Compound identification is a major issue for many scientists but especially practitioners of metabolomics and phytochemists. The methods used, however, only highlight a mass-to-charge ratio and a retention time for identification purposes. This level of information is usually insufficient to identify a metabolite categorically, even when accurate mass systems have been used. Achieving full characterisation of the analyte requires the use of labour-intensive methods for isolation and subsequent analysis by orthogonal analytical techniques such as nuclear magnetic resonance spectroscopy to enable the identification of compounds or for further confirmation of activity by techniques such as bioassays. This paper reports on an automated and rapid method for the monitoring of preparative separation techniques. The described method is based on sequential flow injection analysis with mass spectral monitoring, using either single-stage or mass spectrometry to the nth power (MSn) techniques. The technique allows all the data from a single batch of fractions to be acquired into a single data file.