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Chiu KY, Ai Y, Tanim-Ai Hassan M, Li X, Gunawardena HP, Chen H. Standards-Free Absolute Quantitation of Oxidizable Glycopeptides by Coulometric Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 38815255 DOI: 10.1021/jasms.4c00052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Currently, glycopeptide quantitation is mainly based on relative quantitation due to absolute quantitation requiring isotope-labeled or standard glycopeptides which may not be commercially available or are very costly and time consuming to synthesize. To address this grand challenge, coulometric mass spectrometry (CMS), based on the combination of electrochemistry (EC) and mass spectrometry (MS), was utilized to quantify electrochemically active glycopeptides without the need of using standard materials. In this study, we studied tyrosine-containing glycopeptides, NYIVGQPSS(β-GlcNAc)TGNL-OH and NYSVPSS(β-GlcNAc)TGNL-OH, and successfully quantified them directly with CMS with a discrepancy of less than 5% between the CMS measured amount and the theoretical amount. Taking one step further, we applied this approach to quantify glycopeptides generated from the digestion of NIST mAb, a monoclonal antibody reference material. Through HILIC column separation, five N297 glycopeptides resulting from NIST mAb tryptic digestion were successfully separated and quantified by CMS for an absolute amount without the use of any standard materials. This study indicates the potential utility of CMS for quantitative proteomics research.
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Affiliation(s)
- Kai-Yuan Chiu
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Yongling Ai
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Md Tanim-Ai Hassan
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Xuanwen Li
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Harsha P Gunawardena
- The Janssen Pharmaceutical Companies of Johnson & Johnson, Springhouse, Pennsylvania 19002, United States
| | - Hao Chen
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
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2
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Mastrangeli R, Satwekar A, Bierau H. Innovative Metrics for Reporting and Comparing the Glycan Structural Profile in Biotherapeutics. Molecules 2023; 28:molecules28083304. [PMID: 37110538 PMCID: PMC10143042 DOI: 10.3390/molecules28083304] [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: 03/09/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Glycosylation is a critical quality attribute in biotherapeutics, impacting properties such as protein stability, solubility, clearance rate, efficacy, immunogenicity, and safety. Due to the heterogenic and complex nature of protein glycosylation, comprehensive characterization is demanding. Moreover, the lack of standardized metrics for evaluating and comparing glycosylation profiles hinders comparability studies and the establishment of manufacturing control strategies. To address both challenges, we propose a standardized approach based on novel metrics for a comprehensive glycosylation fingerprint which greatly facilitates the reporting and objective comparison of glycosylation profiles. The analytical workflow is based on a liquid chromatography-mass spectrometry-based multi-attribute method. Based on the analytical data, a matrix of glycosylation-related quality attributes, both at site-specific and whole molecule level, are computed, which provide metrics for a comprehensive product glycosylation fingerprint. Two case studies illustrate the applicability of the proposed indices as a standardized and versatile approach for reporting all dimensions of the glycosylation profile. The proposed approach further facilitates the assessments of risks associated with changes in the glycosylation profile that may affect efficacy, clearance, and immunogenicity.
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Affiliation(s)
- Renato Mastrangeli
- Global CMC Development Technology & Innovation, CMC Science & Intelligence, Merck Serono SpA (An affiliate of Merck KGaA, Darmstadt, Germany), Guidonia Montecelio, 00012 Rome, Italy
| | - Abhijeet Satwekar
- Global CMC Development, Global Analytical Development, Global Analytical-Pharmaceutical Science & Innovation, Merck Serono SpA (An affiliate of Merck KGaA, Darmstadt, Germany), Guidonia Montecelio, 00012 Rome, Italy
| | - Horst Bierau
- Global CMC Development Technology & Innovation, CMC Science & Intelligence, Merck Serono SpA (An affiliate of Merck KGaA, Darmstadt, Germany), Guidonia Montecelio, 00012 Rome, Italy
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3
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Babu N, Bhat MY, John AE, Chatterjee A. The role of proteomics in the multiplexed analysis of gene alterations in human cancer. Expert Rev Proteomics 2021; 18:737-756. [PMID: 34602018 DOI: 10.1080/14789450.2021.1984884] [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: 10/20/2022]
Abstract
INTRODUCTION Proteomics has played a pivotal role in identifying proteins perturbed in disease conditions when compared with healthy samples. Study of dysregulated proteins aids in identifying diagnostic markers and potential therapeutic targets. Cancer is an outcome of interplay of several such disarrayed proteins and molecular pathways which perturb cellular homeostasis, resulting in transformation. In this review, we discuss various facets of proteomic approaches, including tools and technological advancements, aiding in understanding differentially expressed molecules and signaling mechanisms. AREAS COVERED In this review, we have taken the approach of documenting the different methods of proteomic studies, ranging from labeling techniques, data analysis methods, and the nature of molecule detected. We summarize each technique and provide a glimpse of cancer research carried out using them, highlighting the advantages and drawbacks in comparison with others. Literature search using online resources, such as PubMed and Google Scholar were carried out for this approach. EXPERT OPINION Technological advancements in proteomics studies have come a long way from the study of two-dimensional mapping of proteins separated on gels in the early 1970s. Higher precision in molecular identification and quantification (high throughput), and greater number of samples analyzed have been the focus of researchers.
