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,