Disclosed are methods, systems, and computer program products for using liquid chromatography/tandem mass spectrometry (LC-MS/MS) for the analysis of endogenous biomarkers, such as PGD2, in a biological sample. More specifically, the methods, systems, and computer program products are described for detecting and quantifying the amount of an PGD2 in a sample. The quantitative analysis may be helpful in making clinical diagnoses.