In July 1999, two existing units (the Protein Structure Lab and the Facility for Advanced Instrumentation) were combined to form the current Molecular Structure Facility. The PSL served as a core facility that primarily focused on the conventional biochemical techniques for protein analysis including Edman sequencing and amino acid analysis. The FAI instrumentation consisted of electron microscopes and a sector mass spectrometer. This merger was initiated in March 1998 to position the UC Davis campus for the postgenomic research era.

To exploit the proteomics revolution, the MSF acquired several advanced mass spectrometers, LC systems and other instrumentation through the awarded NIH Shared Instrumentation grants (1999-2000), the UC Initiative Fund (2000), funding from the School of Medicine (1998) and campus matching funds (1999-2000). The MSF is located in extensively renovated areas (4000 sq. ft.) in Hutchison Hall. Full operation of the MSF was not completed until early 2003 when the facility was able to appoint qualified scientists. The MSF is finally shifting into a performance stage from its long visionary phase. (1998-2002).