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Advancements in mass spectrometry-based glycoproteomics and glycomics

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National Science Review 2016年第3期3卷 345-364页

作者： haojie lu Ying zhang pengyuan yang department of Systems Biology for Medicine School of Basic Medicine and Institutes of Biomedical SciencesFudan University Key Lab of Glycoconjugate of Ministry of Health and Birth Control Fudan University department of chemistry Fudan University

Protein N-glycosylation plays a crucial role in a considerable number of important biological *** studies on glycoproteomes and glycomes have already characterized many glycoproteins and glycans associated with cell development, life cycle, and disease progression. Mass spectrometry(MS) is the most powerful tool for identifying biomolecules including glycoproteins and glycans, however, utilizing MS-based approaches to identify glycoproteomes and glycomes is challenging due to the technical difficulties associated with glycosylation analysis. In this review, we summarize the most recent developments in MS-based glycoproteomics and glycomics, including a discussion on the development of analytical methodologies and strategies used to explore the glycoproteome and glycome, as well as noteworthy biological discoveries made in glycoproteome and glycome research. This review places special emphasis on china, where scientists have made sizeable contributions to the literature, as advancements in glycoproteomics and glycomincs are occurring quite rapidly.

关键词： mass spectrometry glycoproteomics glycomics

Recent advances in proteolysis and peptide/protein separation by chromatographic strategies

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Science china chemistry 2010年第4期53卷 685-694页

作者： zhang XiangMin1, LIU BaoHong1, zhang LiHua2, ZOU HanFa2, CAO Jing1, GAO MingXia1, TANG Jia1, LIU Yun1, yang pengyuan1 & zhang YuKui2 1department of chemistry and institutes of biomedical sciences, fudan university, shanghai 200433, china 2Dalian Institute of Chemical Physics, Chinese Academy of sciences, Dalian 116023, china 1. department of chemistry and institutes of biomedical sciences Fudan University Shanghai 200433 China2. Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China

This review gives a broad glance on the progress of recent advances on proteolysis and peptide/protein separation by chroma-tographic strategies in the past ten years, covering the main research in these areas especially in china. The reviewed research focused on enzymatic micro-reactors and peptide separation in bottom-up approaches, and protein and peptide separation in top-down approaches. The new enzymatic micro-reactor is able to accelerate proteolytic reaction rate from conventionally a couple of hours to a few seconds, and the multiple dimensional chromatographic-separation with various models or arrays could sufficiently separate the proteomic mixture. These advances have significantly promoted the research of protein/peptide separation and identification in proteomics.

关键词： proteolysis enzymatic digestion chromatographic separation peptide enrichment mass spectrometry

GTF2H4 regulates partial EndMT via NF-κB activation through NCOA3 phosphorylation in ischemic diseases

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The Innovation 2024年第2期5卷 27-41页

作者： Zheyan Fang Gang Zhao Shuang Zhao Xueting Yu Runyang Feng You-en zhang Haomin Li Lei Huang Zhenyang Guo Zhentao zhang Mukaddas Abdurahman Hangnan Hong Peng Li Bing Wu Jinhang Zhu Xin Zhong Dong Huang Hao lu Xin Zhao Zhaoyang Chen Wenbin zhang Junjie Guo Hongchao Zheng Yue He Shengying Qin haojie lu Yun Zhao Xiangdong Wang Junbo Ge Hua Li department of Cardiology Zhongshan HospitalFudan UniversityShanghai Institute of Cardiovascular DiseasesShanghai 200032China department of Cardiology Zhongshan HospitalFudan UniversityShanghai 200032China department of Medical Examination Shanghai Xuhui District Central HospitalShanghai 200031China department of Cardiology and Institute of Clinical Medicine Renmin HospitalHubei University of MedicineShiyan 442000China Clinical Data Center Children’s HospitalZhejiang University School of MedicineNational Clinical Research Center for Child HealthHangzhou 310052China department of Molecular Celland Cancer BiologyUniversity of Massachusetts Chan Medical SchoolWorcesterMA 01605USA Bio-X Institute Key Laboratory for The Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghai 200030China department of Cardiology Heart Center of Fujian ProvinceFujian Medical University Union HospitalFuzhou 350001China department of Cardiology Sir Run Run Shaw Hospitalaffiliated with Zhejiang University School of MedicineHangzhou 310020China department of Cardiology The Affiliated Hospital of Qingdao UniversityQingdao 266003China department of Cardiology Shanghai Xuhui District Central HospitalShanghai 200031China department of Cardiology Shanghai Eighth People’s HospitalShanghai 200235China department of chemistry and institutes of biomedical sciences Fudan UniversityShanghai 200032China State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai 200031China School of Life Science and Technology Shanghai Tech University100 Haike RoadShanghai 201210China Key Laboratory of Systems Health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China department of Pulmonary and Critical Care Medicine Zhongshan Hospital

