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 SilicoApproach to Identify Potential Inhibitors for Axl-Gas6 Signalling
Swathik Clarancia Peter, Jayakanthan Mannu, and Premendu P. Mathur
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.