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

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

doi:10.1016/j.patter.2023.100792

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

Patterns (N Y). 2023 Jul 5;4(7):100792. doi: 10.1016/j.patter.2023.100792. eCollection 2023 Jul 14.

Authors

Zhangzhi Xue^{1

2

3}, Tiansheng Zhu^{1

2

3

4}, Fangfei Zhang^{1

2

3}, Cheng Zhang^{1

2

3}, Nan Xiang⁵, Liujia Qian^{1

2

3}, Xiao Yi⁵, Yaoting Sun^{1

2

3}, Wei Liu⁵, Xue Cai^{1

2

3}, Linyan Wang⁶, Xizhe Dai⁶, Liang Yue^{1

2

3}, Lu Li^{1

2

3}, Thang V Pham⁷, Sander R Piersma⁷, Qi Xiao^{1

2

3}, Meng Luo⁸, Cong Lu⁹, Jiang Zhu⁹, Yongfu Zhao¹⁰, Guangzhi Wang¹⁰, Junhong Xiao¹⁰, Tong Liu¹¹, Zhiyu Liu¹², Yi He¹², Qijun Wu¹³, Tingting Gong¹³, Jianqin Zhu^{14

15}, Zhiguo Zheng^{14

15}, Juan Ye⁶, Yan Li⁸, Connie R Jimenez⁷, Jun A^{1

2

3}, Tiannan Guo^{1

2

3}

Affiliations

¹ 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.
² Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China.
³ Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China.
⁴ College of Mathematics and Computer Science, Zhejiang A & F University, Hangzhou, Zhejiang 311300, China.
⁵ Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou 310024, China.
⁶ Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China.
⁷ OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, VU University, 1011 Amsterdam, the Netherlands.
⁸ Songjiang Research Institute and Songjiang Hospital, Department of Anatomy and Physiology, College of Basic Medical Science, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China.
⁹ Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
¹⁰ Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning Province 116044, China.
¹¹ Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province 150081, China.
¹² Department of Urology, The Second Hospital of Dalian Medical University, No.467 Zhongshan Road, Dalian, Liaoning Province 116044, China.
¹³ Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province 110000, China.
¹⁴ The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310000, China.
¹⁵ Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310000, China.

Abstract

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.