Partial endothelial-to-mesenchymal transition(EndMT)is an intermediate phenotype observed in endothelial cells(ECs)undergoing a transition toward a mesenchymal state to support neovascularization during(patho)physiological ***,we investigated the occurrence of partial EndMT in ECs under hypoxic/ischemic conditions and identified general transcription factor IIH subunit 4(GTF2H4)as a positive regulator of this *** addition,we discovered that GTF2H4 collaborates with its target protein excision repair cross-complementation group 3(ERCC3)to co-regulate partial ***,by using phosphorylation proteomics and site-directed mutagenesis,we demonstrated that GTF2H4 was involved in the phosphorylation of receptor coactivator 3(NCOA3)at serine 1330,which promoted the interaction between NCOA3 and p65,resulting in the transcriptional activation of NF-κB and the NF-kB/Snail signaling axis during partial *** vivo experiments confirmed that GTF2H4 significantly promoted partial EndMT and angiogenesis after ischemic ***,our findings reveal that targeting GTF2H4 is promising for tissue repair and offers potential opportunities for treating hypoxic/ischemic diseases.

关键词： ischemic activation GTF

New lysine-acetylated proteins screened by immunoaffinity and liquid chromatography-mass spectrometry

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Science china chemistry 2010年第1期53卷 238-244页

作者： zhang Bing ZHAO Chao luO KaiXuan YAN GuoQuan YAO Jun WANG YingYin lu haojie FAN HuiZhi yang pengyuan department of chemistry Fudan UniversityShanghai 200433China institutes of biomedical sciences Fudan UniversityShanghai 200032China

The lack of selective extraction specific for lysine-acetylated proteins has been a major problem in the field of acetylation biology,though acetylation plays a key role in many biological *** this paper,we report for the first time the proteomic screening of lysine-acetylated proteins from a mouse liver tissue,by a new approach of immunoaffinity purification of lysine-acetylated peptides combined with nano-HPLC/MS/MS *** have found 20 lysine-acetylated proteins with 21 lysine-acetylated sites,among which 12 lysine-acetylated proteins and 16 lysine-acetylated sites have never been reported ***,three acetyltransferases harboring in mitochondrion are newly discovered acetyltransferases responsible for the acetylation of nonhistone *** have explored the significant patterns of residue preference by the hierarchical clustering analysis of amino acid residues surrounding acetylation sites,which could be helpful to the prediction of new sites of lysine *** findings provide more candidates for studying the important roles played by acetylation in diverse cellular pathways and related human diseases.

关键词： lysine acetylation immunoaffinity purification liquid chromatography mass spectrometry

Comparison of alternative extraction methods for secretome profiling in human hepatocellular carcinoma cells

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Science china(Life sciences) 2011年第1期54卷 34-38页

作者： CAO Jing SHEN ChengPin zhang Jun YAO Jun SHEN HuaLi LIU YinKun lu haojie yang pengyuan institutes of biomedical sciences and department of chemistry Fudan University Shanghai 200032 China Liver Cancer Institute Zhongshan Hospital Fudan University Shanghai 200032 China

Secreted proteins are important sources for early detection and diagnosis of disease, and as such have received considerable attention. The extraction of low concentration proteins from large volumes of culture media, which are rich in salts and other compounds that interfere with most proteomics techniques, presents a problem for secretome studies. Ultrafiltration, precipitation, and dialysis are three major extraction methods that can be used to overcome this problem. The present study for the first time, compared the merits and shortcomings of these three methods, without bias. Centrifugal ultrafiltration provided the best extraction efficiency, and precipitation provided the highest number of identifiable proteins. The three methods yielded closely related, but different, information on the secretome; thus, they should be considered complementary or, at least, supplementary methods. Three hundred and sixty unique proteins were identified, including 211 potential secreted proteins. Compared with previous studies, this study also identified 42 new secreted proteins. The present study not only offers a reference for the selection of secretome extraction methods, but also expands the secretome database for the investigation of hepatocellular carcinoma.

关键词： hepatocellular carcinoma secretome protein extraction ultrafiltration precipitation dialysis LC-MS/MS

Discover the Post-Translational Modification Proteome Using Mass Spectrometry

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Chinese Journal of chemistry 2021年第3期39卷 550-558页

作者： Ying zhang Caiyun Fang Huimin Bao Wenjuan Yuan haojie lu shanghai Cancer Center and institutes of biomedical sciences Fudon UniversityShanghai 200032China department of chemistry and NHC Key Laboratory of Glycoconjugates Research Fudan UniversityShanghai 200032China

Protein post-translational modifications(PTMs)are chemical modifications on *** play a key role in many cellular processes by influencing the structure of proteins and dynamically regulating their ***,characterizing PTMs at proteome level is critical to provide invaluable insight into the functions of proteins underlying different biological *** in modern proteomics technologies including sample preparation,chromatography separation as well as mass spectrometry have propelled the PTMs proteome to further *** the past decade,to better examine the PTMs with high sensitivity and selectivity,our group have developed a series of MS-based novel analytical approaches to study the protein ***,we mainly introduce these approaches developed by our group and discuss how to overcome the technical obstacles of studying various protein PTMs with mass spectrometry.

