About the Book
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
Şule Yılmaz, 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 Begoña Heras
17. In Silico Approach to Identify Potential Inhibitors for Axl-Gas6 Signalling
