The proposed project combines mass spectrometry with already established techniques for protein interaction study, i.e. "foot printing" and "cross linking" in order to simplify and accelerate the characterisation of protein-nucleic acid inter- actions. Two ionisation methods, matrix assisted laser desorp- tion/ionisation (MALDI) and electrospray ionisation (ESI) have recently significantly improved the possibilities for mass spectrometrlc analysis of these biomolecules. High sensitivity (femtomoles) and short analysis time (some minutes) of these techniques have the potential to significantly improve the presently used methods for the study of interaction sites of proteins and nucleic acids. Accurate mass determination and fragment-ion studies in combination with specific chemical and biochemical degradation and modification reactions will be used to generate the needed structure information. Computer assisted combination of these data with information available in sequence data bases (mass spectrometric data as search criteria) will be the final step for the identification of the interaction sites in the participating biopolymers.