Updated project metadata. Endometrial fluid reflects the status of the endometrium, being a good atraumatic source of information on embryo implantation and some pathological conditions. Although some attempts have been made to characterize it, the catalogue of the human endometrial fluid proteins remains incomplete and little has been done regarding the analysis of the containing natural peptides. In this work, we have thoroughly analyzed the protein and natural peptide content of endometrial fluid. Protein content coming from 11 different individuals was analyzed using the novel TIMS TOF Pro mass spectrometer. A total of 4694 proteins were identified with at least one peptide with FDR<1%, of which 2261 were identified in more than 50% of the samples. Besides, a pooled endometrial fluid sample was used for isolating the natural peptides and analyzed by mass spectrometry. Following this method we identified 3899 naturally-occurring peptides from 238 different proteins.