Quantitative proteomic analysis of rat retina with experimental autoimmune uveitis based on tandem mass tag (TMT) peptide labeling coupled with LC-MS/MS

Liu, Bin; Yin, Xuewei; Wei, Huixia; Wang, Zhe; Tang, Hongying; Qiu, Yan; Hao, Yixian; Zhang, Xiuyan; Bi, Hongsheng; Guo, Dadong

doi:10.1016/j.jchromb.2020.122293

Cited by 7 publications

(7 citation statements)

References 33 publications

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“…Programs that utilize peak alignment algorithms, ascertain measurements for a given peptide in runs where the peptide is not identified at the MS/MS level by leveraging information from other runs, and the development of novel intensity determination and normalization procedures (Cox et al, 2014; May et al, 2008) collectively raised the confidence of researchers in label‐free quantifications based on MS peak area measurements. The availability of the method in commercial (e.g., Progenesis LC‐MS and QI, Proteome Discoverer and Mascot), and in open‐source (MaxQant, https://www.maxquant.org; Tyanova et al, 2016) software packages also has contributed to the widespread application of the technique to retina proteomics (Cehofski et al, 2015; Eastlake et al, 2018; Gharbi et al, 2021; Grotegut et al, 2020; Hauck et al, 2010; B. Liu et al, 2020; Ly et al, 2014; Perumal et al, 2020; Ruzafa et al, 2018; Suo et al, 2022; Tu et al, 2015; Zhu et al, 2017—just to mention a few of these studies).…”

Section: Ms‐based Proteomics To Catalog and Measure Protein Expressio...mentioning

confidence: 99%

“…In another study, phosphoprotein staining and in‐gel/cross‐gel 2D‐image analysis were applied to pick spots indicating significant changes in phosphorylation in retinae of optic nerve crush‐injured mouse eyes compared to the control. Tryptic peptides of 29 putative phosphoprotein spots of interest were analyzed after in‐gel digestion both by MALDI‐TOF and TOF/TOF MS/MS (B. Liu et al, 2020). However, larger‐scale retina phosphoproteomics have relied on gel‐free methodology including enrichment of phosphopeptides using TiO 2 beads (Chidiac et al, 2016) or microsphere‐based immobilized‐metal affinity chromatography (IMAC) (Mazanek et al, 2007; H. Zhou et al, 2013).…”

Section: Detection and Identification Of Posttranslational Protein Mo...mentioning

confidence: 99%

“…Additionally, loss of retina‐specific proteins reflecting decrease of vision and an increase in RMG cell‐specific proteins indicating glial reactivity were observed. In a recent TMT labeling‐based quantitative proteomics study relying on a rat EAU model, close to 300 disease‐regulated proteins were found in the isolated retinae (B. Liu et al, 2020). Bioinformatics linked the differentially expressed proteins mainly to acute inflammatory response, visual perception, eye photoreceptor cell differentiation related to complement and coagulation cascades, phagosome, phosphatidylinositol 3‐kinase (PI3K)–protein kinase B (also known as Akt) signaling, and metabolic pathways.…”

Section: Proteomics Studies Focused On Biology Pathology and Therapy ...mentioning

confidence: 99%

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Mass spectrometry‐based retina proteomics

Prókai

Zaman

Prókai-Tátrai

2022

Mass Spectrometry Reviews

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A subfield of neuroproteomics, retina proteomics has experienced a transformative growth since its inception due to methodological advances in enabling chemical, biochemical, and molecular biology techniques. This review focuses on mass spectrometry's contributions to facilitate mammalian and avian retina proteomics to catalog and quantify retinal protein expressions, determine their posttranslational modifications, as well as its applications to study the proteome of the retina in the context of biology, health and diseases, and therapy developments.

