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Raman and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy were used to analyze 208 breast milk samples as part of a larger research study. Comprehensive qualitative and quantitative analysis was carried out using chemometric methods: principal component analysis (PCA) and partial least squares (PLS) regression. The obtained information on the main macronutrients (protein, fat and carbohydrate) were primarily evaluated in relation to the available metadata of the samples, where study location and respective primary food sources revealed a stronger differentiation in fat composition than its absolute content. The limitations and challenges of using both spectroscopic techniques for the type of analysis are also highlighted.