1
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Chen X, Song X, Li J, Wang J, Yan Y, Yang F. Integrated proteomic, phosphoproteomic, and N-glycoproteomic analyses of small extracellular vesicles from C2C12 myoblasts identify specific PTM patterns in ligand-receptor interactions. Cell Commun Signal 2024; 22:273. [PMID: 38755675 PMCID: PMC11097525 DOI: 10.1186/s12964-024-01640-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024] Open
Abstract
Small extracellular vesicles (sEVs) are important mediators of intercellular communication by transferring of functional components (proteins, RNAs, and lipids) to recipient cells. Some PTMs, including phosphorylation and N-glycosylation, have been reported to play important role in EV biology, such as biogenesis, protein sorting and uptake of sEVs. MS-based proteomic technology has been applied to identify proteins and PTM modifications in sEVs. Previous proteomic studies of sEVs from C2C12 myoblasts, an important skeletal muscle cell line, focused on identification of proteins, but no PTM information on sEVs proteins is available.In this study, we systematically analyzed the proteome, phosphoproteome, and N-glycoproteome of sEVs from C2C12 myoblasts with LC-MS/MS. In-depth analyses of the three proteomic datasets revealed that the three proteomes identified different catalogues of proteins, and PTMomic analysis could expand the identification of cargos in sEVs. At the proteomic level, a high percentage of membrane proteins, especially tetraspanins, was identified. The sEVs-derived phosphoproteome had a remarkably high level of tyrosine-phosphorylated sites. The tyrosine-phosphorylated proteins might be involved with EPH-Ephrin signaling pathway. At the level of N-glycoproteomics, several glycoforms, such as complex N-linked glycans and sialic acids on glycans, were enriched in sEVs. Retrieving of the ligand-receptor interaction in sEVs revealed that extracellular matrix (ECM) and cell adhesion molecule (CAM) represented the most abundant ligand-receptor pairs in sEVs. Mapping the PTM information on the ligands and receptors revealed that N-glycosylation mainly occurred on ECM and CAM proteins, while phosphorylation occurred on different categories of receptors and ligands. A comprehensive PTM map of ECM-receptor interaction and their components is also provided.In summary, we conducted a comprehensive proteomic and PTMomic analysis of sEVs of C2C12 myoblasts. Integrated proteomic, phosphoproteomic, and N-glycoproteomic analysis of sEVs might provide some insights about their specific uptake mechanism.
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Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xi Song
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiaran Li
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jifeng Wang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yumeng Yan
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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White MEH, Sinn LR, Jones DM, de Folter J, Aulakh SK, Wang Z, Flynn HR, Krüger L, Tober-Lau P, Demichev V, Kurth F, Mülleder M, Blanchard V, Messner CB, Ralser M. Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics. Nat Biomed Eng 2024; 8:233-247. [PMID: 37474612 DOI: 10.1038/s41551-023-01067-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named 'OxoScan-MS', identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive and untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from patients with COVID-19 and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples.
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Affiliation(s)
- Matthew E H White
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ludwig R Sinn
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Marc Jones
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Joost de Folter
- Software Engineering and Artificial Intelligence Technology Platform, The Francis Crick Institute, London, UK
| | - Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ziyue Wang
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Helen R Flynn
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Lynn Krüger
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Vadim Demichev
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Mülleder
- Core Facility High-throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Véronique Blanchard
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Christoph B Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Precision Proteomic Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland.
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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3
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Takahashi Y, Shiota M, Fujita A, Yamada I, Aoki-Kinoshita KF. GlyComb: A novel glycoconjugate data repository that bridges glycomics and proteomics. J Biol Chem 2024; 300:105624. [PMID: 38176651 PMCID: PMC10850976 DOI: 10.1016/j.jbc.2023.105624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/03/2023] [Accepted: 12/26/2023] [Indexed: 01/06/2024] Open
Abstract
The glycosylation of proteins and lipids is known to be closely related to the mechanisms of various diseases such as influenza, cancer, and muscular dystrophy. Therefore, it has become clear that the analysis of post-translational modifications of proteins, including glycosylation, is important to accurately understand the functions of each protein molecule and the interactions among them. In order to conduct large-scale analyses more efficiently, it is essential to promote the accumulation, sharing, and reuse of experimental and analytical data in accordance with the FAIR (Findability, Accessibility, Interoperability, and Re-usability) data principles. However, a FAIR data repository for storing and sharing glycoconjugate information, including glycopeptides and glycoproteins, in a standardized format did not exist. Therefore, we have developed GlyComb (https://glycomb.glycosmos.org) as a new standardized data repository for glycoconjugate data. Currently, GlyComb can assign a unique identifier to a set of glycosylation information associated with a specific peptide sequence or UniProt ID. By standardizing glycoconjugate data via GlyComb identifiers and coordinating with existing web resources such as GlyTouCan and GlycoPOST, a comprehensive system for data submission and data sharing among researchers can be established. Here we introduce how GlyComb is able to integrate the variety of glycoconjugate data already registered in existing data repositories to obtain a better understanding of the available glycopeptides and glycoproteins, and their glycosylation patterns. We also explain how this system can serve as a foundation for a better understanding of glycan function.
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Affiliation(s)
- Yushi Takahashi
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Tokyo, Japan
| | - Masaaki Shiota
- Glycan and Life Systems Integration Center, Faculty of Science and Engineering, Soka University, Tokyo, Japan
| | - Akihiro Fujita
- Glycan and Life Systems Integration Center, Faculty of Science and Engineering, Soka University, Tokyo, Japan
| | - Issaku Yamada
- Laboratory of Glycoinformatics, The Noguchi Institute, Tokyo, Japan
| | - Kiyoko F Aoki-Kinoshita
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Tokyo, Japan; Glycan and Life Systems Integration Center, Faculty of Science and Engineering, Soka University, Tokyo, Japan.
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4
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Yang T, Xiao H, Chen X, Zheng L, Guo H, Wang J, Jiang X, Zhang CY, Yang F, Ji X. Characterization of N-glycosylation and its functional role in SIDT1-Mediated RNA uptake. J Biol Chem 2024; 300:105654. [PMID: 38237680 PMCID: PMC10850970 DOI: 10.1016/j.jbc.2024.105654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/08/2024] Open
Abstract
The mammalian SID-1 transmembrane family members, SIDT1 and SIDT2, are multipass transmembrane proteins that mediate the cellular uptake and intracellular trafficking of nucleic acids, playing important roles in the immune response and tumorigenesis. Previous work has suggested that human SIDT1 and SIDT2 are N-glycosylated, but the precise site-specific N-glycosylation information and its functional contribution remain unclear. In this study, we use high-resolution liquid chromatography tandem mass spectrometry to comprehensively map the N-glycosites and quantify the N-glycosylation profiles of SIDT1 and SIDT2. Further molecular mechanistic probing elucidates the essential role of N-linked glycans in regulating cell surface expression, RNA binding, protein stability, and RNA uptake of SIDT1. Our results provide crucial information about the potential functional impact of N-glycosylation in the regulation of SIDT1-mediated RNA uptake and provide insights into the molecular mechanisms of this promising nucleic acid delivery system with potential implications for therapeutic applications.
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Affiliation(s)
- Tingting Yang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Haonan Xiao
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Le Zheng
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Hangtian Guo
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Jiaqi Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Xiaohong Jiang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Chen-Yu Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, China.
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, China; Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China; Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, Jiangsu, China.
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5
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Chau TH, Chernykh A, Kawahara R, Thaysen-Andersen M. Critical considerations in N-glycoproteomics. Curr Opin Chem Biol 2023; 73:102272. [PMID: 36758418 DOI: 10.1016/j.cbpa.2023.102272] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 02/10/2023]
Abstract
N-Glycoproteomics, the system-wide study of glycans asparagine-linked to protein carriers, holds a unique and still largely untapped potential to provide deep insights into the complexity and dynamics of the heterogeneous N-glycoproteome. Despite the advent of innovative analytical and informatics tools aiding the analysis, N-glycoproteomics remains challenging and consequently largely restricted to specialised laboratories. Aiming to stimulate discussions of method harmonisation, data standardisation and reporting guidelines to make N-glycoproteomics more reproducible and accessible to the community, we here discuss critical considerations related to the design and execution of N-glycoproteomics experiments and highlight good practices in N-glycopeptide data collection, analysis, interpretation and sharing. Giving the rapid maturation and, expectedly, a wide-spread implementation of N-glycoproteomics capabilities across the community in future years, this piece aims to point out common pitfalls, to encourage good data sharing and documentation practices, and to highlight practical solutions and strategies to enhance the insight into the N-glycoproteome.
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Affiliation(s)
- The Huong Chau
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Anastasia Chernykh
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Rebeca Kawahara
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
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6
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Lohia S, Latosinska A, Zoidakis J, Makridakis M, Mischak H, Glorieux G, Vlahou A, Jankowski V. Glycosylation Analysis of Urinary Peptidome Highlights IGF2 Glycopeptides in Association with CKD. Int J Mol Sci 2023; 24:ijms24065402. [PMID: 36982475 PMCID: PMC10048973 DOI: 10.3390/ijms24065402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/26/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Chronic kidney disease (CKD) is prevalent in 10% of world’s adult population. The role of protein glycosylation in causal mechanisms of CKD progression is largely unknown. The aim of this study was to identify urinary O-linked glycopeptides in association to CKD for better characterization of CKD molecular manifestations. Urine samples from eight CKD and two healthy subjects were analyzed by CE-MS/MS and glycopeptides were identified by a specific software followed by manual inspection of the spectra. Distribution of the identified glycopeptides and their correlation with Age, eGFR and Albuminuria were evaluated in 3810 existing datasets. In total, 17 O-linked glycopeptides from 7 different proteins were identified, derived primarily from Insulin-like growth factor-II (IGF2). Glycosylation occurred at the surface exposed IGF2 Threonine 96 position. Three glycopeptides (DVStPPTVLPDNFPRYPVGKF, DVStPPTVLPDNFPRYPVG and DVStPPTVLPDNFPRYP) exhibited positive correlation with Age. The IGF2 glycopeptide (tPPTVLPDNFPRYP) showed a strong negative association with eGFR. These results suggest that with aging and deteriorating kidney function, alterations in IGF2 proteoforms take place, which may reflect changes in mature IGF2 protein. Further experiments corroborated this hypothesis as IGF2 increased plasma levels were observed in CKD patients. Protease predictions, considering also available transcriptomics data, suggest activation of cathepsin S with CKD, meriting further investigation.
