Secondary ion mass spectrometry instrumentation has improved dramatically over the last decade; however, our understanding of the data is yet to catch up. High mass resolution coupled with enhanced transmission and increases in duty cycle have revealed subtle detail in spectral features indicating that there is a wealth of information in our data that we have yet to take advantage of. Here, we present a collection of approaches that should improve our data interpretation. We cover websites delivering liquid chromatography–tandem mass spectrometry data as web services, allowing us to interact with collections of spectra produced via a similar fragmentation process. We show how simple spectral matching approaches suggest that we can compare data across disparate primary ion sources and mass analyser types, and we show how the management and use of metadata will help us to build resources to the benefit of future researchers. Copyright © 2012 John Wiley & Sons, Ltd.