Proteomic analysis of rat plasma with experimental autoimmune uveitis based on label-free liquid chromatography–tandem mass spectrometry (LC–MS/MS)

• We have developed and validated a rapid, sensitive and accurate LC–MS/MS method to quantify proteins in rat plasma.
• There was a good resolution for peptides for all samples using LC–MS/MS determination.
• Plasma samples in both EAU and control groups have a good correlation between each other when determined by LC–MS/MS.

Uveitis is a severe autoimmune eye disease that can cause intraocular inflammation even lead to severe vision loss, and the occurrence of uveitis can be closely associated with abnormal expression of proteins. However, the abnormally expressed proteins involved in uveitis are not well identified. Using liquid chromatography–tandem mass spectrometry technique, we examined the alterations in proteomic expression profiling in rat plasma specimens related to experimental autoimmune uveitis (EAU) versus normal samples. In addition, the experimental verification was further performed using enzyme-linked immunosorbent assay (ELISA) for abnormally expressed proteins in EAU rat plasma. The results indicate that 62 proteins were upregulated and 106 proteins were downregulated in plasma from EAU rats compared with those in saline-treated samples. In the meantime, we observed that the plasma level of complement component 3 in EAU rats was upregulated versus saline-treated rats (from 92.32 μg/mL to 168.92 μg/mL), whereas the level of interleukin-1 receptor accessory protein was downregulated (from 1120.97 pg/mL to 798.39 pg/mL), and these results were highly in agreement with those of mass spectrometry determination. Taken together, our results indicate that liquid chromatography–tandem mass spectrometry analysis possesses a good resolution for peptides in plasma, and the findings will provide the baseline plasma dataset for EAU rats and the relevant information can contribute to future studies on the understanding the mechanism of uveitis.