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Affiliation(s)
- Sonnal Lohia
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Institute for Molecular Cardiovascular Research, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | | | - Jerome Zoidakis
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Manousos Makridakis
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | | | - Griet Glorieux
- Department of Internal Medicine and Pediatrics, Nephrology Division, Ghent University Hospital, 9000 Gent, Belgium
| | - Antonia Vlahou
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Vera Jankowski
- Institute for Molecular Cardiovascular Research, RWTH Aachen University Hospital, 52074 Aachen, Germany
- Correspondence: ; Tel.: +49-(0241)-80-80580
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7
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Li S, Zhu J, Lubman DM, Zhou H, Tang H. GlycoSLASH: Concurrent Glycopeptide Identification from Multiple Related LC-MS/MS Data Sets by Using Spectral Clustering and Library Searching. J Proteome Res 2023; 22:1501-1509. [PMID: 36802412 PMCID: PMC10164058 DOI: 10.1021/acs.jproteome.3c00066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Liquid chromatography coupled with tandem mass spectrometry is commonly adopted in large-scale glycoproteomic studies involving hundreds of disease and control samples. The software for glycopeptide identification in such data (e.g., the commercial software Byonic) analyzes the individual data set and does not exploit the redundant spectra of glycopeptides presented in the related data sets. Herein, we present a novel concurrent approach for glycopeptide identification in multiple related glycoproteomic data sets by using spectral clustering and spectral library searching. The evaluation on two large-scale glycoproteomic data sets showed that the concurrent approach can identify 105%-224% more spectra as glycopeptides compared to the glycopeptide identification on individual data sets using Byonic alone. The improvement of glycopeptide identification also enabled the discovery of several potential biomarkers of protein glycosylations in hepatocellular carcinoma patients.
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Affiliation(s)
- Sujun Li
- Department of Blood Transfusion, The First Affiliated Hospital of Nanchang University, Nanchang 330000, China.,JiangXi Key Laboratory of Transfusion Medicine, Nanchang 330000, China.,Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
| | - Jianhui Zhu
- Department of Surgery, University of Michigan, Medical Center, Ann Arbor, Michigan 48109, United States
| | - David M Lubman
- Department of Surgery, University of Michigan, Medical Center, Ann Arbor, Michigan 48109, United States
| | - He Zhou
- Shenzhen Dengding Biopharma Co. Ltd., Shenzhen 518000, China
| | - Haixu Tang
- Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
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8
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Mackay S, Hitefield NL, Oduor IO, Roberts AB, Burch TC, Lance RS, Cunningham TD, Troyer DA, Semmes OJ, Nyalwidhe JO. Site-Specific Intact N-Linked Glycopeptide Characterization of Prostate-Specific Membrane Antigen from Metastatic Prostate Cancer Cells. ACS OMEGA 2022; 7:29714-29727. [PMID: 36061737 PMCID: PMC9435049 DOI: 10.1021/acsomega.2c02265] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
The composition of N-linked glycans that are conjugated to the prostate-specific membrane antigen (PSMA) and their functional significance in prostate cancer progression have not been fully characterized. PSMA was isolated from two metastatic prostate cancer cell lines, LNCaP and MDAPCa2b, which have different tissue tropism and localization. Isolated PSMA was trypsin-digested, and intact glycopeptides were subjected to LC-HCD-EThcD-MS/MS analysis on a Tribrid Orbitrap Fusion Lumos mass spectrometer. Differential qualitative and quantitative analysis of site-specific N-glycopeptides was performed using Byonic and Byologic software. Comparative quantitative analysis demonstrates that multiple glycopeptides at asparagine residues 51, 76, 121, 195, 336, 459, 476, and 638 were in significantly different abundance in the two cell lines (p < 0.05). Biochemical analysis using endoglycosidase treatment and lectin capture confirm the MS and site occupancy data. The data demonstrate the effectiveness of the strategy for comprehensive analysis of PSMA glycopeptides. This approach will form the basis of ongoing experiments to identify site-specific glycan changes in PSMA isolated from disease-stratified clinical samples to uncover targets that may be associated with disease progression and metastatic phenotypes.
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Affiliation(s)
- Stephen Mackay
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
- University
of North Carolina, Chapel Hill, North Carolina 27516, United States
| | - Naomi L. Hitefield
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
- University
of Georgia, Athens, Georgia 30602, United
States
| | - Ian O. Oduor
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
| | - Autumn B. Roberts
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
| | - Tanya C. Burch
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
| | - Raymond S. Lance
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Spokane
Urology, Spokane, Washington 99202, United States
| | - Tina D. Cunningham
- School of
Health Professions, Eastern Virginia Medical
School, Norfolk, Virginia 23507, United States
| | - Dean A. Troyer
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
| | - Oliver J. Semmes
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
| | - Julius O. Nyalwidhe
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
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9
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Liu S, Wang H, Jiang X, Ji Y, Wang Z, Zhang Y, Wang P, Xiao H. Integrated N-glycoproteomics Analysis of Human Saliva for Lung Cancer. J Proteome Res 2022; 21:1589-1602. [PMID: 35715216 DOI: 10.1021/acs.jproteome.1c00701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aberrant protein N-glycosylation is a cancer hallmark, which has great potential for cancer detection. However, large-scale and in-depth analysis of N-glycosylation remains challenging because of its high heterogeneity, complexity, and low abundance. Human saliva is an attractive diagnostic body fluid, while few efforts explored its N-glycoproteome for lung cancer. Here, we utilized a zwitterionic-hydrophilic interaction chromatography-based strategy to specifically enrich salivary glycopeptides. Through quantitative proteomics analysis, 1492 and 1234 intact N-glycopeptides were confidently identified from pooled saliva samples of 10 subjects in the nonsmall-cell lung cancer group and 10 subjects in the normal control group. Accordingly, 575 and 404 N-glycosites were revealed for the lung cancer group and normal control group. In particular, 154 N-glycosites and 259 site-specific glycoforms were significantly dysregulated in the lung cancer group. Several N-glycosites located at the same glycoprotein and glycans attached to the same N-glycosites were observed with differential expressions, including haptoglobin, Mucin-5B, lactotransferrin, and α-1-acid glycoprotein 1. These N-glycoproteins were mainly related to inflammatory responses, infectious diseases, and cancers. Our study achieved comprehensive characterization of salivary N-glycoproteome, and dysregulated site-specific glycoforms hold promise for noninvasive detection of lung cancer.
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Affiliation(s)
- Sha Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoteng Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yin Ji
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Pharmaceutical Co., Ltd., Nanjing 210042, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Peng Wang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Pharmaceutical Co., Ltd., Nanjing 210042, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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10
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Polasky DA, Geiszler DJ, Yu F, Nesvizhskii AI. Multi-attribute Glycan Identification and FDR Control for Glycoproteomics. Mol Cell Proteomics 2022; 21:100205. [PMID: 35091091 PMCID: PMC8933705 DOI: 10.1016/j.mcpro.2022.100205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/10/2022] [Accepted: 01/20/2022] [Indexed: 11/18/2022] Open
Abstract
Rapidly improving methods for glycoproteomics have enabled increasingly large-scale analyses of complex glycopeptide samples, but annotating the resulting mass spectrometry data with high confidence remains a major bottleneck. We recently introduced a fast and sensitive glycoproteomics search method in our MSFragger search engine, which reports glycopeptides as a combination of a peptide sequence and the mass of the attached glycan. In samples with complex glycosylation patterns, converting this mass to a specific glycan composition is not straightforward; however, as many glycans have similar or identical masses. Here, we have developed a new method for determining the glycan composition of N-linked glycopeptides fragmented by collisional or hybrid activation that uses multiple sources of information from the spectrum, including observed glycan B-type (oxonium) and Y-type ions and mass and precursor monoisotopic selection errors to discriminate between possible glycan candidates. Combined with false discovery rate estimation for the glycan assignment, we show that this method is capable of specifically and sensitively identifying glycans in complex glycopeptide analyses and effectively controls the rate of false glycan assignments. The new method has been incorporated into the PTM-Shepherd modification analysis tool to work directly with the MSFragger glyco search in the FragPipe graphical user interface, providing a complete computational pipeline for annotation of N-glycopeptide spectra with false discovery rate control of both peptide and glycan components that is both sensitive and robust against false identifications. Identifying the glycan on intact glycopeptides remains difficult in glycoproteomics. We developed a method to assign glycan compositions in N-glycoproteomics searches. We demonstrate well-controlled glycan FDR in multiple sample types. The method annotates more glycopeptide spectra than competing tools. The method is included PTM-Shepherd for a full glycoproteomics workflow in FragPipe.
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Affiliation(s)
- Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
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11
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Chen YJ, Yen TC, Lin YH, Chen YL, Khoo KH, Chen YJ. ZIC-cHILIC-Based StageTip for Simultaneous Glycopeptide Enrichment and Fractionation toward Large-Scale N-Sialoglycoproteomics. Anal Chem 2021; 93:15931-15940. [PMID: 34780171 DOI: 10.1021/acs.analchem.1c03224] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Alterations of protein glycosylation are closely related with pathophysiological regulation. Due to the structural macro- and microheterogeneity, low stoichiometry, and low ionization efficiency of glycopeptides, high-performance tools to enrich glycopeptides, especially the negatively charged and labile sialoglycopeptides, are essential to enhance the identification of the underexplored glycoproteome. Here, we present the first implementation of zwitterionic hydrophilic interaction chromatography with the exposed choline group (ZIC-cHILIC) in StageTip for simultaneous enrichment and fractionation of intact glycopeptides. In a model study using lung cancer cells, early elution by a high percentage of acetonitrile prominently prefilters nonglycopeptides, facilitating high enrichment specificity for glycopeptides (92-96%) and sialoglycopeptides (77-89%) in the subsequent hydrophilic fractions. The stepwise elution shows a high glycopeptide fractionation efficiency by a <10% overlap of glycopeptides between adjacent fractions. Most importantly, the ZIC-cHILIC stepwise strategy demonstrated good reproducibility (>80% in triplicate analysis) as well as superior coverage of 4.6- to 12.0-fold and 2.1- to 35.6-fold more glycopeptides and sialoglycopeptides compared to conventional TiO2 and ZIC-HILIC, respectively. To the best of our knowledge, the result with 2742 sialoglycopeptides among 7367 unique glycopeptides and 166 glycans from 2434 N-glycosites of 1118 glycoproteins (Byonic score > 100) provides one of the deepest glycoproteomic profiles in single-cell type. Without the immunoprecipitation step, the large-scale glycoproteomic atlas also reveals site-specific glycosylation of many druggable receptor proteins, such as EGFR, MET, ERBB2, ERBB3, AXL, and IGF1R. The demonstrated high enrichment specificity and identification depth show that stepwise ZIC-cHILIC is an efficient method to explore the under-represented sialoglycoproteome.
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Affiliation(s)
- Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ta-Chi Yen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Hsien Lin
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yan-Lin Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
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12
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Zeng X, Novotny MV, Clemmer DE, Trinidad JC. A graphical representation of glycan heterogeneity. Glycobiology 2021; 32:201-207. [PMID: 34939082 DOI: 10.1093/glycob/cwab116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 10/26/2021] [Accepted: 10/31/2021] [Indexed: 11/12/2022] Open
Abstract
A substantial shortcoming of large scale datasets is often the inability to easily represent and visualize key features. This problem becomes acute when considering the increasing technical ability to profile large numbers of glycopeptides and glycans in recent studies. Here, we describe a simple, concise graphical representation intended to capture the microheterogeneity associated with glycan modification at specific sites. We illustrate this method by showing visual representations of the glycans and glycopeptides from a variety of species. The graphical representation presented allows one to easily discern the compositions of all glycans, similarities and differences of modifications found in different samples, and, in the case of N-linked glycans, the initial steps in the biosynthetic pathway.