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Affiliation(s)
- Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Mohd Younis Bhat
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | | | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
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4
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Delafield DG, Li L. Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation. Mol Cell Proteomics 2021; 20:100054. [PMID: 32576592 PMCID: PMC8724918 DOI: 10.1074/mcp.r120.002095] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 12/13/2022] Open
Abstract
Growing implications of glycosylation in physiological occurrences and human disease have prompted intensive focus on revealing glycomic perturbations through absolute and relative quantification. Empowered by seminal methodologies and increasing capacity for detection, identification, and characterization, the past decade has provided a significant increase in the number of suitable strategies for glycan and glycopeptide quantification. Mass-spectrometry-based strategies for glycomic quantitation have grown to include metabolic incorporation of stable isotopes, deposition of mass difference and mass defect isotopic labels, and isobaric chemical labeling, providing researchers with ample tools for accurate and robust quantitation. Beyond this, workflows have been designed to harness instrument capability for label-free quantification, and numerous software packages have been developed to facilitate reliable spectrum scoring. In this review, we present and highlight the most recent advances in chemical labeling and associated techniques for glycan and glycopeptide quantification.
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Affiliation(s)
- Daniel G Delafield
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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5
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Kim KH, Lee SY, Kim DG, Lee SY, Kim JY, Yoo JS. Absolute Quantification of N-Glycosylation of Alpha-Fetoprotein Using Parallel Reaction Monitoring with Stable Isotope-Labeled N-Glycopeptide as an Internal Standard. Anal Chem 2020; 92:12588-12595. [DOI: 10.1021/acs.analchem.0c02563] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kwang Hoe Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju 28119, Republic of Korea
| | - Sang Yoon Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju 28119, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Dong Geun Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju 28119, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Soo-Youn Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju 28119, Republic of Korea
| | - Jong Shin Yoo
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju 28119, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
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6
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Knopf JD, Landscheidt N, Pegg CL, Schulz BL, Kühnle N, Chao CW, Huck S, Lemberg MK. Intramembrane protease RHBDL4 cleaves oligosaccharyltransferase subunits to target them for ER-associated degradation. J Cell Sci 2020; 133:jcs243790. [PMID: 32005703 DOI: 10.1242/jcs.243790] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 01/21/2020] [Indexed: 08/31/2023] Open
Abstract
The endoplasmic reticulum (ER)-resident intramembrane rhomboid protease RHBDL4 generates metastable protein fragments and together with the ER-associated degradation (ERAD) machinery provides a clearance mechanism for aberrant and surplus proteins. However, the endogenous substrate spectrum and with that the role of RHBDL4 in physiological ERAD is mainly unknown. Here, we use a substrate trapping approach in combination with quantitative proteomics to identify physiological RHBDL4 substrates. This revealed oligosaccharyltransferase (OST) complex subunits such as the catalytic active subunit STT3A as substrates for the RHBDL4-dependent ERAD pathway. RHBDL4-catalysed cleavage inactivates OST subunits by triggering dislocation into the cytoplasm and subsequent proteasomal degradation. RHBDL4 thereby controls the abundance and activity of OST, suggesting a novel link between the ERAD machinery and glycosylation tuning.
