This dataset originates from untargeted metabolomic profiling of Camelina sativa samples analysed by UHPLC-LTQ-Orbitrap mass spectrometry in negative ionisation mode. A total of 950 LC–MS runs were acquired, including 610 unique biological samples, technical replicates, biological standards, extraction blanks, and recurrent QC injections used for drift correction and data quality assessment. Data-dependent MS2 spectra were collected for all samples to support metabolite annotation.

Raw LC–MS data were processed in MS-DIAL, producing 11,680 RT–m/z features, of which 3,016 high-quality features were retained after blank filtering, signal-to-noise screening and QC-based coefficient of variation filtering. Annotation relied on MS-DIAL MS/MS spectral libraries, yielding 220 Level 2 and 1,446 Level 3 annotations, with remaining features classified as unknowns. This dataset contains those 3,016 features associated to the 950 runs.