Introduction to proteomics : tools for the new biology

Foreword by J. R. Yates, III ..................................................................... v Preface ....................................................................................................... vii I. Proteomics and the Proteome .........................................................1 1. Proteomics and the New Biology .........................................................3 2. The Proteome .....................................................................................15 II. Tools of Proteomics .........................................................................25 3. Overview of Analytical Proteomics ...................................................27 4. Analytical Protein and Peptide Separations .....................................31 5. Protein Digestion Techniques ............................................................49 6. Mass Spectrometers for Protein and Peptide Analysis .....................55 7. Protein Identification by Peptide Mass Fingerprinting ....................77 8. Peptide Sequence Analysis by Tandem Mass Spectrometry ..........................................................................89 9. Protein Identification with Tandem Mass Spectrometry Data...........................................................................99 10. SALSA: An Algorithm for Mining Specific Features of Tandem MS Data.......................................................................109 III. Applications of Proteomics .........................................................123 11. Mining Proteomes ............................................................................125 12. Protein Expression Profiling ...........................................................137 13. Identifying Protein–Protein Interactions and Protein Complexes ..................................................................151 14. Mapping Protein Modifications ......................................................167 15. New Directions in Proteomics .........................................................185