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9. Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis

Author

Kawahara, Rebeca, Chernykh, Anastasia, Alagesan, Kathirvel, Bern, Marshall, Cao, Weiqian, Chalkley, Robert J, Cheng, Kai, Choo, Matthew S, Edwards, Nathan, Goldman, Radoslav, Hoffmann, Marcus, Hu, Yingwei, Huang, Yifan, Kim, Jin Young, Kletter, Doron, Liquet, Benoit, Liu, Mingqi, Mechref, Yehia, Meng, Bo, Neelamegham, Sriram, Nguyen-Khuong, Terry, Nilsson, Jonas, Pap, Adam, Park, Gun Wook, Parker, Benjamin L, Pegg, Cassandra L, Penninger, Josef M, Phung, Toan K, Pioch, Markus, Rapp, Erdmann, Sakalli, Enes, Sanda, Miloslav, Schulz, Benjamin L, Scott, Nichollas E, Sofronov, Georgy, Stadlmann, Johannes, Vakhrushev, Sergey Y, Woo, Christina M, Wu, Hung-Yi, Yang, Pengyuan, Ying, Wantao, Zhang, Hui, Zhang, Yong, Zhao, Jingfu, Zaia, Joseph, Haslam, Stuart M, Palmisano, Giuseppe, Yoo, Jong Shin, Larson, Göran, Khoo, Kai-Hooi, Medzihradszky, Katalin F, Kolarich, Daniel, Packer, Nicolle H, and Thaysen-Andersen, Morten

Subjects
Glycopeptides, Glycoproteins, Glycosylation, Humans, Informatics, Proteome, Proteomics, Research Personnel, Software, Tandem Mass Spectrometry, Biological Sciences, Technology, Medical and Health Sciences, Developmental Biology
Abstract

Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved 'high-coverage' and 'high-accuracy' glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics.

Published
2021

12. Data from Inflammation-Dependent IL18 Signaling Restricts Hepatocellular Carcinoma Growth by Enhancing the Accumulation and Activity of Tumor-Infiltrating Lymphocytes

Author

Markowitz, Geoffrey J., primary, Yang, Pengyuan, primary, Fu, Jing, primary, Michelotti, Gregory A., primary, Chen, Rui, primary, Sui, Jianhua, primary, Yang, Bin, primary, Qin, Wen-Hao, primary, Zhang, Zheng, primary, Wang, Fu-Sheng, primary, Diehl, Anna Mae, primary, Li, Qi-Jing, primary, Wang, Hongyang, primary, and Wang, Xiao-Fan, primary

Published
2023
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14. Supplementary Figure Legends from Inflammation-Dependent IL18 Signaling Restricts Hepatocellular Carcinoma Growth by Enhancing the Accumulation and Activity of Tumor-Infiltrating Lymphocytes

Author

Markowitz, Geoffrey J., primary, Yang, Pengyuan, primary, Fu, Jing, primary, Michelotti, Gregory A., primary, Chen, Rui, primary, Sui, Jianhua, primary, Yang, Bin, primary, Qin, Wen-Hao, primary, Zhang, Zheng, primary, Wang, Fu-Sheng, primary, Diehl, Anna Mae, primary, Li, Qi-Jing, primary, Wang, Hongyang, primary, and Wang, Xiao-Fan, primary

Published
2023
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15. Supplementary Figures and Tables from Inflammation-Dependent IL18 Signaling Restricts Hepatocellular Carcinoma Growth by Enhancing the Accumulation and Activity of Tumor-Infiltrating Lymphocytes

Author

Markowitz, Geoffrey J., primary, Yang, Pengyuan, primary, Fu, Jing, primary, Michelotti, Gregory A., primary, Chen, Rui, primary, Sui, Jianhua, primary, Yang, Bin, primary, Qin, Wen-Hao, primary, Zhang, Zheng, primary, Wang, Fu-Sheng, primary, Diehl, Anna Mae, primary, Li, Qi-Jing, primary, Wang, Hongyang, primary, and Wang, Xiao-Fan, primary

