Application of SWATHTM-based next generation proteomics (NGP) in studying eye growth : opportunities and challenges

Chuen Lam, B. Zuo, S.W. Shan, A. Mcfadden, Yan Yin Tse, J. Bian, K.K. Li, Chi Ho To

Research output: Unpublished conference presentation (presented paper, abstract, poster)Conference presentation (not published in journal/proceeding/book)Academic researchpeer-review

Abstract

Myopia is a multifactorial ocular condition that is characterized byan excessively elongated eyeball. Previous animal studies haveshown that myopic eye growth is regulated by complex biochem-ical signalling cascades that take place locally in the retina, choroidand sclera. Conventional approaches of studying these biochemicalcascades usually target single or a few molecular candidates at atime. They reveal limited global information on the interplay be-tween multiple pathways that orchestrate myopic eye growth. Theproteomic approach is a high throughput technique that allowsthousands of protein changes to be identified in one setting. Earlyattempts using the classical 2D gel electrophoresis technique anddiscovery proteomics have identified some novel proteins, whichmay be involved in myopic eye growth. However, the complexity ofocular proteomes has hindered a more comprehensive understand-ing of the mechanism of myopia development. Emerging advances inMass Spectrometry (MS) with Data Independent Acquisition (DIA) allowidentification and quantitative comparison of over thousands of retinalproteins across different biological samples in a highly sensitive andrepeatable manner.Applying SWATH™MS in studying the retinal tissues from growingguinea pigs (Cavia porcellus) at 3 days old and at 21 days old, acomprehensive SWATH ion-library retina consisted of 3138 non-redundant proteins (at 1 % FDR) were established. 80 % of the pro-teins could be co-identified among all sample replicates to providea large reservoir of protein candidates for quantification. Very simi-lar protein translation modifications (PTMs) could also be detectedfrom identified peptides across all biological groups. In contrast,only 63 % of proteins were commonly detected using the standar-dised shotgun approach. Through integrated group analysis in theOneOmicsTMplatform,48uniqueproteinswerefoundtobesignifi-cantly expressed between the two time points. Pathway analysisindicated their involvement in a number of biochemical processesincluding development, metabolism and signal transduction. Theadvent of SWATH™MS with integration of cloud-based bioinformat-ics provides a high-throughput platform that could contributefurther to our basic understanding of myopia.
Original languageEnglish
DOIs
Publication statusPublished - 2015
EventInternational Myopia Conference [IMC] -
Duration: 1 Nov 2015 → …

Conference

ConferenceInternational Myopia Conference [IMC]
Period1/11/15 → …

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