All-Ion Monitoring-Directed Low-Abundance Protein Quantification Reveals CALB2 as a Key Promoter in Hepatocellular Carcinoma Metastasis

蛋白质组 化学 肝细胞癌 转移 管道(软件) 丰度(生态学) 计算生物学 样品制备 癌症研究 癌症 生物化学 色谱法 计算机科学 生物 医学 内科学 程序设计语言 渔业
作者
Hang Chu,Qun Zhao,Yichu Shan,Shen Zhang,Zhigang Sui,Xiao Li,Fei Fang,Baofeng Zhao,Shijun Zhong,Zhen Liang,Lihua Zhang,Yukui Zhang
出处
期刊:Analytical Chemistry [American Chemical Society]
卷期号:94 (16): 6102-6111 被引量:4
标识
DOI:10.1021/acs.analchem.1c03562
摘要

Because of the wide abundance range of the proteome, achieving high-coverage quantification of low-abundance proteins is always a major challenge. In this study, a complete pipeline focused on all-ion monitoring (AIM) is first constructed with the concept of untargeted parallel-reaction monitoring, including the seamless connection of protein sample preparation, liquid chromatography mass spectrometry (LC-MS) acquisition, and algorithm development to enable the in-depth quantitative analysis of low-abundance proteins. This pipeline significantly improves the reproducibility and sensitivity of sample preparation and LC-MS acquisition for low-abundance proteins, enabling all the precursors ions fragmented and collected. Contributed by the advantages of the AIM method with all the target precursor acquisition by the data-dependent acquisition (DDA) approach, together with the ability of data-independent acquisition to fragment all precursor ions, the quantitative accuracy and precision of low-abundance proteins are greatly enhanced. As a proof of concept, this pipeline is employed to discover the key differential proteins in the mechanism of hepatocellular carcinoma (HCC) metastasis. On the basis of the superiority of AIM, an extremely low-abundance protein, CALB2, is proposed to promote HCC metastasis in vitro and in vivo. We also reveal that CALB2 activates the TRPV2-Ca2+-ERK1/2 signaling pathway to induce HCC cell metastasis. In summary, we provide a universal AIM pipeline for the high-coverage quantification of low-abundance functional proteins to seek novel insights into the mechanisms of cancer metastasis.
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