Proteome Bioinformatics

1. Front Matter

   Pages i-xi

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2. An Introduction to Proteome Bioinformatics

   • Shivakumar Keerthikumar

   Pages 1-3

3. Proteomic Data Storage and Sharing

   • Shivakumar Keerthikumar, Suresh Mathivanan

   Pages 5-15

4. Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data

   • Dhirendra Kumar, Amit Kumar Yadav, Debasis Dash

   Pages 17-29

5. Label-Based and Label-Free Strategies for Protein Quantitation

   • Sushma Anand, Monisha Samuel, Ching-Seng Ang, Shivakumar Keerthikumar, Suresh Mathivanan

   Pages 31-43

6. 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 et al.

   Pages 45-66

7. Unassigned MS/MS Spectra: Who Am I?

   • Mohashin Pathan, Monisha Samuel, Shivakumar Keerthikumar, Suresh Mathivanan

   Pages 67-74

8. Methods to Calculate Spectrum Similarity

   • Şule Yilmaz, Elien Vandermarliere, Lennart Martens

   Pages 75-100

9. Proteotypic Peptides and Their Applications

   • Shivakumar Keerthikumar, Suresh Mathivanan

   Pages 101-107

10. Statistical Evaluation of Labeled Comparative Profiling Proteomics Experiments Using Permutation Test

    • Hien D. Nguyen, Geoffrey J. McLachlan, Michelle M. Hill

    Pages 109-117

11. De Novo Peptide Sequencing: Deep Mining of High-Resolution Mass Spectrometry Data

    • Mohammad Tawhidul Islam, Abidali Mohamedali, Criselda Santan Fernandes, Mark S. Baker, Shoba Ranganathan

    Pages 119-134

12. Phylogenetic Analysis Using Protein Mass Spectrometry

    • Shiyong Ma, Kevin M. Downard, Jason W. H. Wong

    Pages 135-146

13. Bioinformatics Methods to Deduce Biological Interpretation from Proteomics Data

    • Krishna Patel, Manika Singh, Harsha Gowda

    Pages 147-161

14. 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, Shoba Ranganathan

    Pages 163-176

15. Network Tools for the Analysis of Proteomic Data

    • David Chisanga, Shivakumar Keerthikumar, Suresh Mathivanan, Naveen Chilamkurti

    Pages 177-197

16. Determining the Significance of Protein Network Features and Attributes Using Permutation Testing

    • Joseph Cursons, Melissa J. Davis

    Pages 199-208

17. Bioinformatics Tools and Resources for Analyzing Protein Structures

    • Jason J. Paxman, Begoña Heras

    Pages 209-220

18. In Silico Approach to Identify Potential Inhibitors for Axl-Gas6 Signaling

    • Swathik Clarancia Peter, Jayakanthan Mannu, Premendu P. Mathur

    Pages 221-229

19. Back Matter

    Pages 231-233

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This thorough book covers the most recent proteomics techniques, databases, bioinformatics tools, and computational approaches that are used for the identification and functional annotation of proteins and their structure. The most recent proteomic resources widely used in the biomedical scientific community for storage and dissemination of data are discussed. In addition, specific MS/MS spectrum similarity scoring functions and their application in the field of proteomics, statistical evaluation of labeled comparative proteomics using permutation testing, and methods of phylogenetic analysis using MS data are also described in detail. Written for the highly successful Methods in Molecular Biology series, chapters contain the kind of detail and key implementation advice to ensure successful results. 

Authoritative and cutting-edge, Proteome Bioinformatics serves as a useful resource for researchers who are beginners as well as advanced investigators in the field of proteomics.

• Mass spectrometry instrumentation
• MS-based proteomics
• Databases
• Computational approaches
• Tandem MS techniques
• Statistical evaluation
• Phylogenetic analysis

• Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia

  Shivakumar Keerthikumar, Suresh Mathivanan

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