjoyed expeditious growth and development in recent years, as it brings together a range of informatics themes that fortify and support the everincreasing power of LC-MS/MS platforms to tackle important biological questions. Proteins are the vehicles of change in living cells and understanding them is elemental to understanding molecular biology. The complexity of the proteomics workflow, from sample preparation to LC-MS/MS to bioinformatics analyses, is such thatmore often than not, the intricacies and indeed shortcomings of the bioinformatics software are not carefully considered during data interpretation. This is an unwelcome prospect, given that comprehending the inner workings of living systems can be intimately tied to fluctuating patterns of protein expression,which can only be as thoroughly understood as the cumulative proteomics experiment allows. State-of-the-art sample preparation and LC-MS/MS will only be as biologically informative as the informatics methods with which data are interrogated. Proteome informatics is described as the ever increasing collection of bioinformatics methodologies that can be exercised in the analysis of protein expression. The book Proteome informatics, edited byConradBessant and the 5th volume of the Royal Society of Chemistry on New Developments in Mass Spectrometry, describes the bioinformatics of proteome analyses in the very context of proteomics workflows. It is an opportune discussion by leading experts on the current state of this evolving discipline, highlighting the essential fund of knowledge that will enable the proteomics expert, who may or may not be well-versed in computer science or statistics, to exploit and construct algorithms that can effectively interrogate gigabytes of data, while keeping a sharp focus on the limitations of what such software can reasonably underscore about the system being studied. Contents: This book is divided into four main sections, which follow an introductory chapter on proteome informatics. The first section describes protein identification and begins with manual de novo sequencing to more sophisticated de novo algorithms. The book steers into details of peptide spectrum matching by database search and the alternative spectral library search in use today. Despite the established advantages of the latter, the approach is only as good as the population of the library itself, which invariably limits the identification of experimental peptides and their post-translational modifications (PTMs). Discussion proceeds into peptide-spectrum match (PSM) scoring and validation, a lynchpin of proteome informatics which unequivocally dictates the goodness of fit in a given peptide (and subsequently protein) identification. Merits and demerits of common methods are briefly explored. This is proceeded by a chapter on protein grouping, which links identified peptides to identifying proteins. The section concludes with commentary on identification and positioning of the all-important PTMs. Indeed, the hundreds of in vivo PTMs (not to mention the many more possibilities of chemical modifications that may be artificially introduced into the system under investigation) are subject to change with changing cellular milieu, and hence are critical in a comprehensive proteomics study. The second section is dedicated to the quantification of proteins. Algorithms detailing MS1-based quantificati
Conrad Bessant is Professor of Bioinformatics at Queen Mary University of London. He has particular interests in proteomics, software development and machine learning and is striving to ensure that everyone using proteomics data can access the latest analysis methods and knows how to use them in the most effective way.
Introduction to Proteome Informatics; De Novo Sequencing; Peptide-Spectrum Matching; PSM Scoring and Validation; Protein Grouping; Identification and Localisation of Post Translational Modifications; Algorithms for MS1-Based Quantitation; Algorithms for MS2-Based Quantitation; Informatics Solutions for Selected Reaction Monitoring; Data Analysis for Data Independent Acquisition; Mining Proteomics Repositories; Data Formats of the Proteomics Standards Initiative; OpenMS; Using Galaxy for Proteomics; R for Proteomics; Proteogenomics: Proteomics for Genome Annotation; Proteomics Informed by Transcriptomics; Subject Index