TY - JOUR T1 - DPHL: A pan-human protein mass spectrometry library for robust biomarker discovery JF - bioRxiv DO - 10.1101/2020.02.03.931329 SP - 2020.02.03.931329 AU - Tiansheng Zhu AU - Yi Zhu AU - Yue Xuan AU - Huanhuan Gao AU - Xue Cai AU - Sander R. Piersma AU - Thang V. Pham AU - Tim Schelfhorst AU - Richard R Goeij De Haas AU - Irene V. Bijnsdorp AU - Rui Sun AU - Liang Yue AU - Guan Ruan AU - Qiushi Zhang AU - Mo Hu AU - Yue Zhou AU - Winan J. Van Houdt AU - T.Y.S Lelarge AU - J. Cloos AU - Anna Wojtuszkiewicz AU - Danijela Koppers-Lalic AU - Franziska Böttger AU - Chantal Scheepbouwer AU - R.H Brakenhoff AU - G.J.L.H. van Leenders AU - Jan N.M. Ijzermans AU - J.W.M. Martens AU - R.D.M. Steenbergen AU - N.C. Grieken AU - Sathiyamoorthy Selvarajan AU - Sangeeta Mantoo AU - Sze Sing Lee AU - Serene Jie Yi Yeow AU - Syed Muhammad Fahmy Alkaff AU - Nan Xiang AU - Yaoting Sun AU - Xiao Yi AU - Shaozheng Dai AU - Wei Liu AU - Tian Lu AU - Zhicheng Wu AU - Xiao Liang AU - Man Wang AU - Yingkuan Shao AU - Xi Zheng AU - Kailun Xu AU - Qin Yang AU - Yifan Meng AU - Cong Lu AU - Jiang Zhu AU - Jin’e Zheng AU - Bo Wang AU - Sai Lou AU - Yibei Dai AU - Chao Xu AU - Chenhuan Yu AU - Huazhong Ying AU - Tony Kiat-hon Lim AU - Jianmin Wu AU - Xiaofei Gao AU - Zhongzhi Luan AU - Xiaodong Teng AU - Peng Wu AU - Shi’ang Huang AU - Zhihua Tao AU - N. Gopalakrishna Iyer AU - Shuigeng Zhou AU - Wenguang Shao AU - Henry Lam AU - Ding Ma AU - Jiafu Ji AU - Oi Lian Kon AU - Shu Zheng AU - Ruedi Aebersold AU - Connie R. Jimenez AU - Tiannan Guo Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/02/03/2020.02.03.931329.abstract N2 - To answer the increasing need for detecting and validating protein biomarkers in clinical specimens, proteomic techniques are required that support the fast, reproducible and quantitative analysis of large clinical sample cohorts. Targeted mass spectrometry techniques, specifically SRM, PRM and the massively parallel SWATH/DIA technique have emerged as a powerful method for biomarker research. For optimal performance, they require prior knowledge about the fragment ion spectra of targeted peptides. In this report, we describe a mass spectrometric (MS) pipeline and spectral resource to support data-independent acquisition (DIA) and parallel reaction monitoring (PRM) based biomarker studies. To build the spectral resource we integrated common open-source MS computational tools to assemble an open source computational workflow based on Docker. It was then applied to generate a comprehensive DIA pan-human library (DPHL) from 1,096 data dependent acquisition (DDA) MS raw files, and it comprises 242,476 unique peptide sequences from 14,782 protein groups and 10,943 SwissProt-annotated proteins expressed in 16 types of cancer samples. In particular, tissue specimens from patients with prostate cancer, cervical cancer, colorectal cancer, hepatocellular carcinoma, gastric cancer, lung adenocarcinoma, squamous cell lung carcinoma, diseased thyroid, glioblastoma multiforme, sarcoma and diffuse large B-cell lymphoma (DLBCL), as well as plasma samples from a range of hematologic malignancies were collected from multiple clinics in China, the Netherlands and Singapore and included in the resource. This extensive spectral resource was then applied to a prostate cancer cohort of 17 patients, consisting of 8 patients with prostate cancer (PCa) and 9 with benign prostate hyperplasia (BPH), respectively. Data analysis of DIA data from these samples identified differential expressions of FASN, TPP1 and SPON2 in prostate tumors. Thereafter, PRM validation was applied to a larger PCa cohort of 57 patients and the differential expressions of FASN, TPP1 and SPON2 in prostate tumors were validated. As a second application, the DPHL spectral resource was applied to a patient cohort consisting of samples from 19 DLBCL patients and 18 healthy individuals. Differential expressions of CRP, CD44 and SAA1 between DLBCL cases and healthy controls were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supported that DIA-PRM MS pipeline enables robust protein biomarker discoveries. ER -