Differential Hydrogen-Deuterium eXchange Mass Spectrometry (ΔHDX-MS) was performed to determine the binding sites of 5 macrocycles (HL2, HL5, HD4, HHL1, HHD3) targeting Huntingtin (HTT) and HTT-HAP40 complex. To do so, HDX-MS was performed at 0, 0.5, 5, 30 mins using the Waters Select Series Cyclic IMS-MS in HDMSe mode coupled to robotic tool change liquid handling (PAL3, Trajan/LEAP) and ACQUITY UPLC M-Class System with HDX Technology (Waters). HDX labeling was performed using 10 mM Phosphate Buffer pD 7.5, 150 mM NaCl and quenched using 7.5 M Guanidine-HCl, 0.5 M TCEP, 100 mM Phosphate Buffer pH 2.5 at 0 °C for 2 min. These samples were diluted 1:1 with 100 mM Phosphate Buffer, pH 2.5 prior to injection, on-column digestion with 1:1 Nepenthesin 2-Pepsin (Affipro), desalting, and reverse-phase separation. Peptide deuterium uptake was analyzed using DynamX after peptide ID was performed using PLGS. The MS files deposited are in Waters .raw format.