To better guide the development of liquid chromatography/electron capture-atmospheric pressure photoionization-mass spectrometry (LC/EC-APPI-MS) in analysis of low polarity compounds, the ionization mechanism of 19 compounds was studied using dopant assisted negative ion-APPI. Four ionization mechanisms, i.e., EC, dissociative EC, proton transfer, and anion attachment, were identified as being responsible for the ionization of the studied compounds. The mechanisms were found to sometimes compete with each other, resulting in multiple ionization products from the same molecule. However, dissociative EC and proton transfer could also combine to generate the same [M Ϫ H] Ϫ ions. Experimental evidence suggests that O 2 Ϫ· , which was directly observed in the APPI source, plays a key role in the formation of [M Ϫ H] Ϫ ions by way of proton transfer. Introduction of anions more basic than O 2 Ϫ· , i.e., C 6 H 5 CH 2 Ϫ , into the APPI source, via addition of di-tert-butyl peroxide in the solvent and/or dopant, i.e., toluene, enhanced the deprotonation ability of negative ion-APPI. Although the use of halogenated solvents could hinder efficient EC, dissociative EC, and proton transfer of negative ion-APPI due to their EC ability, the subsequently generated halide anions promoted halide attachment to compounds that otherwise could not be efficiently ionized. With the four available ionization mechanisms, it becomes obvious that negative ion-APPI is capable of ionizing a wider range of compounds than negative ion chemical ionization (NICI), negative ion-atmospheric pressure chemical ionization (negative ion-APCI) or negative ion-electrospray ionization (negative ion-ESI). (J Am Soc Mass Spectrom 2007, 18, 1789 -1798) © 2007 American Society for Mass Spectrometry I t is well known that liquid chromatography mass spectrometry (LC/MS) favors the analysis of polar compounds, as acid-base solution reactions are the most commonly observed ionization mechanism when using electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI). Traditionally, gas chromatography mass spectrometry (GC/MS) using both electron ionization (EI) and chemical ionization (CI) is employed for the analysis of volatile and thermostable nonpolar compounds. However, it can become difficult to analyze nonvolatile and/or thermo-labile nonpolar compounds via hyphenated techniques of chromatography and MS.In the year 2000, atmospheric pressure photoionization (APPI) [1] was developed as a complement to LC/ESI-MS and LC/APCI-MS. Presently, two fundamentally different APPI sources are commercially available [1,2]. Syagen Technology (Tustin, CA) produces PhotoMate, and Applied Biosystems/MDS SCIEX (Concord, Ontario, Canada) markets PhotoSpray. In both designs, photons emitted by a krypton discharge lamp are used to initiate a series of gas-phase reactions, which finally lead to analyte ionization. However, they differ in that PhotoMate utilizes a design to enhance direct APPI, while PhotoSpray implements a design using a dopant, usually tolu...