Methods in Molecular Biology

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 Fenyo 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 Vizcaino, Florian Reisinger, Ingvar Eidhammer, and Lennart Martens 17. Automated Data Integration and Determination of Posttranslational Modifications 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 Tolic, Zhixin Tian, Errol W. Robinson, and Ljiljana Pasa-Tolic 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 Ebenhoh, 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