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Affiliation(s)
- Xuyao Zeng
- Department of Chemistry, Indiana University Bloomington, 800 Kirkwood Avenue, Bloomington, IN 47405
| | - Milos V Novotny
- Department of Chemistry, Indiana University Bloomington, 800 Kirkwood Avenue, Bloomington, IN 47405
| | - David E Clemmer
- Department of Chemistry, Indiana University Bloomington, 800 Kirkwood Avenue, Bloomington, IN 47405
| | - Jonathan C Trinidad
- Department of Chemistry, Indiana University Bloomington, 800 Kirkwood Avenue, Bloomington, IN 47405
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13
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Kawahara R, Chernykh A, Alagesan K, Bern M, Cao W, Chalkley RJ, Cheng K, Choo MS, Edwards N, Goldman R, Hoffmann M, Hu Y, Huang Y, Kim JY, Kletter D, Liquet B, Liu M, Mechref Y, Meng B, Neelamegham S, Nguyen-Khuong T, Nilsson J, Pap A, Park GW, Parker BL, Pegg CL, Penninger JM, Phung TK, Pioch M, Rapp E, Sakalli E, Sanda M, Schulz BL, Scott NE, Sofronov G, Stadlmann J, Vakhrushev SY, Woo CM, Wu HY, Yang P, Ying W, Zhang H, Zhang Y, Zhao J, Zaia J, Haslam SM, Palmisano G, Yoo JS, Larson G, Khoo KH, Medzihradszky KF, Kolarich D, Packer NH, Thaysen-Andersen M. Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nat Methods 2021; 18:1304-1316. [PMID: 34725484 DOI: 10.1101/2021.03.14.435332] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/22/2021] [Indexed: 05/18/2023]
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.
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Affiliation(s)
- Rebeca Kawahara
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Anastasia Chernykh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Kathirvel Alagesan
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia
| | | | - Weiqian Cao
- Institutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Robert J Chalkley
- UCSF, School of Pharmacy, Department of Pharmaceutical Chemistry, San Francisco, CA, USA
| | - Kai Cheng
- State University of New York, Buffalo, NY, USA
| | - Matthew S Choo
- Analytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Nathan Edwards
- Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Radoslav Goldman
- Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
- Department of Oncology, Georgetown University, Washington, DC, USA
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Yingwei Hu
- Department of Pathology, The Johns Hopkins University, Baltimore, MD, USA
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Jin Young Kim
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea
| | | | - Benoit Liquet
- Department of Mathematics and Statistics, Macquarie University, Sydney, NSW, Australia
- CNRS, Laboratoire de Mathématiques et de leurs Applications de PAU, E2S-UPPA, Pau, France
| | - Mingqi Liu
- Institutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Bo Meng
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China
| | | | - Terry Nguyen-Khuong
- Analytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jonas Nilsson
- Proteomics Core Facility, Sahlgrenska academy, University of Gothenburg, Gothenburg, Sweden
| | - Adam Pap
- BRC, Laboratory of Proteomics Research, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gun Wook Park
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Benjamin L Parker
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia
| | - Josef M Penninger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Toan K Phung
- School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia
| | - Markus Pioch
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
- glyXera GmbH, Magdeburg, Germany
| | - Enes Sakalli
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Miloslav Sanda
- Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA
- Department of Oncology, Georgetown University, Washington, DC, USA
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia
| | - Nichollas E Scott
- Deparment of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Georgy Sofronov
- Department of Mathematics and Statistics, Macquarie University, Sydney, NSW, Australia
| | - Johannes Stadlmann
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hung-Yi Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Pengyuan Yang
- Institutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China
| | - Hui Zhang
- Department of Pathology, The Johns Hopkins University, Baltimore, MD, USA
| | - Yong Zhang
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Joseph Zaia
- Department of Biochemistry, Boston University Medical Campus, Boston, MA, USA
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, UK
| | - Giuseppe Palmisano
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jong Shin Yoo
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| | - Göran Larson
- Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kai-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Katalin F Medzihradszky
- UCSF, School of Pharmacy, Department of Pharmaceutical Chemistry, San Francisco, CA, USA
- BRC, Laboratory of Proteomics Research, Szeged, Hungary
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia
| | - Nicolle H Packer
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia.
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14
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Yang Y, Yan G, Kong S, Wu M, Yang P, Cao W, Qiao L. GproDIA enables data-independent acquisition glycoproteomics with comprehensive statistical control. Nat Commun 2021; 12:6073. [PMID: 34663801 PMCID: PMC8523693 DOI: 10.1038/s41467-021-26246-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/23/2021] [Indexed: 12/26/2022] Open
Abstract
Large-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data independent acquisition (DIA) is an emerging technology with deep proteome coverage and accurate quantitative capability in proteomics studies, but is still in the early stage of development in the field of glycoproteomics. We propose GproDIA, a framework for the proteome-wide characterization of intact glycopeptides from DIA data with comprehensive statistical control by a 2-dimentional false discovery rate approach and a glycoform inference algorithm, enabling accurate identification of intact glycopeptides using wide isolation windows. We further utilize a semi-empirical spectrum prediction strategy to expand the coverage of spectral libraries of glycopeptides. We benchmark our method for N-glycopeptide profiling on DIA data of yeast and human serum samples, demonstrating that DIA with GproDIA outperforms the data-dependent acquisition-based methods for glycoproteomics in terms of capacity and data completeness of identification, as well as accuracy and precision of quantification. We expect that this work can provide a powerful tool for glycoproteomic studies.
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Affiliation(s)
- Yi Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
| | - Guoquan Yan
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
| | - Siyuan Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
| | - Mengxi Wu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
- The Shanghai Key Laboratory of Medical Epigenetics, Fudan University, Shanghai, 200000, China
- The International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, 200000, China
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200000, China
| | - Weiqian Cao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China.
- The Shanghai Key Laboratory of Medical Epigenetics, Fudan University, Shanghai, 200000, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, 200000, China.
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200000, China.
| | - Liang Qiao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China.
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15
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Hayes AJ, Lewis JM, Davies MR, Scott NE. Burkholderia PglL enzymes are Serine preferring oligosaccharyltransferases which target conserved proteins across the Burkholderia genus. Commun Biol 2021; 4:1045. [PMID: 34493791 PMCID: PMC8423747 DOI: 10.1038/s42003-021-02588-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
Glycosylation is increasingly recognised as a common protein modification within bacterial proteomes. While great strides have been made in identifying species that contain glycosylation systems, our understanding of the proteins and sites targeted by these systems is far more limited. Within this work we explore the conservation of glycoproteins and glycosylation sites across the pan-Burkholderia glycoproteome. Using a multi-protease glycoproteomic approach, we generate high-confidence glycoproteomes in two widely utilized B. cenocepacia strains, K56-2 and H111. This resource reveals glycosylation occurs exclusively at Serine residues and that glycoproteins/glycosylation sites are highly conserved across B. cenocepacia isolates. This preference for glycosylation at Serine residues is observed across at least 9 Burkholderia glycoproteomes, supporting that Serine is the dominant residue targeted by PglL-mediated glycosylation across the Burkholderia genus. Combined, this work demonstrates that PglL enzymes of the Burkholderia genus are Serine-preferring oligosaccharyltransferases that target conserved and shared protein substrates. Hayes et al provide a glycosylation site focused analysis of the glycoproteome of two widely utilized B. cenocepacia strains, K56-2 and H111. This team demonstrates that within these glycoproteomes Serine is the sole residue targeted for protein glycosylation and that glycoproteins/glycosylation sites are highly conserved across B. cenocepacia isolates.
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Affiliation(s)
- Andrew J Hayes
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jessica M Lewis
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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16
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Go EP, Zhang S, Ding H, Kappes JC, Sodroski J, Desaire H. The opportunity cost of automated glycopeptide analysis: case study profiling the SARS-CoV-2 S glycoprotein. Anal Bioanal Chem 2021; 413:7215-7227. [PMID: 34448030 PMCID: PMC8390178 DOI: 10.1007/s00216-021-03621-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/29/2021] [Accepted: 08/16/2021] [Indexed: 11/29/2022]
Abstract
Glycosylation analysis of viral glycoproteins contributes significantly to vaccine design and development. Among other benefits, glycosylation analysis allows vaccine developers to assess the impact of construct design or producer cell line choices for vaccine production, and it is a key measure by which glycoproteins that are produced for use in vaccination can be compared to their native viral forms. Because many viral glycoproteins are multiply glycosylated, glycopeptide analysis is a preferrable approach for mapping the glycans, yet the analysis of glycopeptide data can be cumbersome and requires the expertise of an experienced analyst. In recent years, a commercial software product, Byonic, has been implemented in several instances to facilitate glycopeptide analysis on viral glycoproteins and other glycoproteomics data sets, and the purpose of the study herein is to determine the strengths and limitations of using this software, particularly in cases relevant to vaccine development. The glycopeptides from a recombinantly expressed trimeric S glycoprotein of the SARS-CoV-2 virus were first analyzed using an expert-based analysis strategy; subsequently, analysis of the same data set was completed using Byonic. Careful assessment of instances where the two methods produced different results revealed that the glycopeptide assignments from Byonic contained more false positives than true positives, even when the data were assessed using a 1% false discovery rate. The work herein provides a roadmap for removing the spurious assignments that Byonic generates, and it provides an assessment of the opportunity cost for relying on automated assignments for glycopeptide data sets from viral glycoproteins.
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Affiliation(s)
- Eden P Go
- Department of Chemistry, University of Kansas, Lawrence, KS, 66049, USA
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, 02215, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - John C Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL, 35233, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, 02215, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS, 66049, USA.
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17
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Oliveira T, Thaysen-Andersen M, Packer NH, Kolarich D. The Hitchhiker's guide to glycoproteomics. Biochem Soc Trans 2021; 49:1643-1662. [PMID: 34282822 PMCID: PMC8421054 DOI: 10.1042/bst20200879] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/03/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023]
Abstract
Protein glycosylation is one of the most common post-translational modifications that are essential for cell function across all domains of life. Changes in glycosylation are considered a hallmark of many diseases, thus making glycoproteins important diagnostic and prognostic biomarker candidates and therapeutic targets. Glycoproteomics, the study of glycans and their carrier proteins in a system-wide context, is becoming a powerful tool in glycobiology that enables the functional analysis of protein glycosylation. This 'Hitchhiker's guide to glycoproteomics' is intended as a starting point for anyone who wants to explore the emerging world of glycoproteomics. The review moves from the techniques that have been developed for the characterisation of single glycoproteins to technologies that may be used for a successful complex glycoproteome characterisation. Examples of the variety of approaches, methodologies, and technologies currently used in the field are given. This review introduces the common strategies to capture glycoprotein-specific and system-wide glycoproteome data from tissues, body fluids, or cells, and a perspective on how integration into a multi-omics workflow enables a deep identification and characterisation of glycoproteins - a class of biomolecules essential in regulating cell function.
