Table of Contents

1 Mass Spectrometry and the Proteome.- 2 Basics of Triple-Stage Quadrupole/Ion-Trap Mass Spectrometry: Precursor, Product and Neutral-Loss Scanning. Electrospray Ionisation and Nanospray Ionisation.- 3 The Basics of Matrix-Assisted Laser Desorption, Ionisation Time-of-Flight Mass Spectrometry and Post-Source Decay Analysis.- 4 Data-Controlled Micro-Scale Liquid Chromatography — Tandem Mass Spectrometry of Peptides and Proteins: Strategies for Improved Sensitivity, Efficiency and Effectiveness.- 5 Solid-Phase Extraction-Capillary Zone Electrophoresis-Mass Spectrometry Analysis of Low-Abundance Proteins.- 6 Protein Identification by Peptide-Mass Fingerprinting.- 7 Protein Identification by SEQUEST.- 8 Interpreting Peptide Tandem Mass-Spectrometry Fragmentation Spectra.- 9 Automated Interpretation of Peptide Tandem Mass Spectra and Homology Searching.- 10 Specific Detection and Analysis of Phosphorylated Peptides by Mass Spectrometry.- 11 Glycoproteomics: High-Throughput Sequencing of Oligosaccharide Modifications to Proteins.- 12 Proteomics Databases.- 13 Quo Vadis.