Fragment pathway analysis using automated tandem mass spectrometry on an ion-trap mass spectrometer

A "key-sequence" procedure is presented for the automated tandem mass spectrometric analysis of compounds on a Finnigan ion-trap mass spectrometer. This allows fragmentation pathways of a range of masses or even a complete spectrum to be prepared automatically, obviating the tiresome preparation and optimization of individual scan-editor files. The procedure is limited by the speed of the driving computer; an "IBM-AT", for example, permits more than 10 mass units to be scanned per minute. It is calibrated with perfluorotributylamine and methyl stearate is used to demonstrate its results. The Finnigan ion-trap "programming option" is necessary for implementation of the procedure.