We present annually to subdecadaly resolved GDGT-based (CCaT) sea surface temperature reconstruction from S5 sapropel layer recovered in the sediment core M51/3-SL104 (34.8247°N, 27.2925°E; water depth 2155 m) from the Pliny Trench region of the Eastern Mediterranean. We applied Mass Spectrometry Imaging (MSI) on finely laminated sapropel sediment in 200 µm resolution. We used CCaT ratio that was calibrated to SST. MSI was performed using a 7T solarix XR Fourier transform-ion cyclotron resonance-mass spectrometer (FT-ICR-MS) coupled to a matrix-assisted laser desorption/ionization (MALDI) source equipped with a Smartbeam II laser. The resulting time-series of alkenone-based sea surface temperature covers ~4.800 years in 1-4 year resolution. In the dataset are presented depth, age, CCaT values, calibrated SST time-series and associated uncertainty.