Proteome Bioinformatics

ISBN-13: 9781493967384 / Angielski / Twarda / 2016 / 233 str.

Shivakumar Keerthikumar; Suresh Mathivanan

Opis

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.

Spis treści

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

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

Blurb

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.