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Affiliation(s)
- Julia D Knopf
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Nina Landscheidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Nathalie Kühnle
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Chao-Wei Chao
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Simon Huck
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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7
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Ivleva VB, Cooper JW, Arnold FJ, Lei QP. Overcoming Challenges in Structural Characterization of HIV-1 Envelope Glycoprotein by LC-MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1663-1678. [PMID: 31111416 PMCID: PMC7476438 DOI: 10.1007/s13361-019-02225-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/05/2019] [Accepted: 04/10/2019] [Indexed: 05/30/2023]
Abstract
Characterization of HIV Env glycoprotein with 28 glycosylation sites is the essential step of structure-based vaccine design programs. A comprehensive LC-MS/MS peptide mapping analysis was applied to assess the primary sequence, glycosylation profiles, and glycosite occupancy of Env to ensure the adequate mimicking of the native immunogen. Another structural feature was reported, related to its cleaved subunits within the trimeric assembly. We bring attention to the importance of thorough inspection of the results generated by the informatics tools which are currently available for the biopharmaceutical characterization. The complexity of Env translates into a vast amount of data with occasional information gaps that could not possibly be filled by means of the automatic data analysis. A series of data validation steps was applied, followed by the illustrations on how the high-quality results may be misinterpreted. It was shown that the glycan sites can only be characterized to a certain limit, and that any claim of full structural characterization of this molecule beyond these limits should be treated with caution. Following the result verification, the percent glycan occupancy was reported for 25 N-glycan sites, including 3 critical antibody-recognition sites. The exact glycan profiles were provided for 20 individual sites, whereas only the glycosylation type could be deduced for 5 sites, dictated by their location within Env sequence. The distribution of the unprocessed high mannose-type glycans correlated with the expected "mannose patch." Experimental procedure optimization and a workflow for glycan characterization with a focus on stringent data testing are presented in the current study.
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Affiliation(s)
- Vera B Ivleva
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Jonathan W Cooper
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Frank J Arnold
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Q Paula Lei
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA.
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8
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Jan M, Upadhyay C, Alcami Pertejo J, Hioe CE, Arora SK. Heterogeneity in glycan composition on the surface of HIV-1 envelope determines virus sensitivity to lectins. PLoS One 2018; 13:e0194498. [PMID: 29579062 PMCID: PMC5868795 DOI: 10.1371/journal.pone.0194498] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/05/2018] [Indexed: 01/08/2023] Open
Abstract
Lectins that target N-glycans on the surface of HIV-1 envelope (Env) glycoprotein have the potential for use as antiviral agents. Although progress has been made in deciphering the molecular details of lectin and Env glycan interaction, further studies are needed to better understand Env glycan heterogeneity among HIV-1 isolates and its influence on virus-neutralization sensitivity to lectins. This study evaluated a panel of lectins with fine specificity for distinct oligosaccharides and assessed their ability to inhibit infection of HIV-1 viruses known to have differing sensitivity to anti-HIV Env antibodies. The results showed that HIV-1 isolates have different sensitivity to lectins specific for α1-3Man, α1-6Man, and α1-2Man binding lectins. Considering that lectins exclusively recognize the oligosaccharide components of virus Env, these data suggest that glycan heterogeneity among HIV-1 isolates may explain this differential sensitivity. To evaluate this further, chronic and acute viruses were produced in the presence of different glycosidase inhibitors to express more homogenous glycans. Viruses enriched for α1-2Man terminating Man5-9GlcNAc2 glycans became similarly sensitive to α1-2Man-binding lectins. The α1-3Man- and α1-6Man-binding lectins also were more potent against viruses expressing predominantly Man5GlcNAc2 and hybrid type glycans with terminal α1-3Man and α1-6Man. Furthermore, lectin-mediated inhibition was competitively alleviated by mannan and this effect was augmented by enrichment of mannose-type glycans on the virus. In addition, while Env of viruses enriched with mannose-type glycans were sensitive to Endo-H deglycosylation, Env of untreated viruses were partially resistant, indicating that HIV-1 Env glycans are heterogeneously comprised of complex, hybrid, and mannose types. Overall, our data demonstrate that HIV-1 isolates display differential sensitivity to lectins, in part due to the microheterogeneity of N-linked glycans expressed on the surface of the virus Env glycoprotein.
