In this study a new method was developed for analysis of the low molecular weight protein fraction of milk, allowing a simple and fast overview of the peptide profile of various milk samples. For this purpose, immobilized metal affinity chromatography (IMAC) was coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). By this technique, two major peptides in milk could be identified as fragments of alpha-s1-casein. During heat treatment of raw milk, five new peptides were generated, the origin of which could be assigned to the casein fraction. Storage experiments with extended shelf life milk at 4 degrees C did not show any changes in the peptide profile, whereas in ultra high temperature milk stored at room temperature, one peptide increased significantly, which was identified as the N-terminus of alpha-s1-casein. The peptide was assumed to be formed in an enzymatic reaction, which was confirmed in a storage experiment with sterilized milk. Analyses of different commercially available milk samples confirmed the results obtained with the heated and stored milk. Furthermore, differences in the peptide profiles of the samples, probably due to different cow breeds or lactation stages, were observed. These results establish IMAC prior to MALDI-TOF-MS as a valid tool for the rapid analysis of the peptide profile of milk.