Comprehensive knowledge of intracellular biochemistry is needed to accurately understand, model, and manipulate metabolism for industrial and therapeutic applications. Quantitative metabolomics has been driven by advances in analytical instrumentation and can add valuable knowledge to the understanding of intracellular metabolism. Liquid chromatography coupled to mass spectrometry (LC–MS and LC–MS/MS) has become a reliable means with which to quantify a multitude of intracellular metabolites in parallel with great specificity and accuracy. This work details a method that builds and extends upon existing reverse phase ion-paring liquid chromatography methods for separation and detection of polar and anionic compounds that comprise key nodes of intracellular metabolism by optimizing pH and solvent composition. In addition, the presented method utilizes multiple scan types provided by hybrid instrumentation to improve confidence in compound identification. The developed method was validated for a broad coverage of polar and anionic metabolites of intracellular metabolism.