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Introduction to Proteomics Tools for the New Biology - Daniel C. Liebler

Contents


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
Index .........................................................................................................195

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