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Affiliation(s)
- Tiago Oliveira
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
| | | | - Nicolle H. Packer
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
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18
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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19
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Cui Y, Tabang DN, Zhang Z, Ma M, Alpert AJ, Li L. Counterion Optimization Dramatically Improves Selectivity for Phosphopeptides and Glycopeptides in Electrostatic Repulsion-Hydrophilic Interaction Chromatography. Anal Chem 2021; 93:7908-7916. [PMID: 34042420 DOI: 10.1021/acs.analchem.1c00615] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A well-hydrated counterion can selectively and dramatically increase retention of a charged analyte in hydrophilic interaction chromatography. The effect is enhanced if the column is charged, as in electrostatic repulsion-hydrophilic interaction chromatography (ERLIC). This combination was exploited in proteomics for the isolation of peptides with certain post-translational modifications (PTMs). The best salt additive examined was magnesium trifluoroacetate. The well-hydrated Mg+2 ion promoted retention of peptides with functional groups that retained negative charge at low pH, while the poorly hydrated trifluoroacetate counterion tuned down the retention due to the basic residues. The result was an enhancement in selectivity ranging from 6- to 66-fold. These conditions were applied to a tryptic digest of mouse cortex. Gradient elution produced fractions enriched in peptides with phosphate, mannose-6-phosphate, and N- and O-linked glycans. The numbers of such peptides identified either equaled or exceeded the numbers afforded by the best alternative methods. This method is a productive and convenient way to isolate peptides simultaneously that contain a number of different PTMs, facilitating study of proteins with "crosstalk" modifications. The fractions from the ERLIC column were desalted prior to C-18-reversed phase liquid chromatography-tandem mass spectrometry analysis. Between 47-100% of the peptides with more than one phosphate or sialyl residue or with a mannose-6 phosphate group were not retained by a C-18 cartridge but were retained by a cartridge of porous graphitic carbon. This finding implies that the abundance of such peptides may have been significantly underestimated in some past studies.
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Affiliation(s)
- Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Dylan Nicholas Tabang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Zishan Zhang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Min Ma
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave., Madison, Wisconsin 53705, United States
| | - Andrew J Alpert
- PolyLC Inc., 9151 Rumsey Road, ste. 180, Columbia, Maryland 21045, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave., Madison, Wisconsin 53705, United States
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20
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Tian Y, Tang R, Wang X, Zhou J, Li X, Ma S, Gong B, Ou J. Bioinspired dandelion-like silica nanoparticles modified with L-glutathione for highly efficient enrichment of N-glycopeptides in biological samples. Anal Chim Acta 2021; 1173:338694. [PMID: 34172155 DOI: 10.1016/j.aca.2021.338694] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/23/2021] [Indexed: 02/07/2023]
Abstract
The pretreatment of complicated biological samples to eliminate the interference of nonglycopeptides and improve the efficiency of glycopeptides detection is crucial in glycoproteomics research. Hydrophilic interaction chromatography (HILIC) has been adopted for enrichment of glycosylated peptides following identification with mass spectrometry, but it is still urgent to develop novel hydrophilic materials to save cost and improve enrichment efficiency. Scientists are pursuing to fabricate freestanding intelligent artificial materials. One promising approach is to use biomimic material. In our case, "one-pot" strategy was developed to prepare bioinspired nano-core-shell silica microspheres (CSSMs), employing tetrapropylorthosilicate as the silicon source and phenolic resin as the soft template. The pore structure of the obtained microspheres diverged from the center to the outside with diameter ranged from 150 to 340 nm, and shell layer ranged from 25 to 83 nm by adjusting the preparation parameters. Some of them showed dandelion-like morphology. After hydrophilic modification, these CSSMs exhibited great hydrophilicity and could be used as sorbents for enriching N-glycopeptides from complicated biological samples in HILIC. Up to 594 unique N-glycopeptides and 367 N-glycosylation sites from 182 N-glycoproteins were unambiguously identified from 2 μL of human serum, which was superior to the enrichment performance of many HILIC materials in reported papers, demonstrating great potential advantages in proteomic application.
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Affiliation(s)
- Yang Tian
- College of Chemistry and Chemical Engineering, North Minzu University, Yinchuan, 750021, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Ruizhi Tang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xia Wang
- College of Chemistry and Chemical Engineering, North Minzu University, Yinchuan, 750021, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiahua Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shujuan Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Bolin Gong
- College of Chemistry and Chemical Engineering, North Minzu University, Yinchuan, 750021, China.
| | - Junjie Ou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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21
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Oxonium Ion Guided Analysis of Quantitative Proteomics Data Reveals Site-Specific O-Glycosylation of Anterior Gradient Protein 2 (AGR2). Int J Mol Sci 2021; 22:ijms22105369. [PMID: 34065225 PMCID: PMC8160981 DOI: 10.3390/ijms22105369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/03/2021] [Accepted: 05/14/2021] [Indexed: 01/13/2023] Open
Abstract
Developments in mass spectrometry (MS)-based analyses of glycoproteins have been important to study changes in glycosylation related to disease. Recently, the characteristic pattern of oxonium ions in glycopeptide fragmentation spectra had been used to assign different sets of glycopeptides. In particular, this was helpful to discriminate between O-GalNAc and O-GlcNAc. Here, we thought to investigate how such information can be used to examine quantitative proteomics data. For this purpose, we used tandem mass tag (TMT)-labeled samples from total cell lysates and secreted proteins from three different colorectal cancer cell lines. Following automated glycopeptide assignment (Byonic) and evaluation of the presence and relative intensity of oxonium ions, we observed that, in particular, the ratio of the ions at m/z 144.066 and 138.055, respectively, could be used to discriminate between O-GlcNAcylated and O-GalNAcylated peptides, with concomitant relative quantification between the different cell lines. Among the O-GalNAcylated proteins, we also observed anterior gradient protein 2 (AGR2), a protein which glycosylation site and status was hitherto not well documented. Using a combination of multiple fragmentation methods, we then not only assigned the site of modification, but also showed different glycosylation between intracellular (ER-resident) and secreted AGR2. Overall, our study shows the potential of broad application of the use of the relative intensities of oxonium ions for the confident assignment of glycopeptides, even in complex proteomics datasets.
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22
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Zhang R, Zhu J, Lubman DM, Mechref Y, Tang H. GlycoHybridSeq: Automated Identification of N-Linked Glycopeptides Using Electron Transfer/High-Energy Collision Dissociation (EThcD). J Proteome Res 2021; 20:3345-3352. [PMID: 34010560 PMCID: PMC8185882 DOI: 10.1021/acs.jproteome.1c00245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Glycosylation is
one of the most common post-translational modifications
(PTM) occurring in a large variety of proteins with important biological
functions in human and other higher organisms. Liquid chromatography
tandem mass spectrometry (LC-MS/MS) has been routinely used to characterize
site-specific protein glycosylation at high throughput in complex
glycoproteomic samples. Recently, electron transfer/high-energy collision
dissociation (EThcD) was introduced for glycopeptide identification,
which offers rich structural information on glycopepides with the
fragment ions from the cleavages of both the glycan and the peptide
backbone. Herein, we present the software GlycoHybridSeq for automated
interpretation of EThcD-MS/MS spectra from glycoproteomic data using
a customized scoring function, which enables the functionalities of
identifying glycopeptides, characterizing glycosylation sites, and
distinguishing some isomeric glycans. We evaluate GlycoHybridSeq on
glycoproteomic data collected for cancer biomarker discovery. The
results showed that it achieved comparable or better performance than
that of Byonic and MSFragger. GlycoHybridSeq is released as an open
source software and is ready to be used in large-scale glycoproteomic
data analyses.
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Affiliation(s)
- Rui Zhang
- Department of Computer Science, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana 47405, United States
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Haixu Tang
- Department of Computer Science, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana 47405, United States
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23
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Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells. Cell Rep 2021; 35:109179. [PMID: 34004174 PMCID: PMC8116342 DOI: 10.1016/j.celrep.2021.109179] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 02/16/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
Understanding and eliciting protective immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an urgent priority. To facilitate these objectives, we profile the repertoire of human leukocyte antigen class II (HLA-II)-bound peptides presented by HLA-DR diverse monocyte-derived dendritic cells pulsed with SARS-CoV-2 spike (S) protein. We identify 209 unique HLA-II-bound peptide sequences, many forming nested sets, which map to sites throughout S including glycosylated regions. Comparison of the glycosylation profile of the S protein to that of the HLA-II-bound S peptides reveals substantial trimming of glycan residues on the latter, likely induced during antigen processing. Our data also highlight the receptor-binding motif in S1 as a HLA-DR-binding peptide-rich region and identify S2-derived peptides with potential for targeting by cross-protective vaccine-elicited responses. Results from this study will aid analysis of CD4+ T cell responses in infected individuals and vaccine recipients and have application in next-generation vaccine design.
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24
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Chen Z, Yu Q, Yu Q, Johnson J, Shipman R, Zhong X, Huang J, Asthana S, Carlsson C, Okonkwo O, Li L. In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease. Mol Cell Proteomics 2021; 20:100081. [PMID: 33862227 PMCID: PMC8724636 DOI: 10.1016/j.mcpro.2021.100081] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 01/22/2023] Open
Abstract
As the body fluid that directly interchanges with the extracellular fluid of the central nervous system (CNS), cerebrospinal fluid (CSF) serves as a rich source for CNS-related disease biomarker discovery. Extensive proteome profiling has been conducted for CSF, but studies aimed at unraveling site-specific CSF N-glycoproteome are lacking. Initial efforts into site-specific N-glycoproteomics study in CSF yield limited coverage, hindering further experimental design of glycosylation-based disease biomarker discovery in CSF. In the present study, we have developed an N-glycoproteomic approach that combines enhanced N-glycopeptide sequential enrichment by hydrophilic interaction chromatography (HILIC) and boronic acid enrichment with electron transfer and higher-energy collision dissociation (EThcD) for large-scale intact N-glycopeptide analysis. The application of the developed approach to the analyses of human CSF samples enabled identifications of a total of 2893 intact N-glycopeptides from 511 N-glycosites and 285 N-glycoproteins. To our knowledge, this is the largest site-specific N-glycoproteome dataset reported for CSF to date. Such dataset provides molecular basis for a better understanding of the structure-function relationships of glycoproteins and their roles in CNS-related physiological and pathological processes. As accumulating evidence suggests that defects in glycosylation are involved in Alzheimer's disease (AD) pathogenesis, in the present study, a comparative in-depth N-glycoproteomic analysis was conducted for CSF samples from healthy control and AD patients, which yielded a comparable N-glycoproteome coverage but a distinct expression pattern for different categories of glycoforms, such as decreased fucosylation in AD CSF samples. Altered glycosylation patterns were detected for a number of N-glycoproteins including alpha-1-antichymotrypsin, ephrin-A3 and carnosinase CN1 etc., which serve as potentially interesting targets for further glycosylation-based AD study and may eventually lead to molecular elucidation of the role of glycosylation in AD progression.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Jillian Johnson
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Richard Shipman
- Department of Applied Science, University of Wisconsin-Stout, Menomonie, Wisconsin, USA
| | - Xiaofang Zhong
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Sanjay Asthana
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Cynthia Carlsson
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Ozioma Okonkwo
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA; School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA.
