학술논문
DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery
Document Type
article
Author
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
Source
Genomics, Proteomics & Bioinformatics, Vol 18, Iss 2, Pp 104-119 (2020)
Subject
Language
English
ISSN
1672-0229
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.