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In the present study, a novel approach for mid-infrared (IR)-based prediction of bovine milk fatty acid composition is introduced. A rapid, solvent-free, two-step centrifugation method was applied in order to obtain representative milk fat fractions. IR spectra of pure milk lipids were recorded with attenuated total reflection Fourier-transform infrared (ATR-FT-IR) spectroscopy. Comparison to the IR transmission spectra of whole milk revealed a higher amount of significant spectral information for fatty acid analysis. Partial least squar