Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA.
Center for Systems Biology, University of Iceland, Reykjavik, Iceland.
Sci Data. 2023 Oct 13;10(1):697. doi: 10.1038/s41597-023-02590-5.
Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to extract quantitative data in a targeted approach and have been generated for human, mouse, zebrafish, E. coli and few other organisms. However, a spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, a model organism that contributed to several notable discoveries, is not publicly available yet. Here, we report a comprehensive spectral assay library to measure 2,563 of 2,646 annotated H. salinarum NRC-1 proteins. We demonstrate the utility of this library by measuring global protein abundances over time under standard growth conditions. The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon. Data and spectral assay libraries are available via ProteomeXchange (PXD042770, PXD042774) and SWATHAtlas (SAL00312-SAL00319).
数据非依赖性采集（DIA）是一种基于质谱的方法，可可靠地鉴定和重现定量大量目标蛋白质组。DIA 中采用的以肽为中心的数据分析策略需要事先生成的光谱检测库。这种检测库允许以靶向方式提取定量数据，并且已经针对人类、小鼠、斑马鱼、大肠杆菌和其他一些生物体生成。然而，对于极端嗜盐古菌盐沼盐杆菌 NRC-1 的光谱检测库，该生物体是多个显著发现的模型生物，但尚未公开。在这里，我们报告了一个全面的光谱检测库，用于测量 2646 个注释的盐沼盐杆菌 NRC-1 蛋白中的 2563 个。我们通过在标准生长条件下随时间测量全局蛋白质丰度来证明该库的实用性。盐沼盐杆菌 NRC-1 库包含 21074 个独特的肽段，代表预测蛋白质组的 97%，为测量和定量该古菌的任何蛋白质提供了新的、有价值的资源。数据和光谱检测库可通过 ProteomeXchange（PXD042770、PXD042774）和 SWATHAtlas（SAL00312-SAL00319）获得。
