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. 2021 Apr 29;22(9):4721. doi: 10.3390/ijms22094721

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© 2021 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Schematic workflow of quantitative discovery proteomics in myopic vs. control eyes. Overall, 10 retinal lysates from 5 pigmented guinea pigs (five treatment eyes and five control eyes) were included. Approximately 3 µg of tryptic peptide from 10 pooled samples were used in two technical replicates to establish the proteome library under IDA. The 2 µg digested protein from each sample in three technical replicates under SWATH was analyzed by a Triple-TOF 6600 LCMS. Peptide identification from the 2 IDA was consolidated into an ion library for SWATH analysis. Protein identification and retention time calibration for SWATH quantification were performed using the ProteinPilot, PeakView, and MarkerView software, followed by bioinformatics analysis using online tools.