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The structure of a protein is essential for its function. Therefore, a variety of methods for analyzing protein structure have been developed recently; the most advanced and sensitive techniques have been selected for this manual. The presented procedures are well established and have been found useful in many laboratories; they are easy to perform and thus also suitable for beginners.§Enclosed are protocols on the separation of proteins and peptides, manual and automated microsequencing, electrophoresis and blotting, analysis of amino acids, identification of cysteine residues and lipids as well as on mass spectrometry crystallization of macromolecules.