 For her first postdoc, she remained at UCLA working on protein biochemistry-biophysics for the Jules Stein Eye Institute with advisor, Joseph Horwitz.She then moved to San Diego to work with advisor George Somero on protein chemistry enzymology at the Scripps Institute of Oceanography at the University of California, San Diego.On the side McFall-Ngai had been exploring the Hawaiian bobtail squid as an alternative to the fish she had studied in graduate school and initiated what would become a career-long collaboration with microbiologist, Edward (Ned) Ruby, who had written his dissertation on the squids’ symbionts, "Vibrio fischeri".