Peak fitting (PF) and partial least squares (PLS) regression have been independently developed for estimation of functional groups (FGs) from Fourier transform infrared (FTIR) spectra of ambient aerosol collected on Teflon filters. PF is a model that quantifies the functional group composition of the ambient samples by fitting individual Gaussian line shapes to the aerosol spectra. PLS is a data-driven, statistical model calibrated to laboratory standards of relevant compounds and then extrapolated to ambient spectra. In this work, we compare the FG quantification using the most widely used implementations of PF and PLS, including their model parameters, and also perform a comparison when the underlying laboratory standards and spectral processing are harmonized. We evaluate the quantification of organic FGs (alcohol COH, carboxylic COOH, alkane CH, carbonyl CO) and ammonium, using external measurements (organic carbon (OC) measured by thermal optical reflectance (TOR) and ammonium by balance of sulfate and nitrate measured by ion chromatography). We evaluate our predictions using 794 samples collected in the Interagency Monitoring of PROtected Visual Environments (IMPROVE) network (USA) in 2011 and 238 laboratory standards from Ruthenburg et al. (2014) (available at https://doi.org/10.1016/j.atmosenv.2013.12.034). Each model shows different biases. Overall, estimates of OC by FTIR show high correlation with TOR OC. However, PLS applied to unprocessed (raw spectra) appears to underpredict oxygenated functional groups in rural samples, while other models appear to underestimate aliphatic CH bonds and OC in urban samples. It is possible to adjust model parameters (absorption coefficients for PF and number of latent variables for PLS) within limits consistent with calibration data to reduce these biases, but this analysis reveals that further progress in parameter selection is required. In addition, we find that the influence of scattering and anomalous transmittance of infrared in coarse particle samples can lead to predictions of OC by FTIR which are inconsistent with TOR OC. We also find through several means that most of the quantified carbonyl is likely associated with carboxylic groups rather than ketones or esters. In evaluating state-of-the-art methods for FG abundance by FTIR, we suggest directions for future research.