Gas chromatography coupled to mass spectrometry (GC-MS) is one of the most widely used analytical techniques in metabolomics. While electron ionization (EI) is the common analytical standard for GC-MS, atmospheric pressure chemical ionization (APCI) became more prominent in recent years. The soft APCI ionization preserves molecular information and opens the doors to the world of unidentified metabolites which could not yet be annotated due to missing library data.

We report the application of a novel GC-APCI design coupled with high resolution oTOF-MS to analyse derivatized metabolite extracts and reference standards. Compared with earlier results [1], an improved analytical performance resulted in a higher number of compounds which could be identified in human cancer cell extracts.

Upon comparing previous APCI-I [1] and novel APCI-II ion sources, GC-APCI-II-TOFMS analysis resulted in improved peak shapes and much better peak area reproducibility for fatty acid methyl esters (FAMEs). Furthermore, overall decreased lower limits of quantification in the sub-micromolar range were found for twenty metabolites due to reduced background in the ion source. Meanwhile, the analytical linear working range was either maintained or slightly increased. The improved analytical performance enabled to approximately double the number of extracted peaks with signal-to-noise ratios >20 in cell culture supernatant samples of pancreatic cancer cells. Injecting PFTBA automatically into the source before each GC/MS run, lead to low ppm mass deviations for the standard compounds analyzed in this study. The higher number of peaks extracted and improved mass accuracy resulted in 36% more compounds which could be identified compared to the previous setup.

In summary, APCI-II has a number of notable improvements over APCI-I and holds great promise for further studies in metabolomics.