The immunopeptidomics experimental workflow differs from the bottom-up proteomics workflow based on the way peptides are obtained prior to MS analysis. In immunopeptidomics, peptides are processed in vivo or in vitro inside the cell. The peptide-bound MHC molecules are extracted and the immunopeptides are eluted. In bottom-up proteomics, the peptides are produced during an experimental step where a protease, usually trypsin, is used to produce the peptides. This allows a reduction of the search space based on known digestion rules, which is not possible in immunopeptidomics.