关键词： Proteome Mass spectrometry Post translational modification Qualitative analysis Quantitative analysis

High-throughput site-specific N-glycoproteomics reveals glyco-signatures for liver disease diagnosis

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National Science Review 2023年第1期10卷 214-225页

作者： Zhenyu Sun Bin Fu Guoli Wang Lei zhang Ruofan Xu Ying zhang haojie lu shanghai Cancer Center and institutes of biomedical sciences Fudan University department of chemistry and NHC Key Laboratory of Glycoconjugates Research Fudan University Eleanor Roosevelt College University of California San Diego

The glycoproteome has emerged as a prominent target for screening biomarkers,as altered glycosylation is a hallmark of cancer *** this work,we incorporated tandem mass tag labeling into quantitative glycoproteomics by developing a chemical labeling-assisted complementary dissociation method for the multiplexed analysis of intact *** from the complementary nature of two different mass spectrometry dissociation methods for identification and multiplex labeling for quantification of intact N-glycopeptides,we conducted the most comprehensive site-specific and subclass-specific N-glycosylation profiling of human serum immunoglobulin G(IgG) to *** analysing the serum of 90 human patients with varying severities of liver diseases,as well as healthy controls,we identified that the combination of IgG1-H3N5F1 and IgG4-H4N3 can be used for distinguishing between different stages of liver ***,we used targeted parallel reaction monitoring to successfully validate the expression changes of glycosylation in liver diseases in a different sample cohort that included 45 serum samples.

关键词： glycoproteomics high-throughput quantification N-glycopeptides liver disease

OGP: A Repository of Experimentally Characterized O-glycoproteins to Facilitate Studies on O-glycosylation

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Genomics, Proteomics & Bioinformatics 2021年第4期19卷 611-618页

作者： Jiangming Huang Mengxi Wu yang zhang Siyuan Kong Mingqi Liu Biyun Jiang pengyuan yang Weiqian Cao department of chemistry and institutes of biomedical sciences Fudan UniversityShanghai 200032China The Fifth People’s Hospital Fudan Universityand the Shanghai Key Laboratory of Medical Epigeneticsthe International Co-laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyFudan UniversityShanghai 200032China NHC Key Laboratory of Glycoconjugates Research(fudan university) Shanghai 200032China

Numerous studies on cancers, biopharmaceuticals, and clinical trials have necessitated comprehensive and precise analysis of protein O-glycosylation. However, the lack of updated and convenient databases deters the storage of and reference to emerging O-glycoprotein data. To resolve this issue, an O-glycoprotein repository named OGP was established in this *** was constructed with a collection of O-glycoprotein data from different sources. OGP contains 9354 O-glycosylation sites and 11,633 site-specific O-glycans mapping to 2133 O-glycoproteins, and it is the largest O-glycoprotein repository thus *** on the recorded O-glycosylation sites, an O-glycosylation site prediction tool was developed. Moreover, an OGP-based website is already available(http://***/). The website comprises four specially designed and user-friendly modules:statistical analysis, database search, site prediction, and data submission. The first version of OGP repository and the website allow users to obtain various O-glycoprotein-related information, such as protein accession Nos., O-glycosylation sites,O-glycopeptide sequences, site-specific O-glycan structures, experimental methods, and potential O-glycosylation sites.O-glycosylation data mining can be performed efficiently on this website, which will greatly facilitate related studies. In addition, the database is accessible from OGP website(http://***/***).

关键词： O-glycosylation O-glycoprotein repository Site prediction O-glycoprotein related website Data mining

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Science china chemistry 2016年第3期59卷 380-382页

作者： Li Feng Hong Li yang zhang Huali Shen Hongxiu Yu Fan Zhong lunxiu Qin Fuchu He pengyuan yang Zhaoyou Tang Minhang Hospital Fudan UniversityShanghai201199China department of chemistry Fudan UniversityShanghai200433China institutes of biomedical sciences Fudan UniversityShanghai200032China Zhongshan Hospital Fudan UniversityShanghai200032China

Recently, we have analyzed expressional transcriptome and proteome for a number of cancer cell lines, including 8 hepatocellular carcinoma （HCC） ones [1,2]. These 8 HCC cell lines consist of 6 metastatic （all with mutant p53） and 2 non-metastatic （with a mutant and a lost p53） ones, being all HBV traceable for relatively close genetic-backgrounds. We have analyzed the related dataset and obtained transcrip- tome （16353 genes） and proteome （7861 proteins） of these 8 HCC cell lines, and explored a group of up-regulated and down-regulated genes [3].

关键词： Cell culture Chromosomes Genes Pathology