DPHL v.2：一个经过更新的综合性DIA全人类分析文库，用于定量分析超过14000种蛋白质。
DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.
作者信息
Xue Zhangzhi, Zhu Tiansheng, Zhang Fangfei, Zhang Cheng, Xiang Nan, Qian Liujia, Yi Xiao, Sun Yaoting, Liu Wei, Cai Xue, Wang Linyan, Dai Xizhe, Yue Liang, Li Lu, Pham Thang V, Piersma Sander R, Xiao Qi, Luo Meng, Lu Cong, Zhu Jiang, Zhao Yongfu, Wang Guangzhi, Xiao Junhong, Liu Tong, Liu Zhiyu, He Yi, Wu Qijun, Gong Tingting, Zhu Jianqin, Zheng Zhiguo, Ye Juan, Li Yan, Jimenez Connie R, A Jun, Guo Tiannan
机构信息
iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China.
Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China.
出版信息
Patterns (N Y). 2023 Jul 5;4(7):100792. doi: 10.1016/j.patter.2023.100792. eCollection 2023 Jul 14.
A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS)-based proteomics. DPHL v.1, a previous pan-human library built from 1,096 data-dependent acquisition (DDA) MS data of 16 human tissue types, allows quantifying of 10,943 proteins. Here, we generated DPHL v.2 from 1,608 DDA-MS data. The data included 586 DDA-MS data acquired from 18 tissue types, while 1,022 files were derived from DPHL v.1. DPHL v.2 thus comprises data from 24 sample types, including several cancer types (lung, breast, kidney, and prostate cancer, among others). We generated four variants of DPHL v.2 to include semi-tryptic peptides and protein isoforms. DPHL v.2 was then applied to two colorectal cancer cohorts. The numbers of identified and significantly dysregulated proteins increased by at least 21.7% and 14.2%, respectively, compared with DPHL v.1. Our findings show that the increased human proteome coverage of DPHL v.2 provides larger pools of potential protein biomarkers.
一个全面的泛人类光谱库对于使用基于质谱（MS）的蛋白质组学发现生物标志物至关重要。DPHL v.1是之前从16种人类组织类型的1096个数据依赖采集（DDA）MS数据构建的泛人类库，可对10943种蛋白质进行定量。在此，我们从1608个DDA-MS数据生成了DPHL v.2。这些数据包括从18种组织类型获取的586个DDA-MS数据，而1022个文件来自DPHL v.1。因此，DPHL v.2包含来自24种样本类型的数据，包括几种癌症类型（如肺癌、乳腺癌、肾癌和前列腺癌等）。我们生成了DPHL v.2的四个变体，以纳入半胰蛋白酶肽和蛋白质异构体。然后将DPHL v.2应用于两个结直肠癌队列。与DPHL v.1相比，鉴定出的蛋白质数量和显著失调的蛋白质数量分别至少增加了21.7%和14.2%。我们的研究结果表明，DPHL v.2对人类蛋白质组覆盖范围的增加提供了更大的潜在蛋白质生物标志物库。
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