The development of methods using liquid chromatography coupled to mass spectrometry to analyze glycerol dialkyl glycerol tetraethers (GDGTs) has substantially expanded the biomarker tool box and led to the development of several new proxies. Recent studies have shown that new high performance liquid chromatography methods have substantially improved separation of GDGT isomers and detection of novel isomers. Here we present a chromatographic method based on two ultra-high performance liquid chromatography silica columns capable of separating a wide range of GDGTs with good resolution and which compares favorably with previously published methods. This method was tested on a part of the global calibration set of the TEX86, a proxy for sea water temperature, and on a part of the global calibration set of the MBT5Me, a proxy for air temperature, and CBT', a proxy for soil pH. Our results show that the new high resolution chromatography method leads to a significant but small offset (< 0.01 or < 0.8 °C) in TEX86, especially at low values, while no difference is observed for the CBT'. However, for the MBT5Me a significant difference is observed (< 0.01 or < 3 °C), especially at low values, although this difference is smaller than the calibration error (4.8 °C).