Proteogenomic Tools and Approaches to Explore Protein Coding Landscapes of Eukaryotic Genomes -- Next Generation Sequencing Data and Proteogenomics -- Proteogenomics: Key Driver for Clinical Discovery and Personalized Medicine -- Identification of Small Novel Coding Sequences, a Proteogenomics Endeavor -- Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies -- Mutant Proteogenomics -- Proteogenomic Analysis of Single Amino Acid Polymorphisms in Cancer Research -- Developments for Personalized Medicine of Lung Cancer Subtypes: Mass Spectrometry-based Clinical Proteogenomic Analysis of Oncogenic Mutations -- Proteomics for the Study of Gastrointestinal Stromal Tumors -- Proteogenomics for the Comprehensive Analysis of Human Cellular and Serum Antibody Repertoires -- Antibody-Based Proteomics

This book highlights key technologies and identifies areas for further development in proteogenomics. The utility and usefulness of very large Omics data sets (Next Gen Sequencing of DNA, RNA-seq, ribosome profiling, mass spectrometry- and antibody-based proteomics) is discussed and opportunities and challenges of related bioinformatics applications are outlined. The reader will be able to appreciate the interdisciplinary nature of the continuously evolving area of proteogenomics, which has already grown beyond its original concept of verifying gene annotations by proteomics. The chapters presented in this book are arranged to offer a general overview, rather than to provide detailed descriptions of technologies. The selected applications will provide useful insight into the level of detail that can be obtained in relation to certain diseases areas, including cancer biology and personalized medicine. The readers will find that each chapter delivers a comprehensive approach to proteogenomics, each from the point of view of a specific application. Research scientists interested in innovative processes that can offer a unique and at the same time a more complete access to technological developments and concepts that in turn can contribute to a better understand biological functions should read this book