Functional proteomics provides a powerful approach to screen for molecular responses at the protein level. By combining 2D gels and mass spectrometry with standard molecular pharmacological approaches, responses to specific signal transduction pathways can be monitored. The results reveal novel targets for regulation by post-translational modification, which compliment information from gene array analyses. In addition, synergistic interactions between signaling effectors can be revealed by functional proteomics, providing new insight into combinatorial signaling between pathways. Examples illustrating applications to MAP kinase and Rho GTPase pathways will be presented. In a second study, 2D-gel based approaches reveal proteins that are differentially expressed between melanocyte vs melanoma cultured cell lines. Immunohistochemical analysis shows that expression of one of the identified proteins discriminates malignant melanoma from nontumorigenic melanocytes and nevi in human biopsies, revealing a likely marker of tumor initiation. Finally, recent results using high throughput MS protocols for protein profiling will be presented. These illustrate the powerful approach of multidimensional LC/MS/MS as well as new computational methods towards monitoring protein changes in response to signal transduction.
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