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Rat retinae data for use as spectral library, for pathway remodeling as well as protein mapping
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 spect...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8243017/ https://www.ncbi.nlm.nih.gov/pubmed/34222568 http://dx.doi.org/10.1016/j.dib.2021.107212 |
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author | Reinehr, Sabrina Guntermann, Annika Kuehn, Sandra Palmhof, Marina Grotegut, Pia Serschnitzki, Bettina Steinbach, Simone Dick, H. Burkhard Marcus, Katrin Joachim, Stephanie C. May, Caroline |
author_facet | Reinehr, Sabrina Guntermann, Annika Kuehn, Sandra Palmhof, Marina Grotegut, Pia Serschnitzki, Bettina Steinbach, Simone Dick, H. Burkhard Marcus, Katrin Joachim, Stephanie C. May, Caroline |
author_sort | Reinehr, Sabrina |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8243017 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-82430172021-07-02 Rat retinae data for use as spectral library, for pathway remodeling as well as protein mapping Reinehr, Sabrina Guntermann, Annika Kuehn, Sandra Palmhof, Marina Grotegut, Pia Serschnitzki, Bettina Steinbach, Simone Dick, H. Burkhard Marcus, Katrin Joachim, Stephanie C. May, Caroline Data Brief Data Article 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. Elsevier 2021-06-17 /pmc/articles/PMC8243017/ /pubmed/34222568 http://dx.doi.org/10.1016/j.dib.2021.107212 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Data Article Reinehr, Sabrina Guntermann, Annika Kuehn, Sandra Palmhof, Marina Grotegut, Pia Serschnitzki, Bettina Steinbach, Simone Dick, H. Burkhard Marcus, Katrin Joachim, Stephanie C. May, Caroline Rat retinae data for use as spectral library, for pathway remodeling as well as protein mapping |
title | Rat retinae data for use as spectral library, for pathway remodeling as well as protein mapping |
title_full | Rat retinae data for use as spectral library, for pathway remodeling as well as protein mapping |
title_fullStr | Rat retinae data for use as spectral library, for pathway remodeling as well as protein mapping |
title_full_unstemmed | Rat retinae data for use as spectral library, for pathway remodeling as well as protein mapping |
title_short | Rat retinae data for use as spectral library, for pathway remodeling as well as protein mapping |
title_sort | rat retinae data for use as spectral library, for pathway remodeling as well as protein mapping |
topic | Data Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8243017/ https://www.ncbi.nlm.nih.gov/pubmed/34222568 http://dx.doi.org/10.1016/j.dib.2021.107212 |
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