He returned to the University of Nebraska in late 1945 and completed his M.S. degree in 1947. He went on to work under William Miller at Cornell University where he earned his Ph.D. in 1950. He went on to a postdoctoral researcher position at the University of Iowa with R.L. Shriner.
He took a position at Dow Chemical in Midland, Michigan in 1950 and was in charge of mass spectrometry and gas chromatography from 1950 to 1956. In 1956, he became the Director of Dow’s Eastern Research Lab in Framingham, Massachusetts. During this time, he developed the first GC/MS instruments[2] and developed techniques for determining the structure of organic molecules by mass spectrometry, most notably in the discovery of what is now known as the McLafferty rearrangement.[1]
From 1964 to 1968, he was Professor of Chemistry at Purdue University. In 1968, he returned to his alma mater, Cornell University, to become the Peter J. W. DebyeProfessor of Chemistry. He was elected to the United States National Academy of Sciences in 1982. While at Cornell, McLafferty assembled one of the first comprehensive data bases of mass spectra and pioneered artificial intelligence techniques to interpret GC/MS results.[5] His PBM STIRS program has widespread use to save hours of time consuming work otherwise required to manually analyze GC/MS results.