Published
2023
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17. Supplementary Materials and Methods from Inflammation-Dependent IL18 Signaling Restricts Hepatocellular Carcinoma Growth by Enhancing the Accumulation and Activity of Tumor-Infiltrating Lymphocytes

Author

Markowitz, Geoffrey J., primary, Yang, Pengyuan, primary, Fu, Jing, primary, Michelotti, Gregory A., primary, Chen, Rui, primary, Sui, Jianhua, primary, Yang, Bin, primary, Qin, Wen-Hao, primary, Zhang, Zheng, primary, Wang, Fu-Sheng, primary, Diehl, Anna Mae, primary, Li, Qi-Jing, primary, Wang, Hongyang, primary, and Wang, Xiao-Fan, primary

Published
2023
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19. Supplemental Figure S17 from Inflammation-Dependent IL18 Signaling Restricts Hepatocellular Carcinoma Growth by Enhancing the Accumulation and Activity of Tumor-Infiltrating Lymphocytes

Author

Markowitz, Geoffrey J., primary, Yang, Pengyuan, primary, Fu, Jing, primary, Michelotti, Gregory A., primary, Chen, Rui, primary, Sui, Jianhua, primary, Yang, Bin, primary, Qin, Wen-Hao, primary, Zhang, Zheng, primary, Wang, Fu-Sheng, primary, Diehl, Anna Mae, primary, Li, Qi-Jing, primary, Wang, Hongyang, primary, and Wang, Xiao-Fan, primary

Published
2023
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21. Computational and Mass Spectrometry-Based Approach Identify Deleterious Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) in JMJD6.

Author

Gong, Tianqi, Yang, Lujie, Shen, Fenglin, Chen, Hao, Pan, Ziyue, Zhang, Quanqing, Jiang, Yan, Zhong, Fan, Yang, Pengyuan, and Zhang, Yang

Subjects
JMJD6, computational workflow, deleterious nsSNPs, systematic filtration, Genetics, Cancer, 2.1 Biological and endogenous factors, 5.1 Pharmaceuticals, Generic health relevance, Organic Chemistry, Medicinal and Biomolecular Chemistry, Theoretical and Computational Chemistry
Abstract

The jumonji domain-containing protein 6 (JMJD6) gene catalyzes the arginine demethylation and lysine hydroxylation of histone and a growing list of its known substrate molecules, including p53 and U2AF65, suggesting a possible role in mRNA splicing and transcription in cancer progression. Mass spectrometry-based technology offers the opportunity to detect SNP variants accurately and effectively. In our study, we conducted a combined computational and filtration workflow to predict the nonsynonymous single nucleotide polymorphisms (nsSNPs) present in JMJD6, followed by a liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and validation. The computational approaches SIFT, PolyPhen-2, SNAP, I-Mutant 2.0, PhD-SNP, PANTHER, and SNPS&GO were integrated to screen out the predicted damaging/deleterious nsSNPs. Through the three-dimensional structure of JMJD6, H187R (rs1159480887) was selected as a candidate for validation. The validation experiments showed that the mutation of this nsSNP in JMJD6 obviously affected mRNA splicing or the transcription of downstream genes through the reduced lysyl-hydroxylase activity of its substrates, U2AF65 and p53, further indicating the accuracy of this prediction method. This research provides an effective computational workflow for researchers with an opportunity to select prominent deleterious nsSNPs and, thus, remains promising for examining the dysfunction of proteins.

