The ion composition at high-altitude (3454 m a.s.l.) was measured with an Atmospheric Pressure interface Time of Flight mass spectrometer (APi-TOF) during a period of nine months, from August 2013 to April 2014. The negative mass spectra were dominated by the ions of sulfuric, nitric, malonic and methanesulfonic acid (MSA) as well as SO5- . The most prominent positive ion peaks were from amines. The other cations were mainly organic compounds clustered with a nitrogen-containing ion, which could be either NH4+ or an aminium. Occasionally the positive spectra were characterized by groups of compounds each differing by a methylene group. In the negative spectrum, sulfuric acid was always observed during clear sky conditions following the diurnal cycle of sun irradiation. On many occasions we also saw a high signal of sulfuric acid during night time when clusters up to the tetramer were observed. A plausible reason for these events could be evaporation from particles at low relative humidity. A remarkably strong correlation between the signals of SO5- and CH3SO3- was observed for the full measurement period. The presence of these two ions during both the day and the night suggests a non-photochemical channel of formation which is possibly linked to halogen chemistry. Halogenated species, especially Br– and IO3- , were frequently observed in air masses that originated mainly from the Atlantic Ocean and occasionally from continental areas based on back trajectory analyses. We found I2O5 clustered with an ion, a species that was proposed from laboratory and modelling studies. All halogenated ions exhibited an unexpected diurnal behaviour with low values during day time. New particle formation (NPF) events were observed and characterized by 1) highly oxygenated molecules (HOMs) and low sulfuric acid or 2) ammonia-sulfuric acid clusters. We present characteristic spectra for each of these two event types based on 26 nucleation episodes. The mass spectrum of the ammonia-sulfuric acid nucleation event compares very well with laboratory measurements reported from the CLOUD chamber. A source receptor analysis indicates that new particle formation events at the Jungfraujoch take place within a restricted period of time of 24-48 hours after air masses have had contact with boundary layer. This time frame appears to be crucial to reach an optimal oxidation state and concentration of organic molecules necessary to facilitate nucleation.