Among the new proxies based on the distribution of glycerol dialkyl glycerol tetraethers (GDGTs), the BIT index (Branched and Isoprenoid Tetraether index) is one of the most difficult to determine accurately, as shown by two round-robin GDGT studies. Sensitivity to mass spectrometer settings and tuning, and a diversity of mass spectrometry techniques may explain the relatively large observed interlaboratory scatter. However, the mass defect difference between crenarchaeol and branched GDGTs (brGDGTs) has never been specifically scrutinized. In this study, we analyzed five sediment samples with contrasting BIT values using about 60 m/z values to assess the shape of GDGT peaks using selected ion monitoring. We then assessed the biases in relative GDGT signals and mass spectrometry-derived BIT values under two scenarios which ignore the systematic mass defect difference between crenarchaeol and brGDGTs. Our results show that approximate mass selection for GDGT analysis using selected ion monitoring generates losses of relative GDGT signals of up to 36%. The observed effects on BIT values are maximal for intermediate BIT values, with shifts of BIT values of +/- 0.1 unit. The shifts of BIT values due to approximate mass selection are thus not negligible compared to the interlaboratory scatter evidenced by the latest round-robin GDGT study.