Published
2021

22. Optimized MALDI-TOF MS Strategy for Characterizing Polymers

Author

Wang, Zhenxin, Zhang, Quanqing, Shen, Huali, Yang, Pengyuan, and Zhou, Xinwen

Subjects
Analytical Chemistry, Chemical Sciences, Physical Chemistry, MALDI-TOF MS, polymer, polyvinylpyrrolidone K12, polymer polyol KPOP-5040, polyether polyol DL-4000, polyethylene glycol 6000, Chemical sciences
Abstract

In recent years, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) plays an essential role in the analysis of polymers. To acquire a more reliable strategy for polymer profiling, we characterized four representative polymers including polyethylene glycol 6000, polyvinylpyrrolidone K12, polymer polyol KPOP-5040, and polyether polyol DL-4000. The preparation methods of these four polymer samples have been optimized from six aspects, including matrix, cationization reagent, solvent, mixing ratio of cationization reagent to polymer, mixing ratio of matrix to polymer, and laser intensity. After investigating the effects of seven commonly used matrices on the ionization efficiency of four polymers, trans-2-[3-(4-tert-butylphenyl)-2-methyl-2-propenylidene] malononitrile (DCTB) was found to be the only matrix suitable for the analysis of all the four polymers. Our experimental results suggested that different polymers showed a certain preference for different cationization reagents. For example, the polymer polyol KPOP-5040 was suitable for sodium iodide as the cationization reagent, while polyvinylpyrrolidone K12 was more suitable for silver trifluoroacetate (AgTFA). For the choice of solvent, tetrahydrofuran is a reagent with rapid evaporation and a wide range of dissolution which can achieve the best results for the analysis of four polymers. The optimized method was successfully applied to the identification of DSPE-PEG-NH2 with different polymerized degrees. This MALDI-TOF strategy potentially provided the supplementary function through the polymer's application in biomedical and visible probing.

Published
2021

23. Precision N-Glycoproteomic Profiling of Murine Peritoneal Macrophages After Different Stimulations

Author

Yang, Lujie, Gong, Tianqi, Shen, Huali, Pei, Jiangnan, Zhang, Lei, Zhang, Quanqing, Huang, Yuanyu, Hu, Zuojian, Pan, Ziyue, Yang, Pengyuan, Lin, Ling, and Yu, Hongxiu

Subjects
Biochemistry and Cell Biology, Biomedical and Clinical Sciences, Biological Sciences, Immunology, Vaccine Related, Underpinning research, 1.1 Normal biological development and functioning, Inflammatory and immune system, Good Health and Well Being, Animals, Chromatography, High Pressure Liquid, Computational Biology, Cytokines, Gene Expression Regulation, Gene Regulatory Networks, Glycoproteins, Macrophage Activation, Macrophages, Peritoneal, Mice, Models, Biological, NIH 3T3 Cells, Proteome, Proteomics, RAW 264.7 Cells, macrophage, N-glycosylation, Toll-like receptors, glycoproteomics, inflammatory response, Medical Microbiology, Biochemistry and cell biology, Genetics
Abstract

Macrophages are important immune cells that participate in both innate and adaptive immune responses, such as phagocytosis, recognition of molecular patterns, and activation of the immune response. In this study, murine peritoneal macrophages were isolated and then activated by LPS, HSV and VSV. Integrative proteomic and precision N-glycoproteomic profiling were conducted to assess the underlying macrophage activation. We identified a total of 587 glycoproteins, including 1239 glycopeptides, 526 monosaccharide components, and 8326 intact glycopeptides in glycoproteomics, as well as a total of 4496 proteins identified in proteomic analysis. These glycoproteins are widely involved in important biological processes, such as antigen presentation, cytokine production and glycosylation progression. Under the stimulation of the different pathogens, glycoproteins showed a dramatic change. We found that receptors in the Toll-like receptor pathway, such as Tlr2 and CD14, were increased under LPS and HSV stimulation. Glycosylation of those proteins was proven to influence their subcellular locations.

