Proteome Bioinformatics
The field of proteomics moves rapidly, as new methods, techniques, applications, standards, models and software appear almost on a daily basis. In Proteome Bioinformatics, expert researchers explore this ever-changing field, providing the reader with a mi
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Molecular Biology™
Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For other titles published in this series, go to www.springer.com/series/7651
Proteome Bioinformatics Edited by
Simon J. Hubbard Faculty of Life Sciences, The University of Manchester, Manchester, UK
Andrew R. Jones Department of Pre-clinical Veterinary Science, University of Liverpool, Liverpool, UK
Editor Simon J. Hubbard Faculty of Life Sciences The University of Manchester Manchester M13 9PT UK [email protected]
Andrew R. Jones Department of Pre-clinical Veterinary Science University of Liverpool Liverpool L69 7ZJ UK [email protected]
ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-60761-443-2 e-ISBN 978-1-60761-444-9 DOI 10.1007/978-1-60761-444-9 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2009941056 © Humana Press, a part of Springer Science+Business Media, LLC 2010 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. While the advice and information in this book are believed to be true and accurate at the date of going to press, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Humana Press is a part of Springer Science+Business Media (www.springer.com)
Preface The field of proteomics moves rapidly. New methods, techniques, applications, standards, models and software appear almost on a daily basis. Accompanying this are plenty of texts on the experimental side of the field and a few appearing on the informatic and data analysis side. This latterly includes one in the Methods in Molecular Biology series tackling the specific analysis of “Mass spectrometry data in proteomics” in MMB vol. 376. This current collection builds on this, but takes a broader view of proteome data analysis covering data analysis essentials, but also the databases and data models, as well as practical considerations for analysing database search results, annotating genomes, and speeding up searches. It also digs deeper into some topics, such as decoy database searching and aspects of signal processing in proteomic mass spectrometry. The ai
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