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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.<\/jats:p>","DOI":"10.1016\/j.gpb.2019.11.008","type":"journal-article","created":{"date-parts":[[2020,8,12]],"date-time":"2020-08-12T02:39:22Z","timestamp":1597199962000},"page":"104-119","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":80,"title":["DPHL: A DIA Pan-Human Protein Mass Spectrometry Library for Robust Biomarker Discovery"],"prefix":"10.1093","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7335-9087","authenticated-orcid":false,"given":"Tiansheng","family":"Zhu","sequence":"first","affiliation":[{"name":"Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University , Hangzhou 310024 , China"},{"name":"Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University , Hangzhou 310024 , China"},{"name":"Institute of Basic Medical Sciences, Westlake Institute for Advanced Study , Hangzhou 310024 , China"},{"name":"School of Computer Science, Shanghai Key Laboratory of Intelligent Information Processing, Fudan University , Shanghai 200433 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0429-0802","authenticated-orcid":false,"given":"Yi","family":"Zhu","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University , Hangzhou 310024 , China"},{"name":"Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University , Hangzhou 310024 , China"},{"name":"Institute of Basic Medical Sciences, Westlake Institute for Advanced Study , Hangzhou 310024 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9132-2643","authenticated-orcid":false,"given":"Yue","family":"Xuan","sequence":"additional","affiliation":[{"name":"Thermo Fisher Scientific (BREMEN) GmbH , Bremen 28195 , Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4701-7913","authenticated-orcid":false,"given":"Huanhuan","family":"Gao","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University , Hangzhou 310024 , China"},{"name":"Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University , Hangzhou 310024 , China"},{"name":"Institute of Basic Medical Sciences, Westlake Institute for Advanced Study , Hangzhou 310024 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7427-2100","authenticated-orcid":false,"given":"Xue","family":"Cai","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University , Hangzhou 310024 , China"},{"name":"Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University , Hangzhou 310024 , China"},{"name":"Institute of Basic Medical Sciences, 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