Soft X-ray atmospheric pressure photoionization (soft X-ray APPI) as an ionization method in liquid chromatography–mass spectrometry (LC-MS) is presented. The ionization mechanism was examined with selected test compounds in the negative ion mode, using soft X-ray APPI source emitting 4.9 keV photons. Test compounds with an acidic group were ionized by a proton transfer reaction, producing deprotonated molecules ([M – H] − ), whereas compounds having positive electron affinity were ionized by a charge exchange reaction, producing negative molecular ions (M –• ). Soft X-ray APPI does not require a dopant to achieve high ionization efficiency, which is an advantage compared with vacuum ultraviolet APPI with 10 eV photons, in which a dopant is needed to improve ionization efficiency. The energy of the soft X-ray photons is in the keV range, which is high enough to displace a valence electron and often also inner shell electrons from LC eluents and atmospheric gases, initiating an efficient ionization process in the negative ion mode.