Abstract Lipids are powerful tools for reconstructing paleoenvironments and geologic processes because of their ubiquity and preservation in the rock record. Traditionally, organic geochemistry studies are targeted analyses of known biomarker compounds with known responses to past environmental conditions or geologic processes. With the recent development of the lipidomics field in the biological sciences, there is an opportunity for non‐targeted analysis to identify new biomarkers. However, lipids in the rock record integrate processes from biologic to geologic (i.e., diagenesis, heating, catagenesis) resulting in more chemically complex matrices than biological samples. As non‐targeted “‐omics” approaches are transferred from biology and applied to sediment, soil, and rock samples to perform geolipidomics, they must be evaluated and potentially adapted for geologic samples. Here we compare four non‐targeted methods of extracting features consisting of a peak area and spectrum...