Data on corneal proteome and differentially expressed corneal proteins in highly myopic chicks using a data independent quantification approach

Abstract

Myopia is an abnormal refractive status, explained by an excessive ocular lengthening mostly in posterior segments. Although growing evidence of anterior segments, specifically altered corneal geometries with biomechanical properties in myopes have been reported, the mechanism behind is poorly understood. We hereby prepared experimentally induced highly myopic chicks to investigate the molecular basis of corneal remodeling by applying a novel proteomic approach integrated with information dependent acquisition (IDA) and data independent quantification (SWATH-MS) analysis. As a result, differentially expressed protein biomarkers that might be involved in structural changes were screened based on the first of its kind unique chicken corneal proteome. All generated raw data from IDA and SWATH-MS are accessible at Peptide Atlas public repository (http://www.peptideatlas.org/PASS/PASS01410) for general release.

Corneal proteome and differentially expressed corneal proteins in highly myopic chicks using a label-free SWATH-MS quantification approach

“…Detailed procedures of proteomic analysis workflow have been described in the proteomics data journal 29 and are briefly summarized in Fig. 5 .…”

“…To overcome these limitations, this study included corneas from highly myopic eyes as well as untreated control eyes for generating an in-depth ion spectral library using an offline peptide fractionation technique 28 . By integrating the generated library, differentially expressed corneal proteins in myopic eyes could be screened by applying SWATH-MS coupled to bioinformatics 29 .…”

Omics in Myopia

“…The articles presenting only proteomic findings, without the interpretation thereof, are of lesser value from a clinical perspective. However, they may constitute a reference for future research, serving as a proteome database for various biological materials, such as tears from patients wearing orthokeratological lenses as a treatment for myopia and normal controls [9], chick cornea in FDM [12], chick VH [8] and guinea pig retina [24] during the emmetropization period.…”

“…Animal specimens are easier to obtain than clinical samples, and the amount of analyte is larger. While proteomic analyses of human specimens were limited to vitreous [10,32] and aqueous humor [19,26,28], other materials, such as sclera [22,23], retina [17] and cornea [12], were also included in animal studies. Both studies in humans and those involving animal models can be divided into non-targeted and targeted analyses.…”

“…While the latter analysis used the DDA approach, the SWATH analyses, especially those aimed at the creation of spectral libraries, involved the DIA approach. In most cases, the libraries were created based on vitreous and corneal samples from chicks [8,12] and retina from pigs [24,30]. Furthermore, this method was also used to analyze human tears in patients wearing orthokeratology lenses as myopia treatment [9].…”