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25
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Kearney CJ, Vervoort SJ, Ramsbottom KM, Todorovski I, Lelliott EJ, Zethoven M, Pijpers L, Martin BP, Semple T, Martelotto L, Trapani JA, Parish IA, Scott NE, Oliaro J, Johnstone RW. SUGAR-seq enables simultaneous detection of glycans, epitopes, and the transcriptome in single cells. SCIENCE ADVANCES 2021; 7:7/8/eabe3610. [PMID: 33608275 PMCID: PMC7895430 DOI: 10.1126/sciadv.abe3610] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/05/2021] [Indexed: 05/08/2023]
Abstract
Multimodal single-cell RNA sequencing enables the precise mapping of transcriptional and phenotypic features of cellular differentiation states but does not allow for simultaneous integration of critical posttranslational modification data. Here, we describe SUrface-protein Glycan And RNA-seq (SUGAR-seq), a method that enables detection and analysis of N-linked glycosylation, extracellular epitopes, and the transcriptome at the single-cell level. Integrated SUGAR-seq and glycoproteome analysis identified tumor-infiltrating T cells with unique surface glycan properties that report their epigenetic and functional state.
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Affiliation(s)
- Conor J Kearney
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
| | - Stephin J Vervoort
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
| | - Kelly M Ramsbottom
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Izabela Todorovski
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Emily J Lelliott
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Magnus Zethoven
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Lizzy Pijpers
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Ben P Martin
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Timothy Semple
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Luciano Martelotto
- Centre for Cancer Research, University of Melbourne, Melbourne 3000, VIC, Australia
| | - Joseph A Trapani
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Ian A Parish
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Jane Oliaro
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia.
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Ricky W Johnstone
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
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26
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Ferreira JA, Relvas-Santos M, Peixoto A, M N Silva A, Lara Santos L. Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:25-43. [PMID: 34118464 PMCID: PMC8498922 DOI: 10.1016/j.gpb.2021.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/25/2021] [Accepted: 03/01/2021] [Indexed: 12/24/2022]
Abstract
Molecular-assisted precision oncology gained tremendous ground with high-throughput next-generation sequencing (NGS), supported by robust bioinformatics. The quest for genomics-based cancer medicine set the foundations for improved patient stratification, while unveiling a wide array of neoantigens for immunotherapy. Upfront pre-clinical and clinical studies have successfully used tumor-specific peptides in vaccines with minimal off-target effects. However, the low mutational burden presented by many lesions challenges the generalization of these solutions, requiring the diversification of neoantigen sources. Oncoproteogenomics utilizing customized databases for protein annotation by mass spectrometry (MS) is a powerful tool toward this end. Expanding the concept toward exploring proteoforms originated from post-translational modifications (PTMs) will be decisive to improve molecular subtyping and provide potentially targetable functional nodes with increased cancer specificity. Walking through the path of systems biology, we highlight that alterations in protein glycosylation at the cell surface not only have functional impact on cancer progression and dissemination but also originate unique molecular fingerprints for targeted therapeutics. Moreover, we discuss the outstanding challenges required to accommodate glycoproteomics in oncoproteogenomics platforms. We envisage that such rationale may flag a rather neglected research field, generating novel paradigms for precision oncology and immunotherapy.
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Affiliation(s)
- José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal.
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal
| | - André M N Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal
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27
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Towards structure-focused glycoproteomics. Biochem Soc Trans 2021; 49:161-186. [PMID: 33439247 PMCID: PMC7925015 DOI: 10.1042/bst20200222] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023]
Abstract
Facilitated by advances in the separation sciences, mass spectrometry and informatics, glycoproteomics, the analysis of intact glycopeptides at scale, has recently matured enabling new insights into the complex glycoproteome. While diverse quantitative glycoproteomics strategies capable of mapping monosaccharide compositions of N- and O-linked glycans to discrete sites of proteins within complex biological mixtures with considerable sensitivity, quantitative accuracy and coverage have become available, developments supporting the advancement of structure-focused glycoproteomics, a recognised frontier in the field, have emerged. Technologies capable of providing site-specific information of the glycan fine structures in a glycoproteome-wide context are indeed necessary to address many pending questions in glycobiology. In this review, we firstly survey the latest glycoproteomics studies published in 2018–2020, their approaches and their findings, and then summarise important technological innovations in structure-focused glycoproteomics. Our review illustrates that while the O-glycoproteome remains comparably under-explored despite the emergence of new O-glycan-selective mucinases and other innovative tools aiding O-glycoproteome profiling, quantitative glycoproteomics is increasingly used to profile the N-glycoproteome to tackle diverse biological questions. Excitingly, new strategies compatible with structure-focused glycoproteomics including novel chemoenzymatic labelling, enrichment, separation, and mass spectrometry-based detection methods are rapidly emerging revealing glycan fine structural details including bisecting GlcNAcylation, core and antenna fucosylation, and sialyl-linkage information with protein site resolution. Glycoproteomics has clearly become a mainstay within the glycosciences that continues to reach a broader community. It transpires that structure-focused glycoproteomics holds a considerable potential to aid our understanding of systems glycobiology and unlock secrets of the glycoproteome in the immediate future.
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28
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Ye Z, Vakhrushev SY. The Role of Data-Independent Acquisition for Glycoproteomics. Mol Cell Proteomics 2021; 20:100042. [PMID: 33372048 PMCID: PMC8724878 DOI: 10.1074/mcp.r120.002204] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/26/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Data-independent acquisition (DIA) is now an emerging method in bottom–up proteomics and capable of achieving deep proteome coverage and accurate label-free quantification. However, for post-translational modifications, such as glycosylation, DIA methodology is still in the early stage of development. The full characterization of glycoproteins requires site-specific glycan identification as well as subsequent quantification of glycan structures at each site. The tremendous complexity of glycosylation represents a significant analytical challenge in glycoproteomics. This review focuses on the development and perspectives of DIA methodology for N- and O-linked glycoproteomics and posits that DIA-based glycoproteomics could be a method of choice to address some of the challenging aspects of glycoproteomics. First, the current challenges in glycoproteomics and the basic principles of DIA are briefly introduced. DIA-based glycoproteomics is then summarized and described into four aspects based on the actual samples. Finally, we discussed the important challenges and future perspectives in the field. We believe that DIA can significantly facilitate glycoproteomic studies and contribute to the development of future advanced tools and approaches in the field of glycoproteomics. Protein glycosylation and challenges in glycoproteomics. Data-independent acquisition for deglycosylated and intact N-linked glycopeptides. Unbiased screening of oxonium ions from all glycopeptide precursors. Glyco–data-independent acquisition on mucin-type O-glycopeptides.
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Affiliation(s)
- Zilu Ye
- Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen N, Denmark.
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29
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Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nat Methods 2021; 18:1304-1316. [PMID: 34725484 PMCID: PMC8566223 DOI: 10.1038/s41592-021-01309-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022]
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.
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30
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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31
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Blazev R, Ashwood C, Abrahams JL, Chung LH, Francis D, Yang P, Watt KI, Qian H, Quaife-Ryan GA, Hudson JE, Gregorevic P, Thaysen-Andersen M, Parker BL. Integrated Glycoproteomics Identifies a Role of N-Glycosylation and Galectin-1 on Myogenesis and Muscle Development. Mol Cell Proteomics 2020; 20:100030. [PMID: 33583770 PMCID: PMC8724610 DOI: 10.1074/mcp.ra120.002166] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/20/2020] [Accepted: 09/16/2020] [Indexed: 12/23/2022] Open
Abstract
Many cell surface and secreted proteins are modified by the covalent addition of glycans that play an important role in the development of multicellular organisms. These glycan modifications enable communication between cells and the extracellular matrix via interactions with specific glycan-binding lectins and the regulation of receptor-mediated signaling. Aberrant protein glycosylation has been associated with the development of several muscular diseases, suggesting essential glycan- and lectin-mediated functions in myogenesis and muscle development, but our molecular understanding of the precise glycans, catalytic enzymes, and lectins involved remains only partially understood. Here, we quantified dynamic remodeling of the membrane-associated proteome during a time-course of myogenesis in cell culture. We observed wide-spread changes in the abundance of several important lectins and enzymes facilitating glycan biosynthesis. Glycomics-based quantification of released N-linked glycans confirmed remodeling of the glycome consistent with the regulation of glycosyltransferases and glycosidases responsible for their formation including a previously unknown digalactose-to-sialic acid switch supporting a functional role of these glycoepitopes in myogenesis. Furthermore, dynamic quantitative glycoproteomic analysis with multiplexed stable isotope labeling and analysis of enriched glycopeptides with multiple fragmentation approaches identified glycoproteins modified by these regulated glycans including several integrins and growth factor receptors. Myogenesis was also associated with the regulation of several lectins, most notably the upregulation of galectin-1 (LGALS1). CRISPR/Cas9-mediated deletion of Lgals1 inhibited differentiation and myotube formation, suggesting an early functional role of galectin-1 in the myogenic program. Importantly, similar changes in N-glycosylation and the upregulation of galectin-1 during postnatal skeletal muscle development were observed in mice. Treatment of new-born mice with recombinant adeno-associated viruses to overexpress galectin-1 in the musculature resulted in enhanced muscle mass. Our data form a valuable resource to further understand the glycobiology of myogenesis and will aid the development of intervention strategies to promote healthy muscle development or regeneration.
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Affiliation(s)
- Ronnie Blazev
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher Ashwood
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia; CardiOmics Program, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Jodie L Abrahams
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Long H Chung
- School of Life and Environmental Science, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Deanne Francis
- School of Life and Environmental Science, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Pengyi Yang
- School of Mathematics and Statistics, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia; Computational Systems Biology Group, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Kevin I Watt
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia; Department of Diabetes, Monash University, Melbourne, Victoria, Australia
| | - Hongwei Qian
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Gregory A Quaife-Ryan
- Cardiac Bioengineering Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - James E Hudson
- Cardiac Bioengineering Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Paul Gregorevic
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia; Department of Neurology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Benjamin L Parker
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia; School of Life and Environmental Science, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.
