Resource: Mass Spectrometry-based Methods of Proteome Analysis

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Mass Spectrometry-based Methods of Proteome Analysis --> [Only registered users see links. ]

Boris L. Zybailov and Michael P. Washburn
Stowers Institute for Medical Research, Kansas City, MO, USA

1 Principles and Instrumentation 3
1.1 Proteome and Proteomics 3
1.2 Need for Large-scale Analyses of Gene Products at the Protein Level 3
1.3 General Problems in Proteome Analyses 4
1.4 MS Instrumentation 5
1.4.1 Ionization Methods 6
1.4.2 Mass Analyzers 8
1.4.3 MS/MS 9
1.5 Methods of Sample Fractionation 10
1.5.1 2D-electrophoretic Separation of Complex Protein Mixtures 11
1.5.2 Liquid-phase Separation Methods 12
1.5.3 Affinity Methods (Epitope Tagging) 13
1.6 Protein Identification by MS 14
2 Quantitative Methods of Proteome Analysis Using MS 18
2.1 Metabolic Labeling 18
2.2 Isotope Coded Affinity Tags 20
2.3 18O Labeling 21
2.4 Postdigestion Labeling 22
2.5 Global mRNA and Protein Expression Analyses 23
3 Specific Examples of Applications 23
3.1 Global Proteome Sampling 23
3.1.1 Global Proteome Sampling Based on 2D Page 23
3.1.2 Global Proteome Sampling Based on Multidimensional LC 24
3.1.3 MS-assisted Disease Diagnosis from Serum Samples 25
3.2 Analysis of Protein Modifications by Mass Spectrometry 25
3.2.1 Phosphorylated Proteins 27
3.2.2 Glycosylated Proteins 28
3.2.3 Ubiquitinated Proteins 29
3.3 Analysis of Protein–Protein Interactions by Mass Spectrometry 30
3.3.1 Computational Methods of Protein–Protein Interaction Prediction 30
3.3.2 Yeast 2-hybrid Arrays 30
3.3.3 Direct Analysis of Large Protein Complexes; Composition of the
Yeast Ribosome 31
3.3.4 Analysis of Multisubunit Protein Complexes
Involved in Ubiquitin-dependent Proteolysis by Mass Spectrometry 31
3.3.5 Proteomics of the Nuclear Pore Complex 31
3.3.6 High-throughput Analyses of Protein–Protein Interactions 33
3.3.7 Quantitative Proteomics Methods in the Studies of Protein Complexes 35