Mass Spectrometry Based Proteomics as a Tool for the Analysis of Protein Protein Interactions in Signaling Processes

Waltraud X. Schulze

Max Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany [email protected]

Abstract This chapter focuses on the emerging technology of protein mass spectrometry and how it can be applied to the analysis of signaling pathways. Since proteins undergo posttranslational modifications, the analysis of the regulatory function of protein modification, especially phosphorylation, will be crucial for our view of plant signal transduction pathways. In addition, proteins are part of protein complexes and binary protein-protein interactions which need to be characterized in order to understand signal specificity and cross-talk. This chapter provides outlines of experiments involving (1) screening of interactions specific to protein modifications, (2) isolation of protein complexes, and (3) the analysis of kinases and their substrates. Finally, as signaling events are dynamic processes, the time component needs to be considered. Strategies implying quantitative proteomic methods are presented.

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