In addition to a variety of other techniques used in T-cell epitope identification, mass spectrometery coupled to liquid chromatography have now become an important and sensitive tool in separation, detection, and sequence analysis of highly complex natural major histocompatibility complex (MHC) ligand mixtures. In this article, we present current strategies for the identification of MHC eluted peptides using high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) with a particular recall to those presented in the context of the non classical human leukocytes antigen (HLA) class I molecule HLA-E. In addition we also discuss the advantages and disadvantages of the methods available in the literature to concentrate and fractionate the peptides prior to analysis by mass spectrometry. An application of our method for isolation and characterization of peptides presented in the context of HLA-E is finally reported.