Protein–glycosaminoglycan (GAG) interactions play a central role in tissue engineering and drug delivery. A rapid and efficacious method for screening these interactions is essential. Raman spectroscopy was used to identify chemical interactions and conformational changes occurring upon binding between a synthetic peptide (QRRFMQYSARRF) and two glycosaminoglycans (GAGs), heparin and chondroitin 6-sulfate (C6S). The results identify three main chemical groups that are involved in the binding of the synthetic peptide with heparin and C6S. Tyrosine formed hydrogen bonds with the GAGs via its hydroxyl group. The amide I band demonstrated substantial shifts in Raman wavenumbers when bound to heparin and C6S (Δω = −10.2 ± 0.7 cm<sup>−1</sup> and Δω = −11.9 ± 0.3 cm<sup>−1</sup>, respectively), suggesting that the peptide underwent planar conformational changes after binding occurred. Upon binding to the peptide, the sulfate peak of heparin displayed a substantially greater shift in the Raman wavenumber (−7.5 ± 0.5 cm<sup>−1</sup>) than that of C6S (−2.6 ± 0.5 cm<sup>−1</sup>). The greater amide I and sulfate band shifts seen during peptide–heparin interactions are indicative of a stronger association compared to that between the peptide and C6S. This observation was confirmed by capillary electrophoresis, which demonstrated a lower dissociation constant (<i>K</i><sub>D</sub>) between the peptide and heparin (<i>K</i><sub>D</sub> of 19.2 ± 3.3 μM) than between the peptide and C6S (26.7 ± 2.5 μM). We conclude that the shift in the Raman wavenumbers of amide I and sulfate groups can be used for high-throughput screening of interaction affinities between libraries of peptides and GAGs.

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