Published
2021

26. Anatomically resolved transcriptome and proteome landscapes reveal disease‐relevant molecular signatures and systematic changes in heart function of end‐stage dilated cardiomyopathy

Author

Lin, Ling, primary, Liu, Shanshan, additional, Chen, Zhangwei, additional, Xia, Yan, additional, Xie, Juanjuan, additional, Fu, Mingqiang, additional, Lu, Danbo, additional, Wu, Yuan, additional, Shen, Huali, additional, Yang, Pengyuan, additional, and Qian, Juying, additional

Published
2022
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27. pGlycoQuant with a deep residual network for quantitative glycoproteomics at intact glycopeptide level

Author

Kong, Siyuan, primary, Gong, Pengyun, additional, Zeng, Wen-Feng, additional, Jiang, Biyun, additional, Hou, Xinhang, additional, Zhang, Yang, additional, Zhao, Huanhuan, additional, Liu, Mingqi, additional, Yan, Guoquan, additional, Zhou, Xinwen, additional, Qiao, Xihua, additional, Wu, Mengxi, additional, Yang, Pengyuan, additional, Liu, Chao, additional, and Cao, Weiqian, additional

Published
2022
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29. Contributors

Author

Cai, Zhixiong, primary, Cao, Junji, additional, Chen, Xi, additional, Chen, Xiaofeng, additional, Chen, Xiaomei, additional, Ding, Longjiang, additional, Duan, Wei, additional, Dunn, Andrew, additional, Fang, Yaning, additional, Hou, Li, additional, Huang, Yipeng, additional, Huang, Guoming, additional, Huang, Mengjiao, additional, Huang, Yu, additional, Huang, Rujin, additional, Li, Feiming, additional, Li, Baichuan, additional, Li, Mengmeng, additional, Lian, Ying, additional, Lin, Liping, additional, Lin, Chunshui, additional, Lin, Xucong, additional, Lin, Jou, additional, Lu, Chun-Hua, additional, Pan, Yi, additional, Rong, Mingcong, additional, Shi, Donglu, additional, Wang, Xiaoru, additional, Wang, Weijie, additional, Wang, Xu-dong, additional, Wang, Wei, additional, Wei, Liming, additional, Wu, Xiaoping, additional, Xie, Zenghong, additional, Xu, Wei, additional, Xue, Yitong, additional, Yang, Pengyuan, additional, Yang, Huang-Hao, additional, Yang, Chaoyong, additional, Yao, Qiuhong, additional, Yi, Changqing, additional, Zeng, Jingbin, additional, Zhang, Wei, additional, Zhang, Xiaoai, additional, Zhang, Yinglu, additional, Zhang, Yufei, additional, Zhao, Yuan, additional, and Zhu, Lin, additional

Published
2019
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34. Membrane glycomics reveal heterogeneity and quantitative distribution of cell surface sialylation.

Author

Park, Diane Dayoung, Xu, Gege, Wong, Maurice, Phoomak, Chatchai, Liu, Mingqi, Haigh, Nathan E, Wongkham, Sopit, Yang, Pengyuan, Maverakis, Emanual, and Lebrilla, Carlito B

Subjects
Chemical Sciences
Abstract

Given that unnatural sugar expression is metabolically achieved, the kinetics and disposition of incorporation can lend insight into the temporal and localization preferences of sialylation across the cell surface. However, common detection schemes lack the ability to detail the molecular diversity and distribution of target moieties. Here we employed a mass spectrometric approach to trace the placement of azido sialic acids on membrane glycoconjugates, which revealed substantial variations in incorporation efficiencies between N-/O-glycans, glycosites, and glycosphingolipids. To further explore the propensity for sialylation, we subsequently mapped the native glycome of model epithelial cell surfaces and illustrate that while glycosylation sites span broadly across the extracellular region, a higher number of heterogeneous glycoforms occur on sialylated sites closest to the transmembrane domain. Beyond imaging techniques, this integrative approach provides unprecedented details about the frequency and structure-specific distribution of cell surface sialylation, a critical feature that regulates cellular interactions and homeostatic pathways.

