Modern Proteomics - Sample Preparation, Analysis and Practical Applications

Table of Contents

Preface

1. 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.D

3. Protein Fractionation and Enrichment for Proteomics; Andrew J. Alpert, Ph.D.

4. High Performance Liquid Chromatography; Mark L. Stolowitz, Ph.D

6. Top-Down Mass Spectrometry: Proteomics to Proteoforms; Steven M. Patrie

7. 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.D

9. 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.

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.