Genomics, Proteomics & Bioinformatics (Apr 2020)
DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery
- 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 Böttger,
- 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
Affiliations
- Tiansheng Zhu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China; School of Computer Science, Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, China
- Yi Zhu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China; Corresponding authors.
- Yue Xuan
- Thermo Fisher Scientific (BREMEN) GmbH, Bremen 28195, Germany
- Huanhuan Gao
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Xue Cai
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Sander R. Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, VU University, Amsterdam 1011, The Netherlands
- Thang V. Pham
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, VU University, Amsterdam 1011, The Netherlands
- Tim Schelfhorst
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, VU University, Amsterdam 1011, The Netherlands
- Richard R.G.D. Haas
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, VU University, Amsterdam 1011, The Netherlands
- Irene V. Bijnsdorp
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, VU University, Amsterdam 1011, The Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, Urology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands
- Rui Sun
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Liang Yue
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Guan Ruan
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Qiushi Zhang
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Mo Hu
- Thermo Fisher Scientific, Shanghai 201206, China
- Yue Zhou
- Thermo Fisher Scientific, Shanghai 201206, China
- Winan J. Van Houdt
- The Netherlands Cancer Institute, Surgical Oncology, Amsterdam 1011, The Netherlands
- Tessa Y.S. Le Large
- Amsterdam UMC, Vrije Universiteit Amsterdam, Surgery, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands
- Jacqueline Cloos
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pediatric Oncology/Hematology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands
- Anna Wojtuszkiewicz
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pediatric Oncology/Hematology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands
- Danijela Koppers-Lalic
- Amsterdam UMC, Vrije Universiteit Amsterdam, Hematology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands
- Franziska Böttger
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands
- Chantal Scheepbouwer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Neurosurgery, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands
- Ruud H. Brakenhoff
- Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands
- Geert J.L.H. van Leenders
- Erasmus MC University Medical Center, Pathology, Rotterdam 1016LV, The Netherlands
- Jan N.M. Ijzermans
- Erasmus MC University Medical Center, Surgery, Rotterdam 1016LV, The Netherlands
- John W.M. Martens
- Erasmus MC University Medical Center, Medical Oncology, Rotterdam 1016LV, The Netherlands
- Renske D.M. Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands
- Nicole C. Grieken
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands
- Sathiyamoorthy Selvarajan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169608, Singapore
- Sangeeta Mantoo
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169608, Singapore
- Sze S. Lee
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore 169608, Singapore
- Serene J.Y. Yeow
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore 169608, Singapore
- Syed M.F. Alkaff
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169608, Singapore
- Nan Xiang
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Yaoting Sun
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Xiao Yi
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Shaozheng Dai
- School of Computer Science and Engineering, Beihang University, Beijing 100191, China
- Wei Liu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Tian Lu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Zhicheng Wu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China; School of Computer Science, Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, China
- Xiao Liang
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Man Wang
- MOE Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Translational Research, Peking University Cancer Hospital, Beijing 100142, China
- Yingkuan Shao
- Cancer Institute (MOE Key Laboratory of Cancer Prevention and Intervention, Zhejiang Provincial Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Xi Zheng
- Cancer Institute (MOE Key Laboratory of Cancer Prevention and Intervention, Zhejiang Provincial Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Kailun Xu
- Cancer Institute (MOE Key Laboratory of Cancer Prevention and Intervention, Zhejiang Provincial Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Qin Yang
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Yifan Meng
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cong Lu
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Jiang Zhu
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Jin'e Zheng
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Bo Wang
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
- Sai Lou
- Phase I Clinical Research Center, Zhejiang Provincial People's Hospital, Hangzhou 310014, China
- Yibei Dai
- Department of Laboratory Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Chao Xu
- College of Mathematics and Informatics, Digital Fujian Institute of Big Data Security Technology, Fujian Normal University, Fuzhou 350108, China
- Chenhuan Yu
- Zhejiang Provincial Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou 310015, China
- Huazhong Ying
- Zhejiang Provincial Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou 310015, China
- Tony K. Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169608, Singapore
- Jianmin Wu
- MOE Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Translational Research, Peking University Cancer Hospital, Beijing 100142, China
- Xiaofei Gao
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhongzhi Luan
- School of Computer Science and Engineering, Beihang University, Beijing 100191, China
- Xiaodong Teng
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
- Peng Wu
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Shi'ang Huang
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Zhihua Tao
- Department of Laboratory Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Narayanan G. Iyer
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore 169608, Singapore
- Shuigeng Zhou
- School of Computer Science, Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, China
- Wenguang Shao
- Department of Biology, Institute for Molecular Systems Biology, ETH Zurich, Zurich 8092, Switzerland
- Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China
- Ding Ma
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Jiafu Ji
- MOE Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Translational Research, Peking University Cancer Hospital, Beijing 100142, China
- Oi L. Kon
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore 169608, Singapore
- Shu Zheng
- Cancer Institute (MOE Key Laboratory of Cancer Prevention and Intervention, Zhejiang Provincial Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Ruedi Aebersold
- Department of Biology, Institute for Molecular Systems Biology, ETH Zurich, Zurich 8092, Switzerland; Faculty of Science, University of Zurich, Zurich 8092, Switzerland
- Connie R. Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, VU University, Amsterdam 1011, The Netherlands
- Tiannan Guo
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China; Corresponding authors.
- Journal volume & issue
-
Vol. 18,
no. 2
pp. 104 – 119
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 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.
