Oxylipins, small polar molecules derived from the peroxidation of polyunsaturated fatty acids (PUFAs), serve as biomarkers for diseases and play crucial roles in human physiology and inflammation. Despite their significance, many non-enzymatic oxygenated metabolites of PUFAs (NEO-PUFAs) remain poorly reported, resulting in a lack of public datasets of experimental data and limiting their dereplication in further studies. To overcome this limitation, we constructed a high-resolution tandem mass spectrometry (MS/MS) database comprising pure NEO-PUFA (both commercial and synthesized) and in vitro free radical-induced oxidations of diverse PUFAs and oxylipins. Furthermore, we conducted various molecular networking analyses on these standards, as well as on in vitro free radical-induced oxidations, serum samples, and algae samples. This was done to demonstrate their potential in derreplication and to provide additional putative oxylipins This dataset contains all the data used in this study including the raw data and the MzMine 3 procesed data used to built the molecular networks (i.e. feature tables and MSMS spectra). The folder ‘libraries’ contained the NEO-MSMS library divided into three .mgf files, i.e., the standards obtained with Q-Exactive Focus (i.e. NEOMSMS_QFocus_lib.mgf), Orbitrap ID-X Tribrid (i.e. NEOMSMS_idX_lib.mgf), and from the Watrous et al. study (Cell Chem Biol., 2019; 26(3):433-442) (NEOMSMS_Watrous_lib.mgf). Moreover, the individual .mgf files from each compound was included in three subfolders following the same syntax. The folder ‘oxPUFAs’ contains the raw .mzML files of the LC-MSMS analysis and the mzMine alignment results (i.e., the feature tables and the extracted .mgf files) of the in vitro oxidized PUFAs. The folder ‘algae_serum’ contains the same type of data from the algae and serum samples. The folder ‘oxOxylipins’ contains the raw .mzML files of the LC-MSMS analysis of the miniaturized oxidation of HETE, rearrangement of PGH1 and PGH2. Finally, the ‘putative_lib´ folder contains the putatively annotated oxylipins in the same structure as ‘libraries’ folder.

We would like to express our gratitude to the support of the Région Occitanie through the prematuration project MNE-AGPI-03. Á.S.I. acknowledges the support of Margarita Salas grant [UP2021-044-MS21-084] from the Ministry of Universities of the Government of Spain, financed by the European Union, NextGeneration EU and CIGE/2022/107 research project from Generalitat Valenciana, Conselleria d'Educació, Universitats i Ocupació. All authors also acknowledge the equipment employed to Laboratoire de Mesures Physiques platform at Institut des Biomolécules Max Mousseron (IBMM), UMR 5247-CNRS, Université de Montpellier, Montpellier, France.