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This article describes a mass spectrometric data set from rat retinae spiked with indexed Retention Time (iRT) peptides. The provided data set can be used as a spectral library to investigate for instance eye disorders as well as ocular function by data-independent acquisition (DIA) based mass spectrometry. Consequently, there is no urgent need to create an own spectral library, which requires money, time, effort as well as tissue. Besides the use as a spectral library, this data set can improve our knowledge about proteins present in the rat retina and thus the protein pathways within this tissue. The data set may also help to determine optimal parameters for peptide identification by mass spectrometry. To generate the presented data set, six rat retinae were homogenized with glass beads and pooled. The pooled sample was fractionated by SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) followed by tryptic in-gel digestion. The fractionation of the pooled sample was repeated for further 4 times, to end up with in total 5 technical replicates. Peptide extracts were spiked with iRT peptides and analyzed by data-dependent (DDA) nanoHPLC-ESI-MS/MS resulting in 60 files. All resulting data files are hosted in the public repository ProteomeXchange under the identifier PXD021937., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships, which have, or could be perceived to have, influenced the work reported in this article., (© 2021 The Authors.)