Evidence map›Paper›PMID 34222568›Full record

ArticleData in brief2021

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 and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Data in brief, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Sabrina ReinehrExperimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany.
Annika GuntermannRuhr-University Bochum, Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Germany.
Sandra KuehnExperimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany.
Marina PalmhofExperimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany.
Pia GrotegutExperimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany.
Bettina SerschnitzkiRuhr-University Bochum, Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Germany.
Simone SteinbachRuhr-University Bochum, Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Germany.
H Burkhard DickExperimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany.
Katrin MarcusRuhr-University Bochum, Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Germany.
Stephanie C JoachimExperimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany.
Caroline MayRuhr-University Bochum, Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Germany.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Data-independent acquisitionEye disordersMass spectrometryOcular functionProteomicsRetina mass spectrometryRetina proteomicSpectral library

Identifiers

PMID34222568
PMCPMC8243017

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.