DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

Zhu TIANSHENG; Zhu YI; Xuan YUE; Gao HUANHUAN; Cai XUE; Piersma R SANDER; Pham V THANG; Schelfhorst TIM; Haas RGD RICHARD; Bijnsdorp V IRENE; Sun RUI; Yue LIANG; Ruan GUAN; Zhang QIUSHI; Hu MO; Zhou YUE; Winan J Van Houdt; Tessa YS Le Large; Cloos JACQUELINE; Wojtuszkiewicz ANNA; Koppers-Lalic DANIJELA; B(o)ttger FRANZISKA; Scheepbouwer CHANTAL; Brakenhoff H RUUD; Geert JLH van Leenders; Ijzermans NM JAN; Martens WM JOHN; Steenbergen DM RENSKE; Grieken C NICOLE; Selvarajan SATHIYAMOORTHY; Mantoo SANGEETA; Lee S SZE; Yeow JY SERENE; Alkaff MF SYED; Xiang NAN; Sun YAOTING; Yi XIAO; Dai SHAOZHENG; Liu WEI; Lu TIAN; Wu ZHICHENG; Liang XIAO; Wang MAN; Shao YINGKUAN; Zheng XI; Xu KAILUN; Yang QIN; Meng YIFAN; Lu CONG; Zhu JIANG; Zheng JIN'E; Wang BO; Lou SAI; Dai YIBEI; Xu CHAO; Yu CHENHUAN; Ying HUAZHONG; Lim K TONY; Wu JIANMIN; Gao XIAOFEI; Luan ZHONGZHI; Teng XIAODONG; Wu PENG; Huang SHI'ANG; Tao ZHIHUA; Iyer G NARAYANAN; Zhou SHUIGENG; Shao WENGUANG; Lam HENRY; Ma DING; Ji JIAFU; Kon L OI; Zheng SHU; Aebersold RUEDI; Jimenez R CONNIE; Guo TIANNAN

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DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

Author: Zhu TIANSHENG ^{1
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2
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3
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4} ; Zhu YI ; Xuan YUE ; Gao HUANHUAN ; Cai XUE ; Piersma R. SANDER ; Pham V. THANG ; Schelfhorst TIM ; Haas R.G.D. RICHARD ; Bijnsdorp V. IRENE ; Sun RUI ; Yue LIANG ; Ruan GUAN ; Zhang QIUSHI ; Hu MO ; Zhou YUE ; Winan J. Van Houdt ; Tessa Y.S. Le Large ; Cloos JACQUELINE ; Wojtuszkiewicz ANNA ; Koppers-Lalic DANIJELA ; B(o)ttger FRANZISKA ; Scheepbouwer CHANTAL ; Brakenhoff H. RUUD ; Geert J.L.H. van Leenders ; Ijzermans N.M. JAN ; Martens W.M. JOHN ; Steenbergen D.M. RENSKE ; Grieken C. NICOLE ; Selvarajan SATHIYAMOORTHY ; Mantoo SANGEETA ; Lee S. SZE ; Yeow J.Y. SERENE ; Alkaff M.F. SYED ; Xiang NAN ; Sun YAOTING ; Yi XIAO ; Dai SHAOZHENG ; Liu WEI ; Lu TIAN ; Wu ZHICHENG ; Liang XIAO ; Wang MAN ; Shao YINGKUAN ; Zheng XI ; Xu KAILUN ; Yang QIN ; Meng YIFAN ; Lu CONG ; Zhu JIANG ; Zheng JIN'E ; Wang BO ; Lou SAI ; Dai YIBEI ; Xu CHAO ; Yu CHENHUAN ; Ying HUAZHONG ; Lim K. TONY ; Wu JIANMIN ; Gao XIAOFEI ; Luan ZHONGZHI ; Teng XIAODONG ; Wu PENG ; Huang SHI'ANG ; Tao ZHIHUA ; Iyer G. NARAYANAN ; Zhou SHUIGENG ; Shao WENGUANG ; Lam HENRY ; Ma DING ; Ji JIAFU ; Kon L. OI ; Zheng SHU ; Aebersold RUEDI ; Jimenez R. CONNIE ; Guo TIANNAN
Author Information

1. Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China
2. Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
3. Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
4. School of Computer Science, Shanghai Key Laboratory of Intellige
Keywords: Data-independent acquisi-tion; Parallel reaction monitoring; Spectral library; Prostate cancer; Diffuse large B cell lymphoma
From: Genomics, Proteomics & Bioinformatics 2020;18(2):104-119
CountryChina
Language:Chinese
Abstract: To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipe-line and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to gen-erate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.