Formed in 2002, the Proteomics Core was created by the merger of the Protein Core Facility, which provided peptide synthesis and routine methods for protein analysis and separation, and the Biomedical Mass Spectrometry Core, which provided protein analysis and quantification by mass spectrometry.

Since that time, the Proteomics Core has operated with strong institutional support, and today it exists as one of seven cores within the Medical Genome Facility of the Center for Individualized Medicine at Mayo Clinic that provide consultations and services related to genomics and proteomics technologies. The core is also a shared resource of — and receives funding from — the Mayo Clinic Cancer Center.