Peripheral blood mononuclear cells are accessible through blood collection and represent a useful source for investigations on disease mechanisms and treatment response. Aiming to build a reference proteome database we generated three proteome datasets from mononuclear cells (MNCs) using a combination of SDS-PAGE and nano flow liquid chromatography mass spectrometry (nLC-MS/MS). Experiments were performed in triplicates and 514 unique proteins were identified by at least 2 peptides with 95% confidence for all replicates. Identified proteins are associated with a range of dermatologic, inflammatory and neurological conditions as well as molecular processes such as free radical scavenging and cellular growth and proliferation. Mapping the MNC proteome provides a valuable resource for studies on disease pathogenesis and the identification of therapeutic targets.