Indoles are common building blocks of new pharmacologically active chemical entities in drug discovery and development. Due to their poor ionization in electrospray ionization mass spectrometry, atmospheric pressure chemical ionization (APCI) is the method of choice for LC-MS analysis of simple indoles. Three types of ions, including [M ？ 1]+, , and [M + H]+, can be observed in APCI but the relative intensities of these ions may vary depending upon the structural properties of the indoles and the mass spectral source conditions. We report in this paper the observation of [M ？ 1]+ ions for methylindoles in an Agilent multimode ion source and the investigation into their formation. By means of tandem mass spectrometric experiments performed on a Thermo Fisher Scientific LTQ ion trap mass spectrometer equipped with an APCI source, it was found that [M ？ 1]+ ions can be generated from ions upon-collision induced dissociation. This suggests that the [M ？ 1]+ ions might be the in-source fragmentation product of ions. It was proposed that both [M ？ 1]+ and ions are probably generated through a charge transfer mechanism while [M + H]+ ions are the product of proton transfer. The basicity of the analytes might play an important role in dictating which ionization mechanism is operative. For 3-methylindole, the charge transfer process appears to be more dominant than for 2-methylindole since the former is less basic. As expected, substituting electron withdrawing groups on 3-methylindole, such as fluorine, promotes charge transfer and vice versa. Therefore, it is expected that formation of the [M ？ 1]+ ions is more pronounced for less basic methylindoles. 1. Introduction Liquid chromatography-mass spectrometry (LC-MS) has been an increasingly popular tool for both qualitative and quantitative analysis of drugs and their related substances in all stages of drug development owing to its high sensitivity and specificity [1]. This includes, but is not limited to, the analysis of drug metabolites, degradation products, process impurities, extractables/leachables from packaging materials. Several atmospheric pressure ionization (API) techniques, including electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), atmospheric pressure photoionization (APPI), have been successfully interfaced with various mass spectrometric detectors and are widely used in pharmaceutical analysis. However, no single technique ionizes all types of pharmaceutical compounds. Generally, ESI ionizes polar compounds most efficiently and APPI is more suitable for nonpolar
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