Non-targeted analysis (NTA) is an increasingly popular technique for characterizing undefined chemical analytes. Generating quantitative NTA (qNTA) concentration estimates requires the use of training data from calibration “surrogates”. The use of surrogate training data can yield diminished performance of concentration estimation approaches. In order to evaluate performance differences between targeted and qNTA approaches, we defined new metrics that convey predictive accuracy, uncertainty (using 95% inverse confidence intervals), and reliability (the extent to which confidence intervals contain true values). We calculated and examined these newly defined metrics across five quantitative approaches applied to a mixture of 29 per- and polyfluoroalkyl substances (PFAS). The quantitative approaches spanned a traditional targeted design using chemical-specific calibration curves to a generalizable qNTA design using bootstrap-sampled calibration values from chemical surrogates. This dataset is associated with the following publication: Pu, S., J. McCord, J. Bangma, and J. Sobus. Establishing performance metrics for quantitative non-targeted analysis: a demonstration using per- and polyfluoroalkyl substances. Analytical and Bioanalytical Chemistry. Springer, New York, NY, USA, 416: 1249-1267, (2024).