北京大学王初团队报道了基于数据独立采集的质谱定量化学蛋白质组分析。相关研究成果发表在2022年1月5日出版的《美国化学会杂志》。

在复杂的生物系统中，基于活性的蛋白质分析（ABPP）已成为一种功能强大、用途广泛的工具，用于注释蛋白质功能和发现生物活性配体的靶点。其利用化学探针共价标记蛋白质中的功能位点，以便它们可以富集用于基于质谱（MS）的定量蛋白质组学分析。然而，数据相关采集的半随机性和同位素编码定量试剂相关的高成本损害了ABPP在多维分析和高通量筛选中的能力，因为大量样本需要并行量化。

该文中，研究人员将数据独立采集（DIA）MS与ABPP相结合，开发了一种高效的无标记定量化学蛋白质组学方法，DIA-ABPP，其具有良好的重复性和高通量定量的高精度。研究人员证明了DIA-ABPP在三种不同应用中对功能性半胱氨酸组进行全面分析的能力，包括半胱氨酸对反应性代谢物敏感性的剂量依赖性定量、利用共价片段文库筛选可连接性半胱氨酸，以及半胱氨酸单体在生物钟周期中的波动。DIA-ABPP将为功能蛋白质组的深入和多维分析以及与复杂生物系统中生物活性小分子的相互作用开辟新的机会。

附：英文原文

Title: Quantitative Chemoproteomic Profiling with Data-Independent Acquisition-Based Mass Spectrometry

Author: Fan Yang, Guogeng Jia, Jiuzhou Guo, Yuan Liu, Chu Wang

Issue&Volume: January 5, 2022

Abstract: Activity-based protein profiling (ABPP) has emerged as a powerful and versatile tool to enable annotation of protein functions and discovery of targets of bioactive ligands in complex biological systems. It utilizes chemical probes to covalently label functional sites in proteins so that they can be enriched for mass spectrometry (MS)-based quantitative proteomics analysis. However, the semistochastic nature of data-dependent acquisition and high cost associated with isotopically encoded quantification reagents compromise the power of ABPP in multidimensional analysis and high-throughput screening, when a large number of samples need to be quantified in parallel. Here, we combine the data-independent acquisition (DIA) MS with ABPP to develop an efficient label-free quantitative chemical proteomic method, DIA-ABPP, with good reproducibility and high accuracy for high-throughput quantification. We demonstrated the power of DIA-ABPP for comprehensive profiling of functional cysteineome in three distinct applications, including dose-dependent quantification of cysteines’ sensitivity toward a reactive metabolite, screening of ligandable cysteines with a covalent fragment library, and profiling of cysteinome fluctuation in circadian clock cycles. DIA-ABPP will open new opportunities for in-depth and multidimensional profiling of functional proteomes and interactions with bioactive small molecules in complex biological systems.

DOI: 10.1021/jacs.1c11053

Source: https://pubs.acs.org/doi/10.1021/jacs.1c11053