Expression Pathology and Flagship Biosciences recently announced a services alliance in tissue-based proteomics, combining digital pathology with mass-spec FFPE tissue proteomics. While this collaboration is oriented towards research and companion diagnostics development, mass spec is making rapid inroads in all areas of clinical applications, including tissue. The ability to run protein expression in FFPE instead of fresh tissue is a major enhancement on the road to clinical adoption. Mass spec offers the ability to better characterize post-translational modifications of proteins and various isoforms, high levels of multiplexing, and the avoidance of dependence on a given target epitope or antibody for test results. It does require up to 30,000 cells for protein expression measurements, meaning approximately 2 mm x 4 mm of 10 micron thick tissue sample. Up until now, one of the most manual steps has been the selection of tissue for the microdissection, an obvious application where digital pathology and histology pattern recognition can have advantages. The Mayo Clinic licenses Expression Pathology's approach in the diagnosis and classification of amyloidosis in routine biopsy specimen. A number of large reference laboratories are systematically transitioning their small molecular analysis platforms from the traditional ELISAs that require antibodies to mass spec.