Secondary ion mass spectrometry (SIMS) for biomolecular analysis is greatly enhanced by the instrumental combination of orthogonal extraction time-of-flight mass spectrometry with massive gold cluster primary ion bombardment. Precursor peptide molecular ion yield enhancements of 1000, and signal-to-noise improvements of up to 20, were measured by comparing SIMS spectra obtained using Au(+) and massive Au(400) (4+) cluster primary ion bombardment of neat films of the neuropeptide fragment dynorphin 1-7. Remarkably low damage cross-sections were also measured from dynorphin 1-7 and gramicidin S during prolonged bombardment with 40 keV Au(400) (4+). For gramicidin S, the molecular ion yield increases slightly as a function of Au(400) (4+) beam fluence up to at least 2 x 10(13) Au(400) (4+)/cm(2). This is in marked contrast to the rapid decrease observed when bombarding with ions such as Au(5) (+) and Au(9) (+). When gramicidin S is impinged with Au(5) (+), the molecular ion yield decreases by a factor of 10 after a fluence of only 8 x 10(12) ions/cm(2). Comparison of these damage cross-sections implies that minimal surface damage occurs during prolonged Au(400) (4+) bombardment. Several practical analytical implications are drawn from these observations.