Automated liquid chromatography tandem mass spectrometry (LC-MS/MS) is a well-established technique for identification of components from complex mixtures in shotgun proteomics experiments. Approaches involving the use of matrix-assisted laser desorption/ionization mass spectrometry (LC-MALDI-MS/MS) comprise the preparation of protein extracts, their enzymatic digestion, the separation of the resulting peptides by nanoscale liquid chromatography coupled to a collector that deposits the microfractions onto a MALDI plate, and finally the mass spectrometry analysis of the fractions. Using an LC-MALDI strategy, the rate of the collection of MS/MS data is decoupled from the chromatographic separation, thus allowing high-quality data which are often complementary to electrospray ionization (LC-ESI-MS/MS) techniques.