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

Sabrina Reinehr; Annika Guntermann; Sandra Kuehn; Marina Palmhof; Pia Grotegut; Bettina Serschnitzki; Simone Steinbach; H Burkhard Dick; Katrin Marcus; Stephanie C Joachim; Caroline May

doi:10.1016/j.dib.2021.107212

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

Data Brief. 2021 Jun 17:37:107212. doi: 10.1016/j.dib.2021.107212. eCollection 2021 Aug.

Authors

Sabrina Reinehr¹, Annika Guntermann^{2

3}, Sandra Kuehn¹, Marina Palmhof¹, Pia Grotegut¹, Bettina Serschnitzki^{2

3}, Simone Steinbach^{2

3}, H Burkhard Dick¹, Katrin Marcus^{2

3}, Stephanie C Joachim¹, Caroline May^{2

3}

Affiliations

¹ Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany.
² Ruhr-University Bochum, Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Germany.
³ Ruhr-University Bochum, Medical Faculty, Medizinisches Proteom-Center, Germany.

Abstract

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.

Keywords: Data-independent acquisition; Eye disorders; Mass spectrometry; Ocular function; Proteomics; Retina mass spectrometry; Retina proteomic; Spectral library.