Algorithm-Driven Chromatographic Method for Prostaglandin Isomer Identification via Tandem Mass Spectrometry.

This study explores the computational isolation of prostaglandin (PG) isomers, specifically PG E (PGE) and D (PGD), to enhance method development efficiency and provide insights into their retention behavior during supercritical fluid extraction (SFE) combined with supercritical fluid chromatography (SFC)-tandem mass spectrometry (MS/MS). Although PGE and PGD are positional isomers that yield identical product ions in MS/MS, they serve distinct biological roles. This research illustrates the efficacy of selected reaction monitoring (SRM)-based techniques for differentiating coeluting isomers. Despite the challenges posed by baseline resolution, simplified computational methods successfully distinguished between PGE and PGD, demonstrating the potential for high-throughput PG analysis without the necessity for complete chromatographic peak resolution. By employing least-squares estimation to solve a linear system, the abundance ratio of PGE to PGD was derived from intensity ratios across four SRM transitions, achieving precise quantification even with poorly resolved SFC peaks. The study highlights critical factors affecting PG retention, such as the choice of the stationary phase, temperature regulation, and reduction of stainless steel interactions, which can diminish signal intensity. A significant observation is the concentration-dependent suppression effect of the entrainer when interacting with the hepatocyte matrix, underscoring the importance of effective matrix management in SFE/SFC-MS/MS. These findings advance the development of a robust, high-throughput analytical platform for PG quantification and lipidomics research applications.