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Lippold S, de Ru AH, Nouta J, van Veelen PA, Palmblad M, Wuhrer M, de Haan N. Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification. Beilstein J Org Chem 2020; 16:3038-3051. [PMID: 33363672 PMCID: PMC7736696 DOI: 10.3762/bjoc.16.253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
Glycoproteomic data are often very complex, reflecting the high structural diversity of peptide and glycan portions. The use of glycopeptide-centered glycoproteomics by mass spectrometry is rapidly evolving in many research areas, leading to a demand in reliable data analysis tools. In recent years, several bioinformatic tools were developed to facilitate and improve both the identification and quantification of glycopeptides. Here, a selection of these tools was combined and evaluated with the aim of establishing a robust glycopeptide detection and quantification workflow targeting enriched glycoproteins. For this purpose, a tryptic digest from affinity-purified immunoglobulins G and A was analyzed on a nano-reversed-phase liquid chromatography-tandem mass spectrometry platform with a high-resolution mass analyzer and higher-energy collisional dissociation fragmentation. Initial glycopeptide identification based on MS/MS data was aided by the Byonic software. Additional MS1-based glycopeptide identification relying on accurate mass and retention time differences using GlycopeptideGraphMS considerably expanded the set of confidently annotated glycopeptides. For glycopeptide quantification, the performance of LaCyTools was compared to Skyline, and GlycopeptideGraphMS. All quantification packages resulted in comparable glycosylation profiles but featured differences in terms of robustness and data quality control. Partial cysteine oxidation was identified as an unexpectedly abundant peptide modification and impaired the automated processing of several IgA glycopeptides. Finally, this study presents a semiautomated workflow for reliable glycoproteomic data analysis by the combination of software packages for MS/MS- and MS1-based glycopeptide identification as well as the integration of analyte quality control and quantification.
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Affiliation(s)
- Steffen Lippold
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Jan Nouta
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
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33
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Čaval T, Heck AJR, Reiding KR. Meta-heterogeneity: Evaluating and Describing the Diversity in Glycosylation Between Sites on the Same Glycoprotein. Mol Cell Proteomics 2020; 20:100010. [PMID: 33561609 PMCID: PMC8724623 DOI: 10.1074/mcp.r120.002093] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/14/2020] [Accepted: 07/31/2020] [Indexed: 12/26/2022] Open
Abstract
Mass spectrometry-based glycoproteomics has gone through some incredible developments over the last few years. Technological advances in glycopeptide enrichment, fragmentation methods, and data analysis workflows have enabled the transition of glycoproteomics from a niche application, mainly focused on the characterization of isolated glycoproteins, to a mature technology capable of profiling thousands of intact glycopeptides at once. In addition to numerous biological discoveries catalyzed by the technology, we are also observing an increase in studies focusing on global protein glycosylation and the relationship between multiple glycosylation sites on the same protein. It has become apparent that just describing protein glycosylation in terms of micro- and macro-heterogeneity, respectively, the variation and occupancy of glycans at a given site, is not sufficient to describe the observed interactions between sites. In this perspective we propose a new term, meta-heterogeneity, to describe a higher level of glycan regulation: the variation in glycosylation across multiple sites of a given protein. We provide literature examples of extensive meta-heterogeneity on relevant proteins such as antibodies, erythropoietin, myeloperoxidase, and a number of serum and plasma proteins. Furthermore, we postulate on the possible biological reasons and causes behind the intriguing meta-heterogeneity observed in glycoproteins.
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Affiliation(s)
- Tomislav Čaval
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands.
| | - Karli R Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands.
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Lu L, Riley NM, Shortreed MR, Bertozzi CR, Smith LM. O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nat Methods 2020. [PMID: 33106676 DOI: 10.1101/2020.05.18.102327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
We report O-Pair Search, an approach to identify O-glycopeptides and localize O-glycosites. Using paired collision- and electron-based dissociation spectra, O-Pair Search identifies O-glycopeptides via an ion-indexed open modification search and localizes O-glycosites using graph theory and probability-based localization. O-Pair Search reduces search times more than 2,000-fold compared to current O-glycopeptide processing software, while defining O-glycosite localization confidence levels and generating more O-glycopeptide identifications. Beyond the mucin-type O-glycopeptides discussed here, O-Pair Search also accepts user-defined glycan databases, making it compatible with many types of O-glycosylation. O-Pair Search is freely available within the open-source MetaMorpheus platform at https://github.com/smith-chem-wisc/MetaMorpheus .
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Affiliation(s)
- Lei Lu
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Nicholas M Riley
- Department of Chemistry, University of Stanford, Stanford, CA, USA
| | | | - Carolyn R Bertozzi
- Department of Chemistry, University of Stanford, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI, USA.
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Cui X, Mi W, Hu Z, Li X, Meng B, Zhao X, Qian X, Zhu T, Ying W. Global characterization of modifications to the charge isomers of IgG antibody. J Pharm Anal 2020; 12:156-163. [PMID: 35573890 PMCID: PMC9073142 DOI: 10.1016/j.jpha.2020.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 11/08/2020] [Accepted: 11/17/2020] [Indexed: 11/02/2022] Open
Abstract
Posttranslational modifications of antibody products affect their stability, charge distribution, and drug activity and are thus a critical quality attribute. The comprehensive mapping of antibody modifications and different charge isomers (CIs) is of utmost importance, but is challenging. We intended to quantitatively characterize the posttranslational modification status of CIs of antibody drugs and explore the impact of posttranslational modifications on charge heterogeneity. The CIs of antibodies were fractionated by strong cation exchange chromatography and verified by capillary isoelectric focusing-whole column imaging detection, followed by stepwise structural characterization at three levels. First, the differences between CIs were explored at the intact protein level using a top-down mass spectrometry approach; this showed differences in glycoforms and deamidation status. Second, at the peptide level, common modifications of oxidation, deamidation, and glycosylation were identified. Peptide mapping showed nonuniform deamidation and glycoform distribution among CIs. In total, 10 N-glycoforms were detected by peptide mapping. Finally, an in-depth analysis of glycan variants of CIs was performed through the detection of enriched glycopeptides. Qualitative and quantitative analyses demonstrated the dynamics of 24 N-glycoforms. The results revealed that sialic acid modification is a critical factor accounting for charge heterogeneity, which is otherwise missed in peptide mapping and intact molecular weight analyses. This study demonstrated the importance of the comprehensive analyses of antibody CIs and provides a reference method for the quality control of biopharmaceutical analysis. A stepwise investigation on the diversity and dynamics of modifications of antibody charge isomers (CIs) was performed. The results from SCX-HPLC and cIEF-WCID supported each other. In-depth analysis on glycan variants of CIs was achieved by analyzing the enriched glycopeptides. Sialic acid and deamidation modifications were critical factors for the charge heterogeneity.
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36
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Ahmad Izaham AR, Ang CS, Nie S, Bird LE, Williamson NA, Scott NE. What Are We Missing by Using Hydrophilic Enrichment? Improving Bacterial Glycoproteome Coverage Using Total Proteome and FAIMS Analyses. J Proteome Res 2020; 20:599-612. [PMID: 33125241 DOI: 10.1021/acs.jproteome.0c00565] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hydrophilic interaction liquid chromatography (HILIC) glycopeptide enrichment is an indispensable tool for the high-throughput characterization of glycoproteomes. Despite its utility, HILIC enrichment is associated with a number of shortcomings, including requiring large amounts of starting materials, potentially introducing chemical artifacts such as formylation when high concentrations of formic acid are used, and biasing/undersampling specific classes of glycopeptides. Here, we investigate HILIC enrichment-independent approaches for the study of bacterial glycoproteomes. Using three Burkholderia species (Burkholderia cenocepacia, Burkholderia Dolosa, and Burkholderia ubonensis), we demonstrate that short aliphatic O-linked glycopeptides are typically absent from HILIC enrichments, yet are readily identified in whole proteome samples. Using high-field asymmetric waveform ion mobility spectrometry (FAIMS) fractionation, we show that at high compensation voltages (CVs), short aliphatic glycopeptides can be enriched from complex samples, providing an alternative means to identify glycopeptide recalcitrant to hydrophilic-based enrichment. Combining whole proteome and FAIMS analyses, we show that the observable glycoproteome of these Burkholderia species is at least 25% larger than what was initially thought. Excitingly, the ability to enrich glycopeptides using FAIMS appears generally applicable, with the N-linked glycopeptides of Campylobacter fetus subsp. fetus also being enrichable at high FAIMS CVs. Taken together, these results demonstrate that FAIMS provides an alternative means to access glycopeptides and is a valuable tool for glycoproteomic analysis.
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Affiliation(s)
- Ameera Raudah Ahmad Izaham
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Ching-Seng Ang
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lauren E Bird
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Nicholas A Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
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37
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Lu L, Riley NM, Shortreed MR, Bertozzi CR, Smith LM. O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nat Methods 2020; 17:1133-1138. [PMID: 33106676 PMCID: PMC7606753 DOI: 10.1038/s41592-020-00985-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/21/2020] [Indexed: 11/23/2022]
Abstract
We report O-Pair Search, a new approach to identify O-glycopeptides and localize O-glycosites. Using paired collision- and electron-based dissociation spectra, O-Pair Search identifies O-glycopeptides using an ion-indexed open modification search and localizes O-glycosites using graph theory and probability-based localization. O-Pair Search reduces search times more than 2,000-fold compared to current O-glycopeptide processing software, while defining O-glycosite localization confidence levels and generating more O-glycopeptide identifications. Beyond the mucin-type O-glycopeptides discussed here, O-Pair Search also accepts user-defined glycan databases, making it compatible with many types of O-glycosylation. O-Pair Search is freely available within the open-source MetaMorpheus platform at https://github.com/smith-chem-wisc/MetaMorpheus.
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Affiliation(s)
- Lei Lu
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Nicholas M Riley
- Department of Chemistry, University of Stanford, Stanford, CA, USA
| | | | - Carolyn R Bertozzi
- Department of Chemistry, University of Stanford, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford, CA, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI, USA.
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38
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Yang S, Wang Y, Mann M, Wang Q, Tian E, Zhang L, Cipollo JF, Ten Hagen KG, Tabak LA. Improved online LC-MS/MS identification of O-glycosites by EThcD fragmentation, chemoenzymatic reaction, and SPE enrichment. Glycoconj J 2020; 38:145-156. [PMID: 33068214 DOI: 10.1007/s10719-020-09952-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/16/2020] [Accepted: 10/05/2020] [Indexed: 12/01/2022]
Abstract
O-glycosylation is a highly diverse and complex form of protein post-translational modification. Mucin-type O-glycosylation is initiated by the transfer of N-acetyl-galactosamine (GalNAc) to the hydroxyl group of serine, threonine and tyrosine residues through catalysis by a family of glycosyltransferases, the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (E.C. 2.4.1.41) that are conserved across metazoans. In the last decade, structural characterization of glycosylation has substantially advanced due to the development of analytical methods and advances in mass spectrometry. However, O-glycosite mapping remains challenging since mucin-type O-glycans are densely packed, often protecting proteins from cleavage by proteases. Adding to the complexity is the fact that a given glycosite can be modified by different glycans, resulting in an array of glycoforms rising from one glycosite. In this study, we investigated conditions of solid phase extraction (SPE) enrichment, protease digestion, and Electron-transfer/Higher Energy Collision Dissociation (EThcD) fragmentation to optimize identification of O-glycosites in densely glycosylated proteins. Our results revealed that anion-exchange stationary phase is sufficient for glycopeptide enrichment; however, the use of a hydrophobic-containing sorbent was detrimental to the binding of polar-hydrophilic glycopeptides. Different proteases can be employed for enhancing coverage of O-glycosites, while derivatization of negatively charged amino acids or sialic acids would enhance the identification of a short O-glycopeptides. Using a longer than normal electron transfer dissociation (ETD) reaction time, we obtained enhanced coverage of peptide bonds that facilitated the localization of O-glycosites. O-glycosite mapping strategy via proteases, cut-off filtration and solid-phase chemoenzymatic processing. Glycopeptides are enriched by SPE column, followed by release of N-glycans, collection of higher MW O-glycopeptides via MW cut-off filter, O-glycopeptide release via O-protease, and finally detected by LC-MS/MS using EThcD.
