Proteomics

Preface Introduction Experiments 1. Analysis of Whole-cell Lysates by Two-dimensional Gel Electrophoresis and MALDI Mass Spectrometry 2. Purification of Protein Complexes for Mass Spectrometry Analysis 3. Qualitative and Quantitative Measurement of Peptides with MALDI TOF/TOF Mass Spectrometry 4. Analysis of Protein Complexes: High-sensitivity Liquid Chromatography Coupled with Tandem Mass Spectrometry 5. Phosphopeptide Analysis Using IMAC and Mass Spectrometry 6. Multidimensional Protein Identification Technology (MudPIT) Analysis of Whole-cell Lysates 7. Quantitative Mass Spectrometry Analysis of Whole-cell Extracts (iTRAQ) 8. Analysis and Validation of Tandem Mass Spectra 9. High-throughput Cloning of ORFs: Assembling Large Sets of Expression Constructs 10. Construction of Protein Microarrays Nucleic Acid Programmable Protein Array (NAPPA) 11. Using the Nucleic Acid Programmable Protein Array (NAPPA) for Identifying Protein-Protein Interactions Appendices 1. Setup and Demonstration of a Nanoelectrospray Ionization (nanoESI) Source and Tandem Mass Spectrometry (MS/MS) 2. Solution Protein Digest 3. In-gel Trypsin Digest of Gel Fractionated Proteins 4. Trichloroacetic Acid (TCA) Precipitation of Proteins 5. Monoisotopic and Immonium Ion Masses of Amino Acids 6. Dipeptide Masses of Amino Acids 7. LTQ Instrument Methods 8. Off-line Desalting of Peptide Mixtures 9. Preparing Competent Cells 10. DNA Quantification 11. Cautions Index