Data set containing helium spin-echo (HeSE) measurements of surface phonons on a clean Ag(100) surface and molecular vibrational modes of cobalt phthalocyanine (CoPc) adsorbed on Ag(100). The data support the results presented in the associated publication. MATLAB scripts are provided for analysis and plotting. Raw experimental data files are included in data.zip. Clean Ag(100) data AgPhonon_Reconstruction.m MATLAB script to reconstruct and plot the two-dimensional wavelength–intensity matrix of the measured phonon signal. AgPhononDispersion_plot.m MATLAB script to plot the surface phonon dispersion relation for Ag(100). AgPhonon_AnalysisPlot.m MATLAB script for analysing the phonon linewidth as a function of temperature. AgPhonon_Fit.m MATLAB script containing the Ag(100) linewidth data together with model fits used in the analysis. Data for CoPc molecules adsorbed on Ag(100) CoPc_linewidth_Plot.m MATLAB script to plot the linewidth of the CoPc molecular vibrational modes measured on Ag(100). Data directories data.zip Archive containing the raw measurement data in MATLAB format.