Citation: ZHOU Yuan, ZHANG Shen, YUAN Huiming, ZHANG Lihua, ZHANG Yukui. Establishment and application of integrated platform for proteome quantification[J]. Chinese Journal of Chromatography, ;2014, 32(4): 355-360. doi: 10.3724/SP.J.1123.2014.01002 shu

Establishment and application of integrated platform for proteome quantification

ZHOU Yuan ^1,2 ,
ZHANG Shen ^1,2 ,
YUAN Huiming ¹ ,
ZHANG Lihua ^1,, ,
ZHANG Yukui ¹

1.
1. Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences; National Chromatographic Research and Analysis Center, Dalian 116023, China;

Corresponding author: ZHANG Lihua,
Received Date: 2 January 2014
Available Online: 3 March 2014
Fund Project: 国家重大科学研究计划(2012CB910604)；国家重大科学仪器设备开发专项(2012YQ120044-2)；国家自然科学基金项目(21190043). (2012CB910604)；国家重大科学仪器设备开发专项(2012YQ120044-2)；国家自然科学基金项目(21190043)

To improve the accuracy, throughput and automation of proteome quantification analysis, an integrated platform including a microflow mixed-bed ion exchange column, a hydrophilic immobilized enzymatic reactor (hIMER) and nanoRPLC-electrospray ionization (ESI)-MS/MS system was established. Online separation and digestion of dimethylated proteins, followed by peptide separation, identification and quantification can be realized automatically by this platform. High and light dimethyl-labeled (H/L) proteins with the mass ratio of 1:1 were used to evaluate the quantification performance of the platform. The results showed that the dimethyl labeling efficiency at protein level was 90%. The incomplete digestion resulting from 10 min online digestion by the hIMER column and the non-specific adsorption of protein digests on the column had little adverse effect on the accuracy of protein quantification results. The mean value of H/L (mass ratio) of all the quantified proteins was 1.01. This platform was finally applied to analyze the different protein expression levels of two mice hepatocarcinoma ascites cell lines with high and low lymph node metastasis rates (Hca-F and Hca-P cell lines). Finally 15 up-regulated and 12 down-regulated proteins (Hca-F/Hca-P) were successfully obtained. All these results demonstrated that the integrated platform can be used for proteome quantification with the advantages of high accuracy and high throughput.
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