I. Proteomics and the Proteome 1 Proteomics and the New Biology 2 The Proteome II. Tools of Proteomics 3 Overview of Analytical Proteomics 4 Analytical Protein and Peptide Separations 5 Protein Digestion Techniques 6 Mass Spectrometers for Protein and Peptide Analysis 7 Protein Identification by Peptide Mass Fingerprinting 8 Peptide Sequence Analysis by Tandem Mass Spectrometry 9 Protein Identification with Tandem Mass Spectrometry Data 10 An Algorithm for Mining Specific Features of Tandem MS Data III. Applications of Proteomics 11 Mining Proteomes 12 Protein Expression Profiling 13 Identifying Protein-Protein Interactions and Protein Complexes 14 Mapping Protein Modifications 15 New Directions in Proteomics