In‐source collision‐induced dissociation (IS‐CID): Applications, issues and structure elucidation with single‐stage mass analyzers

Abstract A discussion of the definition, advantages, and issues with the formation of ions in the transition region between an electrospray ionization (ESI) source and the ion optics of a mass analyzer is presented. The various types of ions formed in the so‐called in‐source collision‐induced dissociation (IS‐CID) process are illustrated. Applications of IS‐CID with single‐stage mass analyzers, such as structure elucidation and quantitation, are demonstrated. The discussion is illustrated by examples of the in‐source fragmentation of ginkgolides, which are marker compounds found only in Ginkgo biloba . Supercritical fluid chromatography (SFC) with non‐aqueous eluents was used to achieve a fast resolution of the ginkgolides without the hydrolysis reactions possible with aqueous high‐performance liquid chromatography (HPLC) eluents. In‐source ion generation occurs at relatively high pressures (ca. 1–3 torr) compared to the low pressure normally observed in collision chambers of tandem mass spectrometry (MS/MS). As a result, the fragmentation process is complex and often generates ions other than the fragments observed with classic CID or the same ions at different intensities. The objective of the current tutorial is to illustrate the conditions under which single‐stage, quadrupole or time‐of‐flight mass analyzers with electrospray or in‐air (direct analysis in real time; DART) ionization can be used for quantitation and structure elucidation in a manner similar to that observed with MS/MS. While the low m/z (≤ [M±H] ± ) ions formed in‐source often duplicate the ions observed in MS/MS systems, it is the focus of this discussion to illustrate the utility of in‐source generated fragment ions that may not be observed or observed at different intensities than in the collision cells of MS/MS instruments.