Identification of peptides presented in major histocompatibility complex (MHC) class I molecules after viral infection is of strategic importance for vaccine development. Until recently, mass spectrometric identification of virus-induced peptides was based on comparative analysis of peptide pools isolated from uninfected and virusinfected cells. Here we report on a powerful strategy aiming at the rapid, unambiguous identification of naturally processed MHC class I-associated peptides, which are induced by viral infection. The methodology, stable isotope tagging of epitopes (SITE), is based on metabolic labeling of endogenously synthesized proteins during infection. This is accomplished by culturing virus-infected cells with stable isotope-labeled amino acids that are expected to be anchor residues (i. The adaptive immune response to virus infections is characterized by the generation of CD8 ϩ cytotoxic T lymphocytes (CTLs), 1 which recognize peptides presented by MHC class I molecules of infected cells. The MHC class I molecules display peptides from proteins expressed inside the cell that are usually generated in the classical proteasomal pathway. Under physiological conditions these peptides are derived from self-proteins. During viral infection, the MHC class I display of peptides is affected due to changes in host protein expression and as a result of the production of viral proteins (1, 2). Identification and quantification of such altered MHC-peptide expression is a goal as part of a new field of research referred to as immunoproteomics and is of strategic importance for vaccine development (1, 3-5). The analytical challenge lies in the discrimination between the few disease-related peptides among a majority of nondisease-related peptides (6). Several strategies have been developed to explore changes in the MHC-associated peptide display on antigen-presenting cells. These analyses are generally based on the isolation of the MHC-peptide complexes, acid elution of the bound peptides from the MHC molecules followed by analysis using LC and MS as pioneered by Hunt et al. (7) and adapted for various purposes by other groups (4, 8 -11). We successfully used the mass spectrometric method to identify novel MHC class I-restricted viral epitopes by subtractive analysis of peptide pools isolated from virus-infected and control cells (9). This comparative method, however, needs meticulous parallel sample processing of the infected and control peptide batches, and differences in peptide recovery as well as chromatographic retention and stability between uninfected and infected peptide samples cannot be excluded. This has limited the use of subtractive analysis and might have led to the failure to identify viral epitopes (8, 10).The importance of CD8 ϩ T cells in the recovery from respiratory infections such as measles virus (MV) or respiratory syncytial virus (RSV) is generally acknowledged (12,13