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

doi:10.1016/j.dib.2021.107212

Cited by 1 publication

(4 citation statements)

References 4 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For the characterization of differences within the proteome in consequence of immunization with S100B, a DIA-based mass spectrometry analysis was chosen. To this end, the before-generated retina-specific spectral library served as a consensus template [ 30 ]. It consists of mass spectrometric data of the ocular sinister of six rats acquired by data-dependent acquisition mass spectrometry.…”

Section: Resultsmentioning

confidence: 99%

“…The preparation of 6 pooled retinae samples for the creation of a retina-specific spectral library was described previously by Reinehr et al [ 30 ]. Briefly, the eyes were enucleated, retinae were carefully extracted, and homogenization was performed by sonication.…”

Section: Methodsmentioning

confidence: 99%

“…After finishing the incubation cycle, gel pieces were dried and resuspended in 9.5 µL trypsin solution (0.033 µg/µL; SERVA Electrophoresis GmbH, Heidelberg, Germany) plus 12 µL 50 mM ammonium bicarbonate. Trypsin digestion and the elution of peptides were performed as described earlier [ 30 ]. The resulting peptide extract was completely dried in a vacuum concentrator and resuspended in 30 µL 0.1% ( v / v ) trifluoroacetic acid.…”

Section: Methodsmentioning

confidence: 99%

“…Acquired mass spectrometric data were analyzed with the interface Spectronaut™ Pulsar (Biognosys) with default settings and minor changes, as used in Barkovits et al [ 32 ]. Briefly summarized, the retina sample dataset described previously [ 30 ] was taken to generate a retina-specific spectral library (reference data set). The false discovery rate (called Qvalue) was set to a threshold of 1%.…”

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Proteomic Analysis of Retinal Tissue in an S100B Autoimmune Glaucoma Model

Reinehr

Guntermann

Theile

et al. 2021

Biology

Self Cite

View full text Add to dashboard Cite

Glaucoma is a neurodegenerative disease that leads to damage of retinal ganglion cells and the optic nerve. Patients display altered antibody profiles and increased antibody titer, e.g., against S100B. To identify the meaning of these antibodies, animals were immunized with S100B. Retinal ganglion cell loss, optic nerve degeneration, and increased glial cell activity were noted. Here, we aimed to gain more insights into the pathophysiology from a proteomic point of view. Hence, rats were immunized with S100B, while controls received sodium chloride. After 7 and 14 days, retinae were analyzed through mass spectrometry and immunohistology. Using data-independent acquisition-based mass spectrometry, we identified more than 1700 proteins on a high confidence level for both study groups, respectively. Of these 1700, 43 proteins were significantly altered in retinae after 7 days and 67 proteins revealed significant alterations at 14 days. For example, α2-macroglobulin was found significantly increased not only by mass spectrometry analysis, but also with immunohistological staining in S100B retinae at 7 and 14 days. All in all, the identified proteins are often associated with the immune system, such as heat shock protein 60. Once more, these data underline the important role of immunological factors in glaucoma pathogenesis.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations