Although ion chemistry models1,2 have predicted proton hydrates (PH) that is ions of the form H+(H2O)n, as major ions in the stratosphere, the first in situ mass spectrometric measurements3-5 revealed another ion family, called non-proton hydrates (NPH). The fractional abundance of these NPH, represented by H +Xl(H2O)m, increases from 1 to 90% between 55 and 23 km (refs 1, 5-7). Several proposals5,8,9 have been made for the identity of the molecule X, but high resolution spectra 10 and ion abundance measurements11,12 suggest that X should be acetonitrile (CH3CN). This suggestion has been reinforced by laboratory measurements13,14 and in situ data between 20 and 42 km (refs 6, 7), allowing a determination of the concentration profile of X in this altitude region. Here we report the first positive ion composition data obtained using a balloon-borne instrument between 42 and 46 km altitude. These data extend the density profile of X and give supplementary indications about its identity.