Method for the identification and label-free quantification of at least one MHC ligand peptide in one or more primary tissue samples from at least one mammal, said method comprising a) isolating at least one MHC ligand peptide from at least one first healthy and a second diseased tissue sample corresponding to said primary diseased tissue, b) performing an HPLC-MS analysis on said MHC ligand peptides in order to generate a peptide signal therefor, c) determining the precursor ion signal area for each of said MHC ligand peptide signals, d) identifying the sequences for each of said MHC ligand peptides, by fragment spectra clustering and/or database search, e) determining an average quantity of the MHC ligand peptide by grouping areas between different runs, and normalizing said areas within replicate runs, in order to create an average value for each sample, f) determining relative quantities of the MHC ligand peptide that are comparable between samples, comprising f1) assigning the MHC ligand peptide to an allele-specific sequence subgroup for a comparison between different samples by identifying at least one MHC allele to which the MHC ligand peptide is expected to bind, and f2) normalizing between different samples using the allele-specific subgroups to account for different sample sizes and/or MHC expression levels; and f3) performing a data quality control based on peptide reproducibility for each sample, g) determining overpresentation of the MHC ligand peptide by calculating a presentation profile and/or a presentation score for the MHC ligand peptide of said diseased sample and said healthy sample based on said average and relative quantities of the MHC ligand peptide, and h) label-free quantification of the MHC ligand peptide. a) isolating at least one MHC ligand peptide from at least one first healthy and a second diseased tissue sample corresponding to said primary diseased tissue, b) performing an HPLC-MS analysis on said MHC ligand peptides in order to generate a peptide signal therefor, c) determining the precursor ion signal area for each of said MHC ligand peptide signals, d) identifying the sequences for each of said MHC ligand peptides, by fragment spectra clustering and/or database search, e) determining an average quantity of the MHC ligand peptide by grouping areas between different runs, and normalizing said areas within replicate runs, in order to create an average value for each sample, f) determining relative quantities of the MHC ligand peptide that are comparable between samples, comprising f1) assigning the MHC ligand peptide to an allele-specific sequence subgroup for a comparison between different samples by identifying at least one MHC allele to which the MHC ligand peptide is expected to bind, and f2) normalizing between different samples using the allele-specific subgroups to account for different sample sizes and/or MHC expression levels; and f3) performing a data quality control based on peptide reproducibility for each sample, f1) assigning the MHC ligand peptide to an allele-specific sequence subgroup for a comparison between different samples by identifying at least one MHC allele to which the MHC ligand peptide is expected to bind, and f2) normalizing between different samples using the allele-specific subgroups to account for different sample sizes and/or MHC expression levels; and f3) performing a data quality control based on peptide reproducibility for each sample, g) determining overpresentation of the MHC ligand peptide by calculating a presentation profile and/or a presentation score for the MHC ligand peptide of said diseased sample and said healthy sample based on said average and relative quantities of the MHC ligand peptide, and h) label-free quantification of the MHC ligand peptide.