Hao Piliang, Ren Yan, Pasterkamp Gerard, Moll Frans L, de Kleijn Dominique P V, Sze Siu Kwan
School of Biological Sciences, Nanyang Technological University, Singapore; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.
Proteomics Clin Appl. 2014 Aug;8(7-8):631-5. doi: 10.1002/prca.201400007. Epub 2014 Jul 2.
To increase the proteome coverage of human atherosclerotic plaques and identify low-abundance proteins that may have important functions during the development and progression of atherosclerosis.
Thirty-eight human carotid atherosclerotic plaques were pooled into two samples and analyzed in triplicate using offline multidimensional LC-MS/MS. The collected fractions of trypsin-digested peptides from Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) were analyzed by LC-MS/MS on a Q Exactive (Thermo Fisher, MA, USA).
A total of 4702 proteins were identified from atherosclerotic plaques at a false discovery rate (FDR) of 1%, of which 3846 were identified with at least 2 unique peptides. Many pathways related to the development and progression of atherosclerosis were identified, such as atherosclerosis signaling, toll receptor signaling pathway and inhibition of matrix metalloproteases. Many low-abundance proteins with important functions in atherosclerosis that were previously unidentifiable using mass spectrometry based proteomics methods, such as TGF-β, interleukins and other growth factors, were identified confidently from plaques.
This study has substantially increased the coverage of the atherosclerotic plaque proteome which represents a leap forward in understanding of plaque composition, development and progression. The identification of many low-abundance proteins may also facilitate biomarker discovery.
增加人类动脉粥样硬化斑块的蛋白质组覆盖范围，并鉴定在动脉粥样硬化发生和发展过程中可能具有重要功能的低丰度蛋白质。
将38个人类颈动脉粥样硬化斑块合并为两个样本，并使用离线多维液相色谱-串联质谱进行三次分析。从静电排斥-亲水相互作用色谱（ERLIC）收集的胰蛋白酶消化肽段，在Q Exactive（美国马萨诸塞州赛默飞世尔科技公司）上通过液相色谱-串联质谱进行分析。
在错误发现率（FDR）为1%的情况下，从动脉粥样硬化斑块中总共鉴定出4702种蛋白质，其中3846种蛋白质由至少2个独特肽段鉴定。鉴定出许多与动脉粥样硬化发生和发展相关的通路，如动脉粥样硬化信号传导、Toll受体信号通路和基质金属蛋白酶抑制。从斑块中可靠地鉴定出许多以前使用基于质谱的蛋白质组学方法无法鉴定的、在动脉粥样硬化中具有重要功能的低丰度蛋白质，如转化生长因子-β、白细胞介素和其他生长因子。
本研究大幅增加了动脉粥样硬化斑块蛋白质组的覆盖范围，这在理解斑块组成、发生和发展方面向前迈出了一大步。许多低丰度蛋白质的鉴定也可能有助于生物标志物的发现。