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Affiliation(s)
- Shuang Yang
- Biological Chemistry Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yan Wang
- Mass Spectrometry Facility, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Matthew Mann
- Biological Chemistry Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Qiong Wang
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - E Tian
- Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Liping Zhang
- Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - John F Cipollo
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Kelly G Ten Hagen
- Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lawrence A Tabak
- Biological Chemistry Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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Boll I, Jensen P, Schwämmle V, Larsen MR. Depolarization-dependent Induction of Site-specific Changes in Sialylation on N-linked Glycoproteins in Rat Nerve Terminals. Mol Cell Proteomics 2020; 19:1418-1435. [PMID: 32518069 PMCID: PMC8143646 DOI: 10.1074/mcp.ra119.001896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/08/2020] [Indexed: 12/11/2022] Open
Abstract
Synaptic transmission leading to release of neurotransmitters in the nervous system is a fast and highly dynamic process. Previously, protein interaction and phosphorylation have been thought to be the main regulators of synaptic transmission. Here we show that sialylation of N-linked glycosylation is a novel potential modulator of neurotransmitter release mechanisms by investigating depolarization-dependent changes of formerly sialylated N-linked glycopeptides. We suggest that negatively charged sialic acids can be modulated, similarly to phosphorylation, by the action of sialyltransferases and sialidases thereby changing local structure and function of membrane glycoproteins. We characterized site-specific alteration in sialylation on N-linked glycoproteins in isolated rat nerve terminals after brief depolarization using quantitative sialiomics. We identified 1965 formerly sialylated N-linked glycosites in synaptic proteins and found that the abundances of 430 glycosites changed after 5 s depolarization. We observed changes on essential synaptic proteins such as synaptic vesicle proteins, ion channels and transporters, neurotransmitter receptors and cell adhesion molecules. This study is to our knowledge the first to describe ultra-fast site-specific modulation of the sialiome after brief stimulation of a biological system.
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Affiliation(s)
- Inga Boll
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Pia Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
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40
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Ahmad Izaham AR, Scott NE. Open Database Searching Enables the Identification and Comparison of Bacterial Glycoproteomes without Defining Glycan Compositions Prior to Searching. Mol Cell Proteomics 2020. [PMID: 32576591 DOI: 10.1101/2020.04.21.052845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
Mass spectrometry has become an indispensable tool for the characterization of glycosylation across biological systems. Our ability to generate rich fragmentation of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag behind. Although glycoproteomic informatics approaches using glycan databases have attracted considerable attention, database independent approaches have not. This has significantly limited high throughput studies of unusual or atypical glycosylation events such as those observed in bacteria. As such, computational approaches to examine bacterial glycosylation and identify chemically diverse glycans are desperately needed. Here we describe the use of wide-tolerance (up to 2000 Da) open searching as a means to rapidly examine bacterial glycoproteomes. We benchmarked this approach using N-linked glycopeptides of Campylobacter fetus subsp. fetus as well as O-linked glycopeptides of Acinetobacter baumannii and Burkholderia cenocepacia revealing glycopeptides modified with a range of glycans can be readily identified without defining the glycan masses before database searching. Using this approach, we demonstrate how wide tolerance searching can be used to compare glycan use across bacterial species by examining the glycoproteomes of eight Burkholderia species (B. pseudomallei; B. multivorans; B. dolosa; B. humptydooensis; B. ubonensis, B. anthina; B. diffusa; B. pseudomultivorans). Finally, we demonstrate how open searching enables the identification of low frequency glycoforms based on shared modified peptides sequences. Combined, these results show that open searching is a robust computational approach for the determination of glycan diversity within bacterial proteomes.
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Affiliation(s)
- Ameera Raudah Ahmad Izaham
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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41
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Ahmad Izaham AR, Scott NE. Open Database Searching Enables the Identification and Comparison of Bacterial Glycoproteomes without Defining Glycan Compositions Prior to Searching. Mol Cell Proteomics 2020; 19:1561-1574. [PMID: 32576591 PMCID: PMC8143609 DOI: 10.1074/mcp.tir120.002100] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/27/2020] [Indexed: 12/23/2022] Open
Abstract
Mass spectrometry has become an indispensable tool for the characterization of glycosylation across biological systems. Our ability to generate rich fragmentation of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag behind. Although glycoproteomic informatics approaches using glycan databases have attracted considerable attention, database independent approaches have not. This has significantly limited high throughput studies of unusual or atypical glycosylation events such as those observed in bacteria. As such, computational approaches to examine bacterial glycosylation and identify chemically diverse glycans are desperately needed. Here we describe the use of wide-tolerance (up to 2000 Da) open searching as a means to rapidly examine bacterial glycoproteomes. We benchmarked this approach using N-linked glycopeptides of Campylobacter fetus subsp. fetus as well as O-linked glycopeptides of Acinetobacter baumannii and Burkholderia cenocepacia revealing glycopeptides modified with a range of glycans can be readily identified without defining the glycan masses before database searching. Using this approach, we demonstrate how wide tolerance searching can be used to compare glycan use across bacterial species by examining the glycoproteomes of eight Burkholderia species (B. pseudomallei; B. multivorans; B. dolosa; B. humptydooensis; B. ubonensis, B. anthina; B. diffusa; B. pseudomultivorans). Finally, we demonstrate how open searching enables the identification of low frequency glycoforms based on shared modified peptides sequences. Combined, these results show that open searching is a robust computational approach for the determination of glycan diversity within bacterial proteomes.
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Affiliation(s)
- Ameera Raudah Ahmad Izaham
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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42
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Parker R, Partridge T, Wormald C, Kawahara R, Stalls V, Aggelakopoulou M, Parker J, Doherty RP, Morejon YA, Lee E, Saunders K, Haynes BF, Acharya P, Thaysen-Andersen M, Borrow P, Ternette N. Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32839772 PMCID: PMC7444283 DOI: 10.1101/2020.08.19.255901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Understanding and eliciting protective immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an urgent priority. To facilitate these objectives, we have profiled the repertoire of human leukocyte antigen class II (HLA-II)-bound peptides presented by HLA-DR diverse monocyte-derived dendritic cells pulsed with SARS-CoV-2 spike (S) protein. We identify 209 unique HLA-II-bound peptide sequences, many forming nested sets, which map to sites throughout S including glycosylated regions. Comparison of the glycosylation profile of the S protein to that of the HLA-II-bound S peptides revealed substantial trimming of glycan residues on the latter, likely introduced during antigen processing. Our data also highlight the receptor-binding motif in S1 as a HLA-DR-binding peptide-rich region. Results from this study have application in vaccine design, and will aid analysis of CD4+ T cell responses in infected individuals and vaccine recipients.
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43
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Humoral and circulating follicular helper T cell responses in recovered patients with COVID-19. Nat Med 2020; 26:1428-1434. [PMID: 32661393 DOI: 10.1038/s41591-020-0995-0] [Citation(s) in RCA: 300] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has dramatically expedited global vaccine development efforts1-3, most targeting the viral 'spike' glycoprotein (S). S localizes on the virion surface and mediates recognition of cellular receptor angiotensin-converting enzyme 2 (ACE2)4-6. Eliciting neutralizing antibodies that block S-ACE2 interaction7-9, or indirectly prevent membrane fusion10, constitute an attractive modality for vaccine-elicited protection11. However, although prototypic S-based vaccines show promise in animal models12-14, the immunogenic properties of S in humans are poorly resolved. In this study, we characterized humoral and circulating follicular helper T cell (cTFH) immunity against spike in recovered patients with coronavirus disease 2019 (COVID-19). We found that S-specific antibodies, memory B cells and cTFH are consistently elicited after SARS-CoV-2 infection, demarking robust humoral immunity and positively associated with plasma neutralizing activity. Comparatively low frequencies of B cells or cTFH specific for the receptor binding domain of S were elicited. Notably, the phenotype of S-specific cTFH differentiated subjects with potent neutralizing responses, providing a potential biomarker of potency for S-based vaccines entering the clinic. Overall, although patients who recovered from COVID-19 displayed multiple hallmarks of effective immune recognition of S, the wide spectrum of neutralizing activity observed suggests that vaccines might require strategies to selectively target the most potent neutralizing epitopes.
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44
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Riley NM, Malaker SA, Driessen MD, Bertozzi CR. Optimal Dissociation Methods Differ for N- and O-Glycopeptides. J Proteome Res 2020; 19:3286-3301. [PMID: 32500713 PMCID: PMC7425838 DOI: 10.1021/acs.jproteome.0c00218] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
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Site-specific
characterization of glycosylation requires intact
glycopeptide analysis, and recent efforts have focused on how to best
interrogate glycopeptides using tandem mass spectrometry (MS/MS).
Beam-type collisional activation, i.e., higher-energy collisional
dissociation (HCD), has been a valuable approach, but stepped collision
energy HCD (sceHCD) and electron transfer dissociation with HCD supplemental
activation (EThcD) have emerged as potentially more suitable alternatives.
Both sceHCD and EThcD have been used with success in large-scale glycoproteomic
experiments, but they each incur some degree of compromise. Most progress
has occurred in the area of N-glycoproteomics. There
is growing interest in extending this progress to O-glycoproteomics, which necessitates comparisons of method performance
for the two classes of glycopeptides. Here, we systematically explore
the advantages and disadvantages of conventional HCD, sceHCD, ETD,
and EThcD for intact glycopeptide analysis and determine their suitability
for both N- and O-glycoproteomic
applications. For N-glycopeptides, HCD and sceHCD
generate similar numbers of identifications, although sceHCD generally
provides higher quality spectra. Both significantly outperform EThcD
methods in terms of identifications, indicating that ETD-based methods
are not required for routine N-glycoproteomics even
if they can generate higher quality spectra. Conversely, ETD-based
methods, especially EThcD, are indispensable for site-specific analyses
of O-glycopeptides. Our data show that O-glycopeptides cannot be robustly characterized with HCD-centric
methods that are sufficient for N-glycopeptides,
and glycoproteomic methods aiming to characterize O-glycopeptides must be constructed accordingly.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California 94305-6104, United States
| | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, California 94305-6104, United States
| | - Marc D Driessen
- Department of Chemistry, Stanford University, Stanford, California 94305-6104, United States
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305-6104, United States.,Howard Hughes Medical Institute, Stanford, California 94305-6104, United States
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45
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Pegg CL, Zacchi LF, Recinos DR, Howard CB, Schulz BL. Identification of novel glycosylation events on human serum-derived factor IX. Glycoconj J 2020; 37:471-483. [PMID: 32378017 DOI: 10.1007/s10719-020-09922-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/06/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Human Factor IX is a highly post-translationally modified protein that is an important clotting factor in the blood coagulation cascade. Functional deficiencies in Factor IX result in the bleeding disorder haemophilia B, which is treated with plasma-derived or recombinant Factor IX concentrates. Here, we investigated the post-translational modifications of human serum-derived Factor IX and report previously undescribed O-linked monosaccharide compositions at serine 141 and a novel site of glycosylation. At serine 141 we observed two monosaccharide compositions, with HexNAc1Hex1NeuAc2 dominant and a low level of HexNAc1Hex1NeuAc1. This O-linked site lies N-terminal to the first cleavage site for the activation peptide, an important region of the protein that is removed to activate Factor IX. The novel site is an N-linked site in the serine protease domain with low occupancy in a non-canonical consensus motif at asparagine 258, observed with a HexNAc4Hex5NeuAc2 monosaccharide composition attached. This is the first reported instance of a site of modification in the serine protease domain. The description of these glycosylation events provides a basis for future functional studies and contributes to structural characterisation of native Factor IX for the production of effective therapeutic biosimilars and biobetters.
