Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA.
Departments of Biology and Microbiology, University of Washington, Seattle, WA, USA.
Sci Data. 2020 Nov 12;7(1):389. doi: 10.1038/s41597-020-00724-7.
Data-Independent Acquisition (DIA) is a method to improve consistent identification and precise quantitation of peptides and proteins by mass spectrometry (MS). The targeted data analysis strategy in DIA relies on spectral assay libraries that are generally derived from a priori measurements of peptides for each species. Although Escherichia coli (E. coli) is among the best studied model organisms, so far there is no spectral assay library for the bacterium publicly available. Here, we generated a spectral assay library for 4,014 of the 4,389 annotated E. coli proteins using one- and two-dimensional fractionated samples, and ion mobility separation enabling deep proteome coverage. We demonstrate the utility of this high-quality library with robustness in quantitation of the E. coli proteome and with rapid-chromatography to enhance throughput by targeted DIA-MS. The spectral assay library supports the detection and quantification of 91.5% of all E. coli proteins at high-confidence with 56,182 proteotypic peptides, making it a valuable resource for the scientific community. Data and spectral libraries are available via ProteomeXchange (PXD020761, PXD020785) and SWATHAtlas (SAL00222-28).
数据非依赖性采集（DIA）是一种通过质谱（MS）提高肽和蛋白质一致鉴定和精确定量的方法。DIA 中的靶向数据分析策略依赖于光谱检测库，这些库通常源自对每个物种的肽的先验测量。尽管大肠杆菌（E. coli）是研究最充分的模式生物之一，但到目前为止，还没有公开的该细菌的光谱检测库。在这里，我们使用一维和二维分馏样品以及离子淌度分离生成了 4014 个 4389 个注释的大肠杆菌蛋白质的光谱检测库，实现了深度蛋白质组覆盖。我们通过靶向 DIA-MS 的快速色谱法提高了通量，证明了这个高质量库在大肠杆菌蛋白质组定量方面的稳健性和实用性。该光谱检测库支持以高置信度检测和定量所有大肠杆菌蛋白质的 91.5%，使用 56,182 个蛋白质肽，使其成为科学界的宝贵资源。数据和光谱库可通过 ProteomeXchange（PXD020761，PXD020785）和 SWATHAtlas（SAL00222-28）获取。
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