ArticleGenomics, proteomics & bioinformatics2020
DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery.
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40 citing papers in PubMed, 1 synthesis or guideline pooled it, 94 citations in OpenAlex.
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- Resistance prediction in high-grade serous ovarian carcinoma with neoadjuvant chemotherapy using data-independent acquisition proteomics and an ovary-specific spectral library.Molecular oncology · 2023Article
- DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.Patterns (New York, N.Y.) · 2023Article
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Authors and funding
76 authors at 20 institutions in 6 countries.
Tiansheng ZhuZhejiang 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 ZhuZhejiang 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. Electronic address: zhuyi@westlake.edu.cn.
Yue XuanThermo Fisher Scientific (BREMEN) GmbH, Bremen 28195, Germany.
Huanhuan GaoZhejiang 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 CaiZhejiang 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 PiersmaOncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, VU University, Amsterdam 1011, The Netherlands.
Thang V PhamOncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, VU University, Amsterdam 1011, The Netherlands.
Tim SchelfhorstOncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, VU University, Amsterdam 1011, The Netherlands.
Richard R G D HaasOncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, VU University, Amsterdam 1011, The Netherlands.
Irene V BijnsdorpOncoProteomics 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 SunZhejiang 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 YueZhejiang 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 RuanZhejiang 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 ZhangZhejiang 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 HuThermo Fisher Scientific, Shanghai 201206, China.
Yue ZhouThermo Fisher Scientific, Shanghai 201206, China.
Winan J Van HoudtThe Netherlands Cancer Institute, Surgical Oncology, Amsterdam 1011, The Netherlands.
Tessa Y S Le LargeAmsterdam UMC, Vrije Universiteit Amsterdam, Surgery, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands.
Jacqueline CloosAmsterdam UMC, Vrije Universiteit Amsterdam, Pediatric Oncology/Hematology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands.
Anna WojtuszkiewiczAmsterdam UMC, Vrije Universiteit Amsterdam, Pediatric Oncology/Hematology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands.
Danijela Koppers-LalicAmsterdam UMC, Vrije Universiteit Amsterdam, Hematology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands.
Franziska BöttgerAmsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands.
Chantal ScheepbouwerAmsterdam 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 BrakenhoffAmsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands.
Geert J L H van LeendersErasmus MC University Medical Center, Pathology, Rotterdam 1016LV, The Netherlands.
Jan N M IjzermansErasmus MC University Medical Center, Surgery, Rotterdam 1016LV, The Netherlands.
John W M MartensErasmus MC University Medical Center, Medical Oncology, Rotterdam 1016LV, The Netherlands.
Renske D M SteenbergenAmsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands.
Nicole C GriekenAmsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam 1011, The Netherlands.
Sathiyamoorthy SelvarajanDepartment of Anatomical Pathology, Singapore General Hospital, Singapore 169608, Singapore.
Sangeeta MantooDepartment of Anatomical Pathology, Singapore General Hospital, Singapore 169608, Singapore.
Sze S LeeDivision of Medical Sciences, National Cancer Centre Singapore, Singapore 169608, Singapore.
Serene J Y YeowDivision of Medical Sciences, National Cancer Centre Singapore, Singapore 169608, Singapore.
Syed M F AlkaffDepartment of Anatomical Pathology, Singapore General Hospital, Singapore 169608, Singapore.
Nan XiangZhejiang 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 SunZhejiang 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 YiZhejiang 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 DaiSchool of Computer Science and Engineering, Beihang University, Beijing 100191, China.
Wei LiuZhejiang 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 LuZhejiang 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 WuZhejiang 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 LiangZhejiang 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 WangMOE Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Translational Research, Peking University Cancer Hospital, Beijing 100142, China.
Yingkuan ShaoCancer 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 ZhengCancer 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 XuCancer 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 YangCancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
Yifan MengCancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
Cong LuCenter for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
Jiang ZhuCenter for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
Jin'e ZhengCenter for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
Bo WangDepartment of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
Sai LouPhase I Clinical Research Center, Zhejiang Provincial People's Hospital, Hangzhou 310014, China.
Yibei DaiDepartment of Laboratory Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China.
Chao XuCollege of Mathematics and Informatics, Digital Fujian Institute of Big Data Security Technology, Fujian Normal University, Fuzhou 350108, China.
Chenhuan YuZhejiang Provincial Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou 310015, China.
Huazhong YingZhejiang Provincial Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou 310015, China.
Tony K LimDepartment of Anatomical Pathology, Singapore General Hospital, Singapore 169608, Singapore.
Jianmin WuMOE Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Translational Research, Peking University Cancer Hospital, Beijing 100142, China.
Xiaofei GaoZhejiang 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 LuanSchool of Computer Science and Engineering, Beihang University, Beijing 100191, China.
Xiaodong TengDepartment of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
Peng WuCancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
Shi'ang HuangCenter for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
Zhihua TaoDepartment of Laboratory Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China.
Narayanan G IyerDivision of Medical Sciences, National Cancer Centre Singapore, Singapore 169608, Singapore.
Shuigeng ZhouSchool of Computer Science, Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, China.
Wenguang ShaoDepartment of Biology, Institute for Molecular Systems Biology, ETH Zurich, Zurich 8092, Switzerland.
Henry LamDepartment of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China.
Ding MaCancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
Jiafu JiMOE Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Translational Research, Peking University Cancer Hospital, Beijing 100142, China.
Oi L KonDivision of Medical Sciences, National Cancer Centre Singapore, Singapore 169608, Singapore.
Shu ZhengCancer 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 AebersoldDepartment of Biology, Institute for Molecular Systems Biology, ETH Zurich, Zurich 8092, Switzerland; Faculty of Science, University of Zurich, Zurich 8092, Switzerland.
Connie R JimenezOncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, VU University, Amsterdam 1011, The Netherlands.
Tiannan GuoZhejiang 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. Electronic address: guotiannan@westlake.edu.cn.
Westlake University · CNAmsterdam University Medical Centers · NLAmsterdam UMC Location Vrije Universiteit Amsterdam · NLFudan University · CNNational Cancer Centre Singapore · SGSingapore General Hospital · SGTongji Hospital · CNUnion Hospital · CNErasmus MC · NLPeking University · CNZhejiang University · CNBeihang University · CNFirst Affiliated Hospital Zhejiang University · CNSecond Affiliated Hospital of Zhejiang University · CNThermo Fisher Scientific (China) · CNZhejiang Academy of Medical Sciences · CNETH Zurich · CHFujian Normal University · CNHong Kong University of Science and Technology · HKThe Netherlands Cancer Institute · NL
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Mass SpectrometryBiomarkers, TumorCell Line, TumorHumansLymphoma, Large B-Cell, DiffuseMaleNeoplasm ProteinsPeptidesProstatic NeoplasmsProteomicsReproducibility of ResultsBiomarkers, TumorNeoplasm ProteinsPeptidesData-independent acquisitionDiffuse large B cell lymphomaParallel reaction monitoringProstate cancerSpectral library
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