Bioinformatics for Comparative Proteomics

2011
ISBN: 978-1-60761-976-5
Verlag: Humana Press

Buch, Englisch, Band 694, 387 Seiten, Format (B × H): 183 mm x 260 mm, Gewicht: 954 g

Reihe: Methods in Molecular Biology

With the rapid development of proteomic technologies in the life sciences and in clinical applications, many bioinformatics methodologies, databases, and software tools have been developed to support comparative proteomics study. In Bioinformatics for Comparative Proteomics, experts in the field highlight the current status, challenges, open problems, and future trends for developing bioinformatics tools and resources for comparative proteomics research in order to deliver a definitive reference providing both the breadth and depth needed on the subject. Structured in three major sections, this detailed volume covers basic bioinformatics frameworks relating to comparative proteomics, bioinformatics databases and tools for proteomics data analysis, and integrated bioinformatics systems and approaches for studying comparative proteomics in the systems biology context. Written for the highly successful Methods in Molecular Biology™ series, the contributions in this book provide the meticulous, step-by-step description and implementation advice that is crucial for getting optimal results in the lab.

Comprehensive and easy-to-use, Bioinformatics for Comparative Proteomics serves all readers who wish to learn about state-of-the-art bioinformatics databases and tools, novel computational methods and future trends in proteomics data analysis, and comparative proteomics in systems biology.

Zielgruppe

Professional/practitioner

Autoren/Hrsg.

Chen, Chuming

Wu, Cathy H.

Fachgebiete

• Naturwissenschaften Biowissenschaften Angewandte Biologie Bioinformatik
• Naturwissenschaften Biowissenschaften Biowissenschaften Genetik und Genomik (nichtmedizinisch)
• Naturwissenschaften Biowissenschaften Proteinforschung
• Mathematik | Informatik EDV | Informatik Angewandte Informatik Bioinformatik
• Naturwissenschaften Biowissenschaften Biochemie (nichtmedizinisch)
• Mathematik | Informatik EDV | Informatik Informatik

Inhaltsverzeichnis

Part I: Bioinformatics Framework for Comparative Proteomics

1. Protein Bioinformatics Databases and Resources
Chuming Chen, Hongzhan Huang, and Cathy H. Wu

2. A Guide to UniProt for Protein Scientists
Claire O’Donovan and Rolf Apweiler

3. InterPro Protein Classification
Jennifer McDowall and Sarah Hunter

4. Reactome Knowledgebase of Human Biological Pathways and Processes
Peter D'Eustachio

5. eFIP: A Tool for Mining Functional Impact of Phosphorylation from Literature
Cecilia N. Arighi, Amy Y. Siu, Catalina O. Tudor, Jules A. Nchoutmboube, Cathy H. Wu, and Vijay K. Shanker

6. A Tutorial on Protein Ontology Resources for Proteomic Studies
Cecilia N. Arighi

7. Structure-Guided Rule-Based Annotation of Protein Functional Sites in UniProt Knowledgebase
Sona Vasudevan, C.R. Vinayaka, Darren A. Natale, Hongzhan Huang, Robel Y. Kahsay, and Cathy H. Wu

Part II: Proteomic Bioinformatics

8. Modeling Mass Spectrometry-Based Protein Analysis
Jan Eriksson and David Fenyö

9. Protein Identification from Tandem Mass Spectra by Database Searching
Nathan J. Edwards

10. LC-MS Data Analysis for Differential Protein Expression Detection
Rency S. Varghese and Habtom W. Ressom

11. Protein Identification by Spectral Networks Analysis
Nuno Bandeira

12. Software Pipeline and Data Analysis for MS/MS Proteomics: The Trans-Proteomic Pipeline
Andrew Keller and David Shteynberg

13. Analysis of High-Throughput ELISA Microarray Data
Amanda M. White, Don S. Daly, and Richard C. Zangar

14. Proteomics Databases and Repositories
Lennart Martens

15. Preparing Molecular Interaction Data for Publication
Sandra Orchard and Henning Hermjakob

16. Submitting Proteomics Data to PRIDE Using PRIDE Converter
Harald Barsnes, Juan Antonio Vizcaíno, Florian Reisinger, Ingvar Eidhammer, and Lennart Martens

17. Automated Data Integration and Determination of Posttranslational Modiï¬cations with the Protein Inference Engine
Stuart R. Jefferys and Morgan C. Giddings

18. An Integrated Top-Down and Bottom-Up Strategy for Broadly Characterizing Protein Isoforms and Modifications
Si Wu, Nikola Tolić, Zhixin Tian, Errol W. Robinson, and Ljiljana Pasa-Tolić

Part III: Comparative Proteomics in Systems Biology

19. Phosphoproteome Resource for Systems Biology Research
Bernd Bodenmiller and Ruedi Aebersold

20. Protein-Centric Data Integration for Functional Analysis of Comparative Proteomics Data
Peter B. McGarvey, Jian Zhang, Darren A. Natale, Cathy H. Wu, and Hongzhan Huang

21. Integration of Proteomic and Metabolomic Profiling as well as Metabolic Modeling for the Functional Analysis of Metabolic Networks
Patrick May, Nils Christian, Oliver Ebenhöh, Wolfram Weckwerth, and Dirk Walther

22. Time Series Proteome Profiling
Catherine A. Formolo, Michelle Mintz, Asako Takanohashi, Kristy J. Brown, Adeline Vanderver, Brian Halligan, and Yetrib Hathout