Proteome Bioinformatics

1. An Introduction to Proteome Bioinformatics Shivakumar Keerthikumar 2. Proteomic Data Storage and Sharing Shivakumar Keerthikumar and Suresh Mathivanan 3. Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data Dhirendra Kumar, Amit Kumar Yadav, and Debasis Dash 4. Label-Based and Label-Free Strategies for Protein Quantitation Sushma Anand, Monisha Samuel, Ching-Seng Ang, Shivakumar Keerthikumar, and Suresh Mathivanan 5. TMT One Stop Shop: From Reliable Sample Preparation to Computational Analysis Platform Mehdi Mirzaei, Dana Pascovici, Jemma X. Wu, Joel Chick, Yunqi Wu, Brett Cooke, Paul Haynes, and Mark P. Molloy 6. Unassigned MS/MS Spectra: Who Am I? Mohashin Pathan, Monisha Samuel, Shivakumar Keerthikumar, and Suresh Mathivanan 7. Methods to Calculate Spectrum Similarity Sule Yilmaz, Elien Vandermarliere, and Lennart Martens 8. Proteotypic Peptides and Their Applications Shivakumar Keerthikumar and Suresh Mathivanan 9. Statistical Evaluation of Labeled Comparative Profiling Proteomics Experiments Using Permutation Test Hien D. Nguyen, Geoffrey J. McLachlan, and Michelle M. Hill 10. De Novo Peptide Sequencing: Deep Mining of High-Resolution Mass Spectrometry Data Mohammad Tawhidul Islam, Abidali Mohamedali, Criselda Santan Fernandes, Mark S. Baker, and Shoba Ranganathan 11. Phylogenetic Analysis Using Protein Mass Spectrometry Shiyong Ma, Kevin M. Downard, and Jason W.H. Wong 12. Bioinformatics Methods to Deduce Biological Interpretation from Proteomics Data Krishna Patel, Manika Singh, and Harsha Gowda 13. A Systematic Bioinformatics Approach to Identify High Quality Mass Spectrometry Data and Functionally Annotate Proteins and Proteomes Mohammad Tawhidul Islam, Abidali Mohamedali, Seong Beom Ahn, Ishmam Nawar, Mark S. Baker, and Shoba Ranganathan 14. Network Tools for the Analysis of Proteomic Data David Chisanga, Shivakumar Keerthikumar, Suresh Mathivanan, and Naveen Chilamkurti 15. Determining the Significance of Protein Network Features and Attributes Using Permutation Testing Joseph Cursons and Melissa J. Davis 16. Bioinformatics Tools and Resources for Analyzing Protein Structures Jason J. Paxman and Begona Heras 17. In Silico Approach to Identify Potential Inhibitors for Axl-Gas6 Signalling Swathik Clarancia Peter, Jayakanthan Mannu, and Premendu P. Mathur