New and Improved Tools for the Omics Crew.
New and Improved Tools for the Omics Crew.
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为 Omics 团队提供的新工具和改进工具。
DOI：
10.1021/acs.jproteome.0c00328
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发表时间：
2020
影响因子：
4.4
通讯作者：
LaBaer,Joshua
中科院分区：
文献类型：
--
作者：
Florens,Laurence;Dong,Meng-Qiu;LaBaer,Joshua
这个两年一期的特刊汇编了37项研究，描述了组学研究中使用的新方法，或者至少是显著更新的方法。尽管这个问题是从回答相当松散定义的公开呼吁的提交中收集的，但本文所述的方法改进了典型组学分析物表征流水线的（至少）一个主要步骤：样品制备、样品处理、数据采集和数据分析。我们围绕这四个按时间顺序排列的步骤策划了这一问题，并根据其新奇或改进的主要领域对手稿进行了分类（图1）.样品制备，定义为在表征之前富集或耗尽生物样品中特定类别的分析物的步骤为了捕获RNA相互作用蛋白，Lemmens等人巧妙地将使用激酶底物传感器系统（KISS）的双杂交方法与三杂交方法结合起来，利用MS 2 RNA和外壳蛋白之间的特异性相互作用来检测蛋白质-蛋白质相互作用。Y. Zhang等人使用亲水相互作用液相色谱（HILIC）捕获N-糖肽，而Young等人使用Histagged版本的peptidisc膜模拟物亲和纯化重构的膜蛋白。Iliuk等人设计了一种从血浆中捕获细胞外囊泡的化学亲和方法（EVtrap）。在富集硬币的另一面，Nakajima等人使用碳酸钠沉淀（SCP）进行预处理，以从干血斑（DBS）中去除丰富的亲水性蛋白，从而富集疏水性蛋白。S. Zhang等人评估了其最丰富蛋白质的免疫耗竭血浆样品如何影响感兴趣的特定蛋白质的鉴定和定量。虽然描述新的或改进的样品制备方案的六份手稿中有五份属于蛋白质组学类别，但Zougman等人介绍了一种无去污剂的方法，通过使用“同时捕获”（SiTrap）从一个样品中制备蛋白质和代谢物。
This biennial special issue compiles 37 studies describing novel, or at least significantly updated, methods used in omics research. Whereas this issue was assembled from submissions answering a fairly loosely defined open call, the methods described herein improve (at least) one of the main steps of a typical omics analyte characterization pipeline: sample preparation, sample processing, data acquisition, and data analysis. We have curated this issue around these four chronological steps and sorted the manuscripts according to their primary area of novelty or improvement (Figure 1).Sample Preparation, Defined as the Step Where Specific Classes of Analytes in a Biological Sample Are Enriched or Depleted Prior to Characterization To capture RNA-interacting proteins, Lemmens et al. cleverly combine a two-hybrid approach using the kinase substrate sensor system (KISS) to detect protein− protein interactions with the tribrid method, making use of the specific interaction between MS2 RNA and coat protein. Y. Zhang et al. use hydrophilic interaction liquid chromatography (HILIC) to capture N-glycopeptides, while Young et al. implement a Histagged version of the peptidisc membrane mimetic to affinitypurify reconstituted membrane proteins. Iliuk et al. devise a chemical affinity approach to capture extracellular vesicles from plasma (EVtrap). On the opposite side of the enrichment coin, Nakajima et al. perform a pretreatment using sodium carbonate precipitation (SCP) to remove abundant hydrophilic proteins from dried blood spots (DBSs), hence enriching for hydrophobic proteins. S. Zhang et al. assess how immunodepleting plasma samples of their most abundant proteins may influence the identification and quantitation of specific proteins of interest. Whereas five of the six manuscripts describing new or improved sample preparation protocols fall in the proteomics category, Zougman et al. introduce a detergent-free method to prepare both proteins and metabolites from one sample by using “simultaneous trapping”(SiTrap).