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Affiliation(s)
- Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Lucia F Zacchi
- Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Dinora Roche Recinos
- Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Christopher B Howard
- Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia. .,Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia.
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46
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Huang J, Jiang B, Zhao H, Wu M, Kong S, Liu M, Yang P, Cao W. Development of a Computational Tool for Automated Interpretation of Intact O-Glycopeptide Tandem Mass Spectra from Single Proteins. Anal Chem 2020; 92:6777-6784. [PMID: 32275135 DOI: 10.1021/acs.analchem.0c01091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Precise and automated analysis of site-specific O-glycosylation on single proteins is crucial for comprehensive characterization of some important glycoproteins, such as tumor biomarkers and recombinant drug proteins. Mass spectrometry has been proven to be a powerful technique for protein sequencing and N-glycosylation analysis. However, challenges remain in developing computational tools for intact O-glycopeptide analysis, which has greatly hindered the development of mass-spectrometry-based O-glycosylation analysis. Herein, an integrated strategy together with a dedicated automated computational tool termed AOGP was developed for intact O-glycopeptide analysis on single proteins. AOGP utilized de novo sequencing for O-glycans and a database search strategy for peptide backbones. The false discovery rate (FDR) of the identification results was controlled and validated by a mixed Gaussian distribution estimation method. AOGP exhibited superior performance in identifying intact O-glycopeptides of the human erythropoietin with a total of 188 O-glycopeptide spectra reported under 1% FDR. AOGP is developed in Python, is fully open-sourced, and is equipped with a user-friendly interface. Such an easy-operating and robust tool would greatly facilitate O-glycosylation analysis on single proteins in tumor biomarker and recombinant drug protein development.
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47
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Klein J, Zaia J. Relative Retention Time Estimation Improves N-Glycopeptide Identifications by LC-MS/MS. J Proteome Res 2020; 19:2113-2121. [PMID: 32223173 DOI: 10.1021/acs.jproteome.0c00051] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Glycopeptides identified by tandem mass spectrometry rely on the identification of the peptide backbone sequence and the attached glycan(s) by the incomplete fragmentation of both moieties. This may lead to ambiguous identifications where multiple structures could explain the same spectrum equally well due to missing information in the mass spectrum or incorrect precursor mass determination. To date, approaches to solving these problems have been limited, and few inroads have been made to address these issues. We present a technique to address some of these challenges and demonstrate it on previously published data sets. We use a linear modeling approach to learn the influence of the glycan composition on the retention time of a glycopeptide and use these models to validate glycopeptides within the same experiment, detecting over 400 incorrect cases during the MS/MS search and correcting 75 cases that could not be identified based on mass alone. We make this technique available as a command line executable program, written in Python and C, freely available at https://github.com/mobiusklein/glycresoft in source form, with precompiled binaries for Windows.
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Affiliation(s)
- Joshua Klein
- Program for Bioinformatics, Boston University, Boston, Massachusetts 02215, United States
| | - Joseph Zaia
- Program for Bioinformatics, Boston University, Boston, Massachusetts 02215, United States.,Department of Biochemistry, Boston University, Boston, Massachusetts 02215, United States
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48
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Zhu J, Lin YH, Dingess KA, Mank M, Stahl B, Heck AJR. Quantitative Longitudinal Inventory of the N-Glycoproteome of Human Milk from a Single Donor Reveals the Highly Variable Repertoire and Dynamic Site-Specific Changes. J Proteome Res 2020; 19:1941-1952. [PMID: 32125861 PMCID: PMC7252941 DOI: 10.1021/acs.jproteome.9b00753] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein N-glycosylation on human milk proteins assists in protecting an infant's health and functions among others as competitive inhibitors of pathogen binding and immunomodulators. Due to the individual uniqueness of each mother's milk and the overall complexity and temporal changes of protein N-glycosylation, analysis of the human milk N-glycoproteome requires longitudinal personalized approaches, providing protein- and N-site-specific quantitative information. Here, we describe an automated platform using hydrophilic-interaction chromatography (HILIC)-based cartridges enabling the proteome-wide monitoring of intact N-glycopeptides using just a digest of 150 μg of breast milk protein. We were able to map around 1700 glycopeptides from 110 glycoproteins covering 191 glycosites, of which 43 sites have not been previously reported with experimental evidence. We next quantified 287 of these glycopeptides originating from 50 glycoproteins using a targeted proteomics approach. Although each glycoprotein, N-glycosylation site, and attached glycan revealed distinct dynamic changes, we did observe a few general trends. For instance, fucosylation, especially terminal fucosylation, increased across the lactation period. Building on the improved glycoproteomics approach outlined above, future studies are warranted to reveal the potential impact of the observed glycosylation microheterogeneity on the healthy development of infants.
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Affiliation(s)
- Jing Zhu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Beijing Institute of Nutritional Resources, 100069 Beijing, China
| | - Yu-Hsien Lin
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Kelly A Dingess
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Marko Mank
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, The Netherlands
| | - Bernd Stahl
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, The Netherlands.,Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CG Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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49
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Hinneburg H, Pedersen JL, Bokil NJ, Pralow A, Schirmeister F, Kawahara R, Rapp E, Saunders BM, Thaysen-Andersen M. High-resolution longitudinal N- and O-glycoprofiling of human monocyte-to-macrophage transition. Glycobiology 2020; 30:679-694. [DOI: 10.1093/glycob/cwaa020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/18/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Abstract
Protein glycosylation impacts the development and function of innate immune cells. The glycophenotypes and the glycan remodelling associated with the maturation of macrophages from monocytic precursor populations remain incompletely described. Herein, label-free porous graphitised carbon–liquid chromatography–tandem mass spectrometry (PGC-LC-MS/MS) was employed to profile with high resolution the N- and O-glycome associated with human monocyte-to-macrophage transition. Primary blood-derived CD14+ monocytes were differentiated ex vivo in the absence of strong anti- and proinflammatory stimuli using a conventional 7-day granulocyte-macrophage colony-stimulating factor differentiation protocol with longitudinal sampling. Morphology and protein expression monitored by light microscopy and proteomics validated the maturation process. Glycomics demonstrated that monocytes and macrophages display similar N-glycome profiles, comprising predominantly paucimannosidic (Man1-3GlcNAc2Fuc0–1, 22.1–30.8%), oligomannosidic (Man5-9GlcNAc2, 29.8–35.7%) and α2,3/6-sialylated complex-type N-glycans with variable core fucosylation (27.6–39.1%). Glycopeptide analysis validated conjugation of these glycans to human proteins, while quantitative proteomics monitored the glycoenzyme expression levels during macrophage differentiation. Significant interperson glycome variations were observed suggesting a considerable physiology-dependent or heritable heterogeneity of CD14+ monocytes. Only few N-glycome changes correlated with the monocyte-to-macrophage transition across donors including decreased core fucosylation and reduced expression of mannose-terminating (paucimannosidic-/oligomannosidic-type) N-glycans in macrophages, while lectin flow cytometry indicated that more dramatic cell surface glycan remodelling occurs during maturation. The less heterogeneous core 1-rich O-glycome showed a minor decrease in core 2-type O-glycosylation but otherwise remained unchanged with macrophage maturation. This high-resolution glycome map underpinning normal monocyte-to-macrophage transition, the most detailed to date, aids our understanding of the molecular makeup pertaining to two vital innate immune cell types and forms an important reference for future glycoimmunological studies.
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Affiliation(s)
- Hannes Hinneburg
- Department of Molecular Sciences, Macquarie University, NSW 2109 Sydney, Australia
- Biomolecular Discovery Research Centre, Macquarie University, NSW 2109 Sydney, Australia
| | - Jessica L Pedersen
- School of Life Sciences, Faculty of Science, University of Technology, NSW 2007 Sydney, Australia
| | - Nilesh J Bokil
- School of Life Sciences, Faculty of Science, University of Technology, NSW 2007 Sydney, Australia
| | - Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems (Bioprocess Engineering), 39106 Magdeburg, Germany
| | | | - Rebeca Kawahara
- Department of Molecular Sciences, Macquarie University, NSW 2109 Sydney, Australia
- Biomolecular Discovery Research Centre, Macquarie University, NSW 2109 Sydney, Australia
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems (Bioprocess Engineering), 39106 Magdeburg, Germany
- GlyXera GmbH, 39120 Magdeburg, Germany
| | - Bernadette M Saunders
- School of Life Sciences, Faculty of Science, University of Technology, NSW 2007 Sydney, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, NSW 2109 Sydney, Australia
- Biomolecular Discovery Research Centre, Macquarie University, NSW 2109 Sydney, Australia
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50
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Wang Y, Tian Z. New Energy Setup Strategy for Intact N-Glycopeptides Characterization Using Higher-Energy Collisional Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:651-657. [PMID: 31967800 DOI: 10.1021/jasms.9b00089] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
With the optional setting of multiple stepped collisional energies (NCEs), higher-energy collisional dissociation (HCD) as available on Orbitrap instruments is a widely adopted dissociation method for intact N-glycopeptides characterization, where peptide backbones and N-glycan moieties are selectively fragmented at high and low NCEs, respectively. Initially, a dependent setting of a central value plus minus a variation is available to the users to set up NCEs, and the combination of 30 ± 10% to give the energies 20%/30%/40% has been mostly adopted in the literature. With the recent availability of an independent NCEs setup, we found that the combination of 20%/30%/30% is better than 20%/30%/40%; in the analysis of complex intact N-glycopeptides enriched from gastric cancer tissues, total IDs with spectrum-level FDR ≤ 1%, site-specific IDs with site-determining fragment ions, and structure-specific IDs with structure-diagnostic fragment ions were increased by 42% (4,767 → 6,746), 57% (599 → 942), and 97% (1771 → 3495), respectively. This finding will benefit all the coming N-glycoproteomics studies using HCD as the dissociation method.
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Affiliation(s)
- Yue Wang
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
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