Affinity Depletion of Plasma and Serum for Mass Spectrometry-Based Proteome Analysis -- Tissue Sample Preparation for Biomarker Discovery -- Subcellular Fractionation for Identification of Biomarkers: Serial Detergent Extraction by Subcellular Accessibility and Solubility -- Analysis of Secreted Proteins -- Preparation of Human Cerebrospinal Fluid for Proteomics Biomarker Analysis -- Proteomic Analysis of Frozen Tissue Samples Using Laser Capture Microdissection -- Use of Formalin Fixed, Paraffin Embedded Tissue for Proteomic Biomarker Discovery -- Phosphopeptide Enrichment Using Offline Titanium Dioxide Columns for Phosphoproteomics -- iTRAQ-Labeling for Biomarker Discovery -- Analysis of Glycoproteins for Biomarker Discovery -- SILAC in Biomarker Discovery -- Trypsin-mediated 18O/16O Labeling for Biomarker Discovery -- Two-dimensional SDS-PAGE Fractionation of Biological Samples for Biomarker Discovery -- Informatics of Protein and Post-Translational Modification Detection via Shotgun Proteomics -- Quantitation of C-Met Tyrosine Phosphorylation Using MRM-MS -- Preparation of Human Serum for Prolactin Measurement by Multiple Reaction Monitoring Mass Spectrometry -- Label-Free Quantitative Shotgun Proteomics Using Normalized Spectral Abundance Factors -- Employment of Complementary Dissociation Techniques for Body Fluid Characterization and Biomarker Discovery -- DPhosphopeptide Microarrays for Comparative Proteomic Profiling of Cellular Lysates -- Tissue Preparation for MALDI MS Imaging of Protein and Peptides -- Plant Proteogenomics: From Protein Extraction to Improved Gene Predictions -- Label-free Differential Analysis of Murine Postsynaptic Densities -- Fractionation of Peptides by Strong Cation Exchange Liquid Chromatography.

With the advent of proteomics came the development of technologies, primarily mass spectrometry, which allowed high-throughput identification of proteins in complex mixtures.  While the mass spectrometer resides at the heart of proteomics, its ability to characterize biological samples is only as good as the sample preparation and data analysis tools used in any study.  In Proteomics for Biomarker Discovery, expert researchers in the field detail many of the methods which are now commonly used to study proteomics. These methods and techniques include both label-free approaches and those that utilize stable isotopes incorporated both during cell growth or added via a chemical reaction once the proteome is extracted from the cell. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.     Authoritative and practical, Proteomics for Biomarker Discovery seeks to aid scientists in the further study of the different sample preparation and data analysis tools used in proteomics today.