Proteins are understood to be the main workhorses in the cell, participating in a wide variety of activities from cell structure to inter- and intra-cellular transport. This work integrates key technologies and identifies areas for further development in proteogenomics. Focuses on a comprehensive approach that combines large-scale proteomic data with genomic and/or transcriptomics data in genome annotation refinement and the elucidation of novel regulatory mechanisms.
Author(s): Mohamed A. Selmy
Publisher: Delve Publishing
Year: 2018
Language: English
Pages: 300
City: Oakville
Cover
Half Title Page
Title Page
Copyright Page
About The Author
Table of Contents
List of Figures
List of Tables
List of Abbreviations
Preface
Chapter 1 Introduction to Proteogenomics
References
Chapter 2 Modern Omic Technologies
2.1. Genomic Technologies
2.2. Transcriptome Analysis
2.3. Proteomic Analysis
References
Chapter 3 Proteomics Bioinformatics Tools in Proteogenomics Studies
3.1. Introduction
3.2. Database Search Engines
3.3. Results Integration
3.4. Limitations In Database Searching
3.5. Application To Proteogenomics
3.6. Conclusion
References
Chapter 4 Proteogenomics Softwares
4.1. Proteogenomics Software
References
Chapter 5 Mutant Proteogenomics
5.1. Introduction
5.2. Theoretical Considerations
5.3. Methodologies For Detection Of Mutant Proteins
5.4. Biological Findings
References
Chapter 6 Proteogenomics Analysis In Cancer Research
6.1. Introduction
6.2. Bioinformatics Tools For SAP In Cancer Detection
6.3. Proteogenomics Methods For The Identification of SAPs Using Shotgun Experiments
6.4. Summary
References
Chapter 7 Proteogenomics Analysis Of Oncogenic Mutations
7.1. Introduction
7.2. Lung Cancer Subtypes And Mutations
7.3. Clinical Proteogenomics
7.4. Development Of Proteogenomics Technologies To Identify/Quantify Mutated Proteins
7.5. Cellular Pathways Affected By Somatic Mutations
7.6. Drug Resistance And Gatekeeper Mutations
7.7. Perspective
References
Chapter 8 Proteogenomics For Environmental Microbiology
8.1. Introduction
8.2 An Evaluation Of Errors Occurring During Genome Sequencing and Annotation
8.3. Proteogenomics Is Targeting At Better Annotation of Gene Structures
8.4. N-Terminomics Is The Tool To Success
8.5. Should We Trust In Proteogenomics Results?
8.6. Extending The Notions of Proteogenomics
8.7. Potentials In Environmental Microbiology
References
Chapter 9 Proteogenomics For The Analysis Of Human
Antibody Repertoires
9.1. Introduction
9.2. Proteogenomics
9.3. Analysis Methods For Sequencing Immunoglobulin Genes
9.4. De Novo Protein Sequencing of Monoclonal Antibodies
9.5. Native Mass Spectrometry
9.6. Clinical Potentials of Proteogenomics Approaches
9.7. Conclusions
References
Chapter 10 Concluding Marks
Index
