We present combination of capillary electrophoresis (CE) with fluorescence and matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) detection for protein analysis and identification. After separation in CE column, proteins are deposited on MALDI target. The position of protein bands can be found using native fluorescence excited with a 266 nm laser. The proteins in the bands of interest are digested directly on MALDI target and, after addition of MALDI matrix, identified from peptide fingerprint using MALDI MS. Addition of matrix after separation enables true decoupling and independent optimization of CE and MALDI MS. The presented arrangement is an alternative approach to commonly used methods, such as combination of gel electrophoresis and MALDI MS.