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Section: Ms‐based Proteomics To Catalog and Measure Protein Expressio...mentioning

confidence: 99%

Section: Detection and Identification Of Posttranslational Protein Mo...mentioning

confidence: 99%

Section: Proteomics Studies Focused On Biology Pathology and Therapy ...mentioning

confidence: 99%

See 1 more Smart Citation

Mass spectrometry‐based retina proteomics

Prókai

Zaman

Prókai-Tátrai

2022

Mass Spectrometry Reviews

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“…This step provides a basis for the exploration of toxicity and efficacy mechanism. Among these, tandem mass tag (TMT)-labeled proteomics based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) can accurately identify and quantitatively compare peptide-specific amino acids ( Liu et al, 2020 ), which is of great significance to determine the drug toxicity and efficacy mechanism ( Zhao et al, 2021 ; Song et al, 2022 ). In the present study, TMT-labeled LC-MS/MS technology was applied to explore the possible mechanism of reproductive toxicity caused by TGT to establish a basis for the clinical application of TGT.…”

Section: Introductionmentioning

confidence: 99%

Proteomic Study on the Reproductive Toxicity of Tripterygium Glycosides in Rats

et al. 2022

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Tripterygium glycoside tablet (TGT) is a common clinically used and effective non-steroidal immunosuppressant. However, its reproductive toxicity limits its application in pediatric immune diseases, warranting the study of the molecular mechanism behind its reproductive toxicity. In the present study, 4-week-old male Sprague Dawley (SD) rats were provided TGT through continuous gavage with a clinically equivalent dose of 12 mg/kg for 12 weeks. The reproductive toxicity of TGT was recorded, and its toxicity mechanism was verified through experimental validation and proteomics analyses. Our results demonstrated that TGT could significantly reduce the testosterone level in the serum as well as the concentration and survival rate of sperms. Pathological sections of the testis revealed that TGT could reduce spermatocytes at different levels and make the convoluted meridians vacuolated. Based on tandem mass tag (TMT)-labeled quantitative rats testicular tissue proteomics, 34 differential proteins were screened, involving protein digestion and absorption, PPAR signaling pathway, PI3K-Akt, and other pathways, among which PI3K-Akt plays an important role in the study of reproductive injury. Western blotting results revealed that TGT could significantly downregulate the Col1A1, Col1A2, p-PI3K, and p-Akt expressions and inhibit the expression of proteins related to the PI3K-Akt signaling pathway. In summary, the clinically equivalent dose of TGT induced reproductive toxicity of 4-week-old male SD rats, possibly in relation to the inhibition of the PI3K-Akt pathway expression.

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“…Furthermore, at the protein level, tandem mass tag peptide labeling coupled with LC-MS/MS quantitative proteomics technique has been applied. The differentially expressed proteins in EAU rat retinas were mainly associated with complement and coagulation cascades and metabolic pathways ( Liu et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Integrated Transcriptome Analysis of Iris Tissues in Experimental Autoimmune Uveitis

Chang

Han

et al. 2022

Front. Genet.

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Uveitis is a severe ocular inflammatory disease that affects the uvea and frequently results in visual impairment, even irreversible blindness. The current treatments for uveitis have exhibited adverse side effects. To find novel targets of this disease, we perform comparative transcriptome analysis using normal (n = 4) and experimental autoimmune uveitis (EAU) (n = 4) rat iris samples. We mainly focus on the expression profiles of mRNAs and long non-coding RNAs, and identify NOD-like receptor signaling pathway as the one that plays a key role in the pathological changes of the EAU irises. Our work demonstrates that the EAU iris transcriptome can be mined to uncover novel targetable pathways for uveitis. The molecules in NOD-like receptor signaling pathway could be novel therapeutic targets for autoimmune uveitis.

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Quantitative proteomic analysis of rat retina with experimental autoimmune uveitis based on tandem mass tag (TMT) peptide labeling coupled with LC-MS/MS

Cited by 7 publications

References 33 publications

Mass spectrometry‐based retina proteomics

Mass spectrometry‐based retina proteomics

Proteomic Study on the Reproductive Toxicity of Tripterygium Glycosides in Rats

Integrated Transcriptome Analysis of Iris Tissues in Experimental Autoimmune Uveitis

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