Table of ContentsPreface1. Sample Origin, Stephen R. Pennington, Ph.D.2. Sample Preparation for Proteomic Analyses by Mass Spectrometry, John C. Rogers, Ph.D.2.2 Plant structure and specificity - challenges and sample preparation considerations for proteomics, Sophie Alavarez, Ph.D3. Protein Fractionation and Enrichment for Proteomics, Andrew J. Alpert, Ph.D.4. High Performance Liquid Chromatography, Mark L. Stolowitz, Ph.D5. Mass Analyzers, Anthony M. Haag, Ph.D.6. Top-Down Mass Spectrometry: Proteomics to Proteoforms, Steven M. Patrie7. Platforms and pipelines for Proteomics Data Management and Analysis, Sven Nahnsen, Ph.D.8.1 Visualization, inspection and interpretation of shotgun proteomics identification results, Marc Vaudel, Ph.D. and Harald Barsnes, Ph.D.8.2 Tandem mass spectrum sequencing: an alternative to database search engines in shotgun proteomics, Marc Vaudel, Ph.D. and Harald Barsnes, Ph.D.8.3 Protein Inference, Zengyou He, Ph.D.8.4 Modification Site Localization in Peptides, Robert J. Chalkley, Ph.D9. Quantification, Yun Chen, Ph.D.10. Bioinformatics Tools for the Analysis of Proteomics Data, Karla Grisel Calderón-González, Ph.D.11. Useful Web Resources, Maria D. Persons, Ph.D.12. Top-Down Mass Spectrometry: Proteomics to Proteoforms, Stephen Patrie, Ph.D.13. Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments through an MRM-with-Standard-Peptides Quantitative Approach, Andrew J. Percy, Ph.D. and Christoph H. Borchers, Ph.D.14. Posttranslational Modifications (PTMs) analysis, Ruijun Tian, Ph.D.15. Protein-Protein Interaction, Stephen R. Pennington, Ph.D.16. Structural Analysis, Antonio Artigues, Ph.D.17. Introduction to Proteomic-Derived Biomarkers, John E. Wiktorowicz, Ph.D.18. Discovery of Candidate Biomarkers, John E. Wiktorowicz, Ph.D.19. Statistical Approaches to Candidate Biomarker Panel Selection, John E. Wiktorowicz, Ph.D.20. Qualification and Verification of biomarker candidates, John E. Wiktorowicz, Ph.D.... Mehr