TY - JOUR
T1 - DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery
AU - Zhu, Tiansheng
AU - Zhu, Yi
AU - Xuan, Yue
AU - Gao, Huanhuan
AU - Cai, Xue
AU - Piersma, Sander R.
AU - Pham, Thang V.
AU - Schelfhorst, Tim
AU - Haas, Richard R. G. D.
AU - Bijnsdorp, Irene V.
AU - Sun, Rui
AU - Yue, Liang
AU - Ruan, Guan
AU - Zhang, Qiushi
AU - Hu, Mo
AU - Zhou, Yue
AU - van Houdt, Winan J.
AU - le Large, Tessa Y. S.
AU - Cloos, Jacqueline
AU - Wojtuszkiewicz, Anna
AU - Koppers-Lalic, Danijela
AU - Böttger, Franziska
AU - Scheepbouwer, Chantal
AU - Brakenhoff, Ruud H.
AU - van Leenders, Geert J. L. H.
AU - Ijzermans, Jan N. M.
AU - Martens, John W. M.
AU - Steenbergen, Renske D. M.
AU - Grieken, Nicole C.
AU - Selvarajan, Sathiyamoorthy
AU - Mantoo, Sangeeta
AU - Lee, Sze S.
AU - Yeow, Serene J. Y.
AU - Alkaff, Syed M. F.
AU - Xiang, Nan
AU - Sun, Yaoting
AU - Yi, Xiao
AU - Dai, Shaozheng
AU - Liu, Wei
AU - Lu, Tian
AU - Wu, Zhicheng
AU - Liang, Xiao
AU - Wang, Man
AU - Shao, Yingkuan
AU - Zheng, Xi
AU - Xu, Kailun
AU - Yang, Qin
AU - Meng, Yifan
AU - Lu, Cong
AU - Zhu, Jiang
AU - Zheng, Jin'e
AU - Wang, Bo
AU - Lou, Sai
AU - Dai, Yibei
AU - Xu, Chao
AU - Yu, Chenhuan
AU - Ying, Huazhong
AU - Lim, Tony K.
AU - Wu, Jianmin
AU - Gao, Xiaofei
AU - Luan, Zhongzhi
AU - Teng, Xiaodong
AU - Wu, Peng
AU - Huang, Shi'ang
AU - Tao, Zhihua
AU - Iyer, Narayanan G.
AU - Zhou, Shuigeng
AU - Shao, Wenguang
AU - Lam, Henry
AU - Ma, Ding
AU - Ji, Jiafu
AU - Kon, Oi L.
AU - Zheng, Shu
AU - Aebersold, Ruedi
AU - Jimenez, Connie R.
AU - Guo, Tiannan
PY - 2020/4
Y1 - 2020/4
N2 - 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.
AB - 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.
KW - Data-independent acquisition
KW - Diffuse large B cell lymphoma
KW - Parallel reaction monitoring
KW - Prostate cancer
KW - Spectral library
UR - https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85090480476&origin=inward
UR - https://www.ncbi.nlm.nih.gov/pubmed/32795611
U2 - 10.1016/j.gpb.2019.11.008
DO - 10.1016/j.gpb.2019.11.008
M3 - Article
C2 - 32795611
VL - 18
JO - Genomics, Proteomics and Bioinformatics
JF - Genomics, Proteomics and Bioinformatics
SN - 1672-0229
IS - 2
ER -