Published
2018

44. Circulating proteomic panels for risk stratification of intracranial aneurysm and its rupture

Author

Xiong, Yueting, primary, Zheng, Yongtao, additional, Yan, Yan, additional, Yao, Jun, additional, Liu, Hebin, additional, Shen, Fenglin, additional, Kong, Siyuan, additional, Yang, Shuang, additional, Yan, Guoquan, additional, Zhao, Huanhuan, additional, Zhou, Xinwen, additional, Hu, Jia, additional, Zhou, Bin, additional, Jin, Tao, additional, Shen, Huali, additional, Leng, Bing, additional, Yang, Pengyuan, additional, and Liu, Xiaohui, additional

Published
2022
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45. Intratumoral stem-like CCR4+ regulatory T cells orchestrate the immunosuppressive microenvironment in HCC associated with hepatitis B

Author

Gao, Yanan, primary, You, Maojun, additional, Fu, Junliang, additional, Tian, Meijie, additional, Zhong, Xinyue, additional, Du, Chengzhi, additional, Hong, Zhixian, additional, Zhu, Zhenyu, additional, Liu, Junliang, additional, Markowitz, Geoffrey J., additional, Wang, Fu-Sheng, additional, and Yang, Pengyuan, additional

Published
2022
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48. Author Correction: Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis

Author

Kawahara, Rebeca, primary, Chernykh, Anastasia, additional, Alagesan, Kathirvel, additional, Bern, Marshall, additional, Cao, Weiqian, additional, Chalkley, Robert J., additional, Cheng, Kai, additional, Choo, Matthew S., additional, Edwards, Nathan, additional, Goldman, Radoslav, additional, Hoffmann, Marcus, additional, Hu, Yingwei, additional, Huang, Yifan, additional, Kim, Jin Young, additional, Kletter, Doron, additional, Liquet, Benoit, additional, Liu, Mingqi, additional, Mechref, Yehia, additional, Meng, Bo, additional, Neelamegham, Sriram, additional, Nguyen-Khuong, Terry, additional, Nilsson, Jonas, additional, Pap, Adam, additional, Park, Gun Wook, additional, Parker, Benjamin L., additional, Pegg, Cassandra L., additional, Penninger, Josef M., additional, Phung, Toan K., additional, Pioch, Markus, additional, Rapp, Erdmann, additional, Sakalli, Enes, additional, Sanda, Miloslav, additional, Schulz, Benjamin L., additional, Scott, Nichollas E., additional, Sofronov, Georgy, additional, Stadlmann, Johannes, additional, Vakhrushev, Sergey Y., additional, Woo, Christina M., additional, Wu, Hung-Yi, additional, Yang, Pengyuan, additional, Ying, Wantao, additional, Zhang, Hui, additional, Zhang, Yong, additional, Zhao, Jingfu, additional, Zaia, Joseph, additional, Haslam, Stuart M., additional, Palmisano, Giuseppe, additional, Yoo, Jong Shin, additional, Larson, Göran, additional, Khoo, Kai-Hooi, additional, Medzihradszky, Katalin F., additional, Kolarich, Daniel, additional, Packer, Nicolle H., additional, and Thaysen-Andersen, Morten, additional

Published
2021
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50. pGlycoQuant with a deep residual network for precise and minuscule-missing-value quantitative glycoproteomics enabling the functional exploration of site-specific glycosylation

Author

Cao, Weiqian, primary, Kong, Siyuan, additional, Zeng, Wenfeng, additional, Gong, Pengyun, additional, Jiang, Biyun, additional, Hou, Xinhang, additional, Zhang, Yang, additional, Zhao, Huanhuan, additional, Liu, Mingqi, additional, Qiao, Xihua, additional, Wu, Mengxi, additional, Yan, Guoquan, additional, Liu, Chao, additional, and Yang, Pengyuan, additional

Published
2021
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