DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins

• DOI: 10.1016/j.patter.2023.100792
• Publication Date: 2023-07-05T14:51:34Z
• Authors: Zhangzhi Xue; Tiansheng Zhu; Fangfei Zhang; Cheng Zhang; Nan Xiang; Liujia Qian; Xiao Yi; Yaoting Sun; Wei Liu; Xue Cai; Linyan Wang; Xizhe Dai; Liang Yue; Lu Li; Thang V. Pham; Sander R. Piersma; Qi Xiao; Meng Luo; Cong Lu; Jiang Zhu; Yongfu Zhao; Guangzhi Wang; Junhong Xiao; Tong Liu; Zhiyu Liu; Yi He; Qijun Wu; Tingting Gong; Jianqin Zhu; Zhiguo Zheng; Juan Ye; Yan Li; Connie R. Jimenez; Jun A; Tiannan Guo
• Keywords: Human proteome project; Proteome; Biomarker Discovery

A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS)-based proteomics. DPHL v.1, a previous built from 1,096 data-dependent acquisition (DDA) MS data of 16 human tissue types, allows quantifying 10,943 proteins. Here, we generated v.2 1,608 DDA-MS data. The included 586 acquired 18 while 1,022 files were derived v.1. thus comprises 24 sample including several cancer types (lung, breast, kidney, and prostate cancer, among others). We four variants to include semi-tryptic peptides protein isoforms. was then applied two colorectal cohorts. numbers identified significantly dysregulated proteins increased by at least 21.7% 14.2%, respectively, compared with Our findings show that the proteome coverage provides larger pools potential biomarkers.