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

作　　者：Tiansheng Zhu Yi Zhu Yue Xuan Huanhuan Gao Xue Cai Sander R.Piersma Thang V.Pham Tim Schelfhorst Richard R.G.D.Haas Irene V.Bijnsdorp Rui Sun Liang Yue Guan Ruan Qiushi Zhang Mo Hu Yue Zhou Winan J.Van Houdt Tessa Y.S.Le Large Jacqueline Cloos Anna Wojtuszkiewicz Danijela Koppers-Lalic Franziska Bottger Chantal Scheepbouwer Ruud H.Brakenhoff Geert J.L.H.van Leenders Jan N.M.Ijzermans John W.M.Martens Renske D.M.Steenbergen Nicole C.Grieken Sathiyamoorthy Selvarajan Sangeeta Mantoo Sze S.Lee Serene J.Y.Yeow Syed M.F.Alkaff Nan Xiang Yaoting Sun Xiao Yi Shaozheng Dai Wei Liu Tian Lu Zhicheng Wu Xiao Liang Man Wang Yingkuan Shao Xi Zheng Kailun Xu Qin Yang Yifan Meng Cong Lu Jiang Zhu Jin'e Zheng Bo Wang Sai Lou Yibei Dai Chao Xu Chenhuan Yu Huazhong Ying Tony K.Lim Jianmin Wu Xiaofei Gao Zhongzhi Luan Xiaodong Teng Peng Wu Shi'ang Huang Zhihua Tao Narayanan G.Iyer Shuigeng Zhou Wenguang Shao Henry Lam Ding Ma Jiafu Ji Oi L.Kon Shu Zheng Ruedi Aebersold Connie R.Jimenez Tiannan Guo 

机构地区：[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 Intelligent Information Processing,Fudan University,Shanghai 200433,China [5]Thermo Fisher Scientific(BREMEN)GmbH,Bremen 28195,Germany [6]OncoProteomics Laboratory,Department of Medical Oncology,VU University Medical Center,VU University,Amsterdam 1011,The Netherlands [7]Amsterdam UMC,Vrije Universiteit Amsterdam,Urology,Cancer Center Amsterdam,Amsterdam 1011,The Netherlands [8]Thermo Fisher Scientific,Shanghai 201206,China [9]The Netherlands Cancer Institute,Surgical Oncology,Amsterdam 1011,The Netherlands [10]Amsterdam UMC,Vrije Universiteit Amsterdam,Surgery,Cancer Center Amsterdam,Amsterdam 1011,The Netherlands [11]Amsterdam UMC,Vrije Universiteit Amsterdam,Pediatric Oncology/Hematology,Cancer Center Amsterdam,Amsterdam 1011,The Netherlands [12]Amsterdam UMC,Vrije Universiteit Amsterdam,Hematology,Cancer Center Amsterdam,Amsterdam 1011,The Netherlands [13]Amsterdam UMC,Vrije Universiteit Amsterdam,Medical Oncology,Cancer Center Amsterdam,Amsterdam 1011,The Netherlands [14]Amsterdam UMC,Vrije Universiteit Amsterdam,Neurosurgery,Cancer Center Amsterdam,Amsterdam 1011,The Netherlands [15]Amsterdam UMC,Vrije Universiteit Amsterdam,Pathology,Cancer Center Amsterdam,Amsterdam 1011,The Netherlands [16]Amsterdam UMC,Vrije Universiteit Amsterdam,Otolaryngology/Head and Neck Surgery,Cancer Center Amsterdam,Amsterdam 1011,The Netherlands [17]Erasmus MC University Medical Center,Pathology,Rotterdam 1016LV,The Netherlands [18]Erasmus MC University Medical Center,Surgery,Rotterdam 1016LV,The Netherlands [19]Erasmus MC University Medical Center,Medical Oncology,Rotterdam 1016LV,The Netherlands [20]Department of Anatomical Pathology,Singapo

出　　处：《Genomics, Proteomics & Bioinformatics》2020年第2期104-119,共16页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by the National Natural Science Foundation of China(Grant No.81972492);National Science Fund for Young Scholars(Grant No.21904107);Zhejiang Provincial Natural Science Foundation for Distinguished Young Scholars(Grant No.LR19C050001);Hangzhou Agriculture and Society Advancement Program(Grant No.20190101A04);Westlake Startup Grant;research funds from the National Cancer Centre Singapore and Singapore General Hospital,Singapore;the National Key R&D Program of China(Grant No.2016YFC0901704);Zhejiang Innovation Discipline Project of Laboratory Animal Genetic Engineering(Grant No.201510);the Netherlands Cancer Society(Grant No.NKI 2014-6651);The Netherlands Organization for Scientific Research(NWO)-Middelgroot(Grant No.91116017)

摘　　要：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 dataindependent 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 pipeline 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 generate 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.

关 键 词：Data-independent acquisition Parallel reaction monitoring Spectral library Prostate cancer Diffuse large B cell lymphoma 

分 类 号：R341[医药卫生—基础医学]