Proteomics – in the post-genomics era

Protein identification:
One-dimensional gels (for example, analysis after affinity purification)
Two-dimensional gels (for example, analysis after affinity purification, body fluids, etc.)
Protein chips (chips coated with, for example, proteins or antibodies)
Proteins/protein complexes in solution (identification without electrophoresis)

Post-translational modifications
Phosphorylation
Glycosylation

Determining Function
Assays for enzymatic activity or determining substrates 
Bioassays for cytokines, receptor/ligand-binding assays
Localization within the cells (GFP fusions)
Proteomic analysis using large-scale mouse knockouts or RNA interference.
Phenotypic analysis using deletion strains 

Molecular Medicine (no longer just pharmaceuticals)
Finding molecular (protein) drug targets
Disrupting protein–protein interactions using drugs
Large-scale animal assays for recombinant proteins, antibodies and inhibitors

Differential display by two-dimensional gels (superseded by DNA-based array in many situations)
Limited applications in:
    Body fluids (for example, serum and urine)
    Variants resulting from post-translational modifications