Overview
- Editors:
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Simon J. Hubbard
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Fac. Life Sciences, University of Manchester, Manchester, United Kingdom
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Andrew R. Jones
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Fac. Veterinary Science, University of Liverpool, Liverpool, United Kingdom
- Includes cutting-edge informatics methods for identifying and quantifying proteins
- Provides descriptions of the main proteomics databases and guidance on proteomic data standards
- Gives an overview of statistics and scoring methods used in proteomics software
- Includes supplementary material: sn.pub/extras
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Table of contents (25 protocols)
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- Andrew R. Jones, Simon J. Hubbard
Pages 1-5
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- Zhao Song, Luonan Chen, Dong Xu
Pages 7-22
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- Markus Brosch, Jyoti Choudhary
Pages 43-53
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- Joshua E. Elias, Steven P. Gygi
Pages 55-71
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- Ashley C. Gucinski, Eric D. Dodds, Wenzhou Li, Vicki H. Wysocki
Pages 73-94
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- Henry Lam, Ruedi Aebersold
Pages 95-103
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- Christopher Hughes, Bin Ma, Gilles A. Lajoie
Pages 105-121
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- J. C. Wright, R. J. Beynon, S. J. Hubbard
Pages 123-135
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- Bindu Nanduri, Nan Wang, Mark L. Lawrence, Susan M. Bridges, Shane C. Burgess
Pages 137-144
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- Rene Hussong, Andreas Hildebrandt
Pages 145-161
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- Daniel Coca, Istvan Bogdan, Robert J. Beynon
Pages 163-185
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- Jennifer A. Chem (Mead), Luca Bianco, Conrad Bessant
Pages 187-199
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- Knut Reinert, Oliver Kohlbacher
Pages 201-211
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- Andrew W. Dowsey, Jeffrey S. Morris, Howard B. Gutstein, Guang-Zhong Yang
Pages 239-255
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- Wen-Lian Hsu, Ting-Yi Sung
Pages 257-272
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- Jason W. H. Wong, Gerard Cagney
Pages 273-283
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About this book
The feld 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 feld and a few appearing on the informatic and data analysis side. This latterly includes one in the Methods in Molecular Biology series tackling the specifc 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 consid- ations 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 aim of the volume is to provide the reader with a mix of reviews and methodology chapters, which build from the essentials of database searching in proteomics, on through specifc data processing challenges to databases, data standards and data models.
Editors and Affiliations
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Fac. Life Sciences, University of Manchester, Manchester, United Kingdom
Simon J. Hubbard
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Fac. Veterinary Science, University of Liverpool, Liverpool, United Kingdom
Andrew R. Jones
