Proteogenomics Methods and Protocols

This volume presents an up-to-date overview of the current state-of-the-art protocols, and aims to put proteogenomics into a broader perspective. The chapters in this book detail methods and techniques ranging from mass spectrometry to proteomics and proteogenomics and their biomedical implications and applications. Written in the highly successful Methods in Molecular Biology series format, the chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. A highlight for everyone new to the field are the chapters, which put proteogenomics to use to answer biomedical questions.

Authoritative and accessible, Proteogenomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.

De Novo Sequencing of Peptides from Tandem Mass Spectra and Applications in Proteogenomics.- Genome Annotation.- Comprehensive Peptide Mapping is Crucial for Proteogenomics and Proteomics.- A Review of Protein Inference.- From Gene to Whole Cell: Modelling, Visualization, and Analysis.- Introduction to Integrated Proteogenomic Pipeline for Dealing with Pathogenic Missense SNPs.- Discovering Novel Proteoforms using Proteogenomic Workflows within the Galaxy Bioinformatics Platform.- Comparative Proteomics of Bacteria under Stress Conditions.- The Functional Comparison of Eukaryotic Proteomes: Implications for Choosing an Appropriate Model Organism to Probe Human Biology.- Sample Preparation for Proteogenomics of Aquatic Invertebrates.- Proteogenomics for Non-Model Ocean-Derived Fungi.- Deciphering Cancer Complexity: Integrative Proteogenomics and Proteomics Approaches for Biomarker Discovery.- Biomarker Discovery via N-Glycoproteomics.- Proteogenomic Approaches for Diseasome Studies.- Comparative Proteogenomic Approaches for Mapping the Global Proteome of the Unsequenced Leishmania Vector Phlebotomus papatasi.- A Proteogenomic Approach for the Identification of Virulence Factors in Leishmania Parasites.- Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics.- Evaluation of Eukaryotic mRNA Coding Potential.