Rat retinae data for use as spectral library, for pathway remodeling as well as protein mapping.

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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. 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All samples were digested with trypsin. The samples were measured using nanoHPLC-MS/MS in DDA mode."], ["Data source location", "Ruhr-University Bochum, Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Bochum, Germany (51°26′43.4″N 7°15′27.9″E)"], ["Data accessibility", "Repository name: ProteomeXchangeData identification number: PXD021937Direct URL to data: http://www.proteomexchange.org/Excel file of analyzed data in the supplement"], ["Related research article", "[3] Noristani, R.; Kuehn, S.; Stute, G.; et al. (2016): Retinal and Optic Nerve Damage is Associated with Early Glial Responses in an Experimental Autoimmune Glaucoma Model. J Mol Neurosci 58, 4, 470-482. http://dx.doi.org/10.1007/s12031-015-0707-2.[4] Reinehr, S.; Reinhard, J.; Gandej, M.; et al. (2018): S100B immunization triggers NFκB and complement activation in an autoimmune glaucoma model. Sci Rep 8, 1, 9821. http://dx.doi.org/10.1038/s41598-018-28183-6.Benning L, Reinehr S, Grotegut P, Kuehn S, Stute G, Dick HB, Joachim SC. Synapse and Receptor Alterations in Two Different S100B-Induced Glaucoma-Like Models. 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