Table I Model systems and paradigms used in large-scale phosphoproteomic studies
Model systems or paradigmsExamplesAdvantagesLimitations
Growth factors and other agonistsInsulin, EGF, serum, DNA damaging agents, metforminAllows for acute stimulations as well as temporal studiesSpecificity will vary. Needs to be combined with more specific approaches (i.e., inhibitors or RNAi).
Constitutively activated protein kinaseOncogenes (e.g., activated B-Raf or PI3K)Specific activation of a particular pathway. Often, clinically relevant mutations can be used.May lead to the identification of indirect mechanisms
Loss-of-function of pathway inhibitorsTumor suppressors (e.g., TSC2, PTEN)Specific activation of a particular pathway. Often, clinically relevant mutation can be used.May lead to the identification of indirect mechanisms
Pharmacological inhibitorsVarious (e.g., rapamycin, PI-103, PD184352)Allows for acute inhibition and temporal studies. May be very specific or target several related proteins.Specificity could be an issue
RNA interferenceshRNA or siRNACan be highly specific. Possibility of use in vivo and with an inducible system.May lead to the identification of indirect mechanisms