Proteome bioinformatics / edited by Simon J. Hubbard and Andrew R. Jones.

Includes bibliographical references and index.

1. An introduction to proteome bioinformatics / Andrew R. Jones and Simon J. Hubbard -- 2. Bioinformatics methods for protein identifiction using peptide mass fingerprinting / Zhao Song, Luonan Chen, and Dong Xu -- 3. Computational approaches to peptide identification via tandem MS / Simon J. Hubbard --4. Scoring and validation of tandem MS peptide identification methods / Markus Brosch and Jyoti Choudhary -- 5. Target-decoy search strategy for mass spectrometry-based proteomics / Joshua E. Elias and Steven P. Gygi -- 6. Understanding and exploiting peptide fragment ion intensities using experimental and informatic approaches / Ashley C. Gucinski [and others] -- 7. Spectral library searching for peptide identification via tandem MS / Henry Lam and Ruedi Aebersold -- 8. De Novo sequencing methods in proteomics / Christopher Hughes, Bin Ma, and Gilles A. Lajoie -- 9. Cross species proteomics / J.C. Wright, R.J. Beynon, and S.J. Hubbard -- 10. Gene model detection using mass spectrometry / Bindu Nanduri [and others] -- 11. Signal processing in proteomics / Rene Hussong and Andreas Hildebrandt -- 12. A High performance reconfigurable computing solution for peptide mass fingerprinting / Daniel Coca, Istvan Bogdan, and Robert J. Beynon -- 13. Mining proteomic MS/MS data for MRM transitions / Jennifer A. Chem (Mead), Luca Bianco, and Conrad Bessant -- 14. OpenMS and TOPP: Open source software for LC-MS data analysis / Knut Reinert and Oliver Kohlbacher -- 15. Trans-Proteomic pipeline: a pipeline for proteomic analysis / Patrick G.A. Pedrioli -- 16. Informatics and statistics for analyzing 2-D gel electrophoresis images / Andrew W. Dowsey ... et al. -- 17. Automated generic analysis tools for protein quantitation using stable isotope labeling / Wen-Lian Hsu and Ting-Yi Sung -- 18. An Overview of label-free quantitation methods in proteomics by mass spectrometry / Jason W.H. Wong and Gerard Cagney -- 19. The PeptideAtlas Project / Eric W. Deutsch -- 20. Using the PRIDE proteomics identifications database for knowledge discovery and data analysis / Philip Jones and Lennart Martens -- 21. Molecular interactions and data standardisation / Sandra Orchard and Samuel Kerrien -- 22. Mass spectrometer ouput file format mxML / Eric W. Deutsch -- 23. Managing experimental data using FuGE / Andrew R. Jones and Allyson L. Lister -- 24. Proteomics data collection (ProDaC): Publishing and collection proteomics data sets in public repositories using standard formats / Christian Stephan [and others] -- 25. Computational resources for the prediction and analysis of native disorder in proteins / Melissa M. Pentony, Jonathan Ward, and David T. Jones.

Annotation 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 mix of review and methodology chapters which address the fundamentals of analysis methods, algorithms, data standards and databases. Chapters include practical considerations for analyzing database search results, annotating genomes, speeding up searches, and responding to specific data processing challenges. As a volume of the highly successful Methods in Molecular Biology series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results.Comprehensive and ground-breaking, Proteome Bioinformatics is an essential guidebook for the novice and expert alike, covering topics that address a wide range of data analysis and management problems.

Print version record.

English.