The analysis of organic and biological substances by secondary-ion mass spectrometry (SIMS) has greatly benefited from the use of cluster ions as primary bombarding species. Thereby, depth profiling and three-dimensional (3D) imaging of such systems became feasible. Large Arn+ cluster ions may constitute a further improvement in this direction. To explore this option, size-selected Arn+ cluster ions with 300 ≤ n ≤ 2200 (bombarding energies 5.5 and 11 keV) were used to investigate the emission of positive secondary ions from four amino acid specimens (arginine, glycine, phenylalanine, and tyrosine) by time-of-flight SIMS. For all cluster sizes, the protonated molecule of the respective amino acid is observed in the mass spectra. With increasing cluster size the number of fragment ions decreases strongly in relation to the intact molecules, to the extent that the fraction of fragment ions amounts to less than 10% in some cases. Such ‘soft’ emission processes also lead the ejection of dimers and even multimers of the amino acid molecules. In the case of the phenylalanine, secondary ion species composed of up to at least seven phenylalanine moieties were observed. Tentatively, the ionization probability of the emitted molecules is envisaged to depend on the presence of free protons in the emission zone. Their number can be expected to decrease concurrently with the decreasing amount of fragmentation for large Arn+ cluster ions (i.e. for low energies per cluster atom). Copyright © 2011 John Wiley & Sons, Ltd.