Jiang Yuming, Rex Devasahayam Arokia Balaya, Schuster Dina, Neely Benjamin A, Rosano Germán L, Volkmar Norbert, Momenzadeh Amanda, Peters-Clarke Trenton M, Egbert Susan B, Kreimer Simion, Doud Emma H, Crook Oliver M, Yadav Amit Kumar, Vanuopadath Muralidharan, Mayta Martín L, Duboff Anna G, Riley Nicholas M, Moritz Robert L, Meyer Jesse G
Department of Computational Biomedicine, Cedars Sinai Medical Center.
Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
ArXiv. 2023 Nov 13:arXiv:2311.07791v1.
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods to aid the novice and experienced researcher. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this work to serve as a basic resource for new practitioners in the field of shotgun or bottom-up proteomics.
蛋白质组学是通过蛋白质鉴定和定量对生物系统中的蛋白质结构和功能进行大规模研究。“鸟枪法蛋白质组学”或“自下而上蛋白质组学”是目前流行的策略，其中蛋白质被水解成肽，然后通过质谱进行分析。蛋白质组学研究可应用于从简单的蛋白质鉴定到蛋白质异构体、蛋白质-蛋白质相互作用、蛋白质结构改变、蛋白质绝对和相对定量、翻译后修饰以及蛋白质稳定性等各种研究。为了实现这一系列不同的实验，有多种蛋白质组分析策略。蛋白质组学工作流程的细微差别对于新从业者来说可能难以理解。在这里，我们提供了不同蛋白质组学方法的全面概述，以帮助新手和经验丰富的研究人员。我们涵盖了从生物化学基础和蛋白质提取到生物学解释和正交验证的内容。我们希望这项工作能成为鸟枪法或自下而上蛋白质组学领域新从业者的基础资源。
