Finnigan founded the Scientific Instruments Division of Electronic Associates, Inc., producing the first commercial quadrupole mass spectrometer in 1964.

He then formed Finnigan Instruments Corporation to combine a computer system with a quadrupole mass spectrometer and gas chromatograph.

Finnigan's GC/MS/computer systems are used to detect and identify trace organic compounds, making them important instruments for the monitoring and protection of the environment.

They were adopted by the United States Environmental Protection Agency as a standard instrument for monitoring water quality and were fundamental to the work of the EPA.

[5] Finnigan entered the United States Naval Academy in Annapolis, Maryland, in June 1945,[3]: 16  graduating in 1949 with a Bachelor of Science.

[3]: iii  On April 1, 1950, he married Bette Earl Van Horn at Perrin Air Force Base in Sherman, Texas.

[4][3]: 23 Because of his strong interest and aptitude in electrical engineering, he was able to enroll in an Air Force Institute of Technology program that sent qualified officers to graduate school.

[7][3] His master's thesis work with Edward C. Jordan used the ILLIAC to solve complex mathematical functions in antenna theory.

[3]: 28–38 [7] In 1962, Finnigan and one of his coworkers, physicist and nuclear engineer P. Michael Uthe Jr., left Livermore to work for the Stanford Research Institute (SRI) in Palo Alto, California.

The main research department of the company was based in Princeton, New Jersey, but Finnigan founded a new Scientific Instruments Division in Palo Alto, California.

[7] Finnigan's vision involved creation of a broad-based line of process-control instruments, beginning with the quadrupole mass spectrometer.

[3]: 47  Based on previous research at SRI, Finnigan was convinced that a market existed, but EAI and other companies such as IBM and Beckman Instruments were not interested in developing the quadrupole as a product at that time.

[9] Finnigan wanted to pursue development of computer-controlled instrumentation for a combined gas chromatograph (GC) and quadrupole mass spectrometer (MS).

The target machine was projected as having the ability to scan for pesticides with a resolving power of 1,000 to 10,000, across a broad range of 10 nanograms to one microgram.

[1][14][15] The models most generally used were Finnigan Corporation's 1015 and 3000 series of quadrupole mass spectrometers with a data system based on DEC's PDP-8 computers.

[14] The EPA also based its instruction manuals and standards for environmental testing on the Finnigan GC/MS, publishing the results in the Federal Register in 1979.