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Affiliation(s)
- Muzafar Jan
- Department of Immunopathology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- James J. Peters VA Medical Center, Bronx, New York, United States of America
| | - Chitra Upadhyay
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - José Alcami Pertejo
- Imunopatologia Del SIDA, Centro Nacional De Microbiologia, Instituo De Salud Carlos III, Madrid, Spain
| | - Catarina E. Hioe
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- James J. Peters VA Medical Center, Bronx, New York, United States of America
| | - Sunil K. Arora
- Department of Immunopathology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
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9
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine , Leiden University Medical Center , 2333 ZA Leiden , The Netherlands
| | - Gege Xu
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Qiongyu Li
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elisha Goonatilleke
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Carlito B Lebrilla
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States.,Department of Biochemistry and Molecular Medicine , University of California, Davis , Davis , California 95616 , United States.,Foods for Health Institute , University of California, Davis , Davis , California 95616 , United States
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10
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Thygesen C, Boll I, Finsen B, Modzel M, Larsen MR. Characterizing disease-associated changes in post-translational modifications by mass spectrometry. Expert Rev Proteomics 2018; 15:245-258. [DOI: 10.1080/14789450.2018.1433036] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Camilla Thygesen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Inga Boll
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Bente Finsen
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Maciej Modzel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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11
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Kilpatrick LE, Phinney KW. Quantification of Total Vitamin-D-Binding Protein and the Glycosylated Isoforms by Liquid Chromatography–Isotope Dilution Mass Spectrometry. J Proteome Res 2017; 16:4185-4195. [DOI: 10.1021/acs.jproteome.7b00560] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Lisa E. Kilpatrick
- National Institute of Standards and Technology, Material Measurement
Laboratory, Biomolecular Measurement Division, 100 Bureau Drive, Stop 8314, Gaithersburg, Maryland 20899, United States
| | - Karen W. Phinney
- National Institute of Standards and Technology, Material Measurement
Laboratory, Biomolecular Measurement Division, 100 Bureau Drive, Stop 8314, Gaithersburg, Maryland 20899, United States
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12
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Quantification of N-glycosylation site occupancy status based on labeling/label-free strategies with LC-MS/MS. Talanta 2017; 170:509-513. [PMID: 28501204 DOI: 10.1016/j.talanta.2017.04.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 12/30/2022]
Abstract
Protein N-glycosylation plays important roles in physiological and pathological processes. Characterizing the site-specific N-glycosylation including N-glycan macroheterogeneity (glycosylation site occupancy) and microheterogeneity (site-specific glycan structure) is important for understanding of glycoprotein biosynthesis and function. N-Glycan macroheterogeneity is a physiological property of glycoprotein and the technical obstacles have restricted research into the regulation and functions of this heterogeneity. Quantification of N-glycosylation site occupancy would uncover the critical role of macroheterogeneity in a variety of biological properties. Liquid chromatography (LC)- mass spectrometry (MS)-based quantification is emerging as a powerful tool for glycosylation characterization. This review summarizes the labeling and label-free quantitative MS approaches for quantifying N-glycosylation site occupancy, including its quantification for target glycoproteins in recent years.
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13
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Global site-specific N-glycosylation analysis of HIV envelope glycoprotein. Nat Commun 2017; 8:14954. [PMID: 28348411 PMCID: PMC5379070 DOI: 10.1038/ncomms14954] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/15/2017] [Indexed: 02/07/2023] Open
Abstract
HIV-1 envelope glycoprotein (Env) is the sole target for broadly neutralizing antibodies (bnAbs) and the focus for design of an antibody-based HIV vaccine. The Env trimer is covered by ∼90N-linked glycans, which shield the underlying protein from immune surveillance. bNAbs to HIV develop during infection, with many showing dependence on glycans for binding to Env. The ability to routinely assess the glycan type at each glycosylation site may facilitate design of improved vaccine candidates. Here we present a general mass spectrometry-based proteomics strategy that uses specific endoglycosidases to introduce mass signatures that distinguish peptide glycosites that are unoccupied or occupied by high-mannose/hybrid or complex-type glycans. The method yields >95% sequence coverage for Env, provides semi-quantitative analysis of the glycosylation status at each glycosite. We find that most glycosites in recombinant Env trimers are fully occupied by glycans, varying in the proportion of high-mannose/hybrid and complex-type glycans. The analysis of site-specific glycosylation of HIV Envelope glycoprotein (Env) is challenging as it contains 25–30 glycosylation sites with multiple glycan forms at each site. Here the authors present a generally applicable mass spectrometry-based method for site-specific analysis of protein glycosylation that they apply to the analysis of the HIV-1 Env.
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14
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Largy E, Cantais F, Van Vyncht G, Beck A, Delobel A. Orthogonal liquid chromatography-mass spectrometry methods for the comprehensive characterization of therapeutic glycoproteins, from released glycans to intact protein level. J Chromatogr A 2017; 1498:128-146. [PMID: 28372839 DOI: 10.1016/j.chroma.2017.02.072] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/04/2017] [Accepted: 02/28/2017] [Indexed: 01/16/2023]
Abstract
Proteins are increasingly used as therapeutics. Their characterization is challenging due to their size and inherent heterogeneity notably caused by post-translational modifications, among which glycosylation is probably the most prominent. The glycosylation profile of therapeutic proteins must therefore be thoroughly analyzed. Here, we illustrate how the use of a combination of various cutting-edge LC or LC/MS(/MS) methods, and operating at different levels of analysis allows the comprehensive characterization of both the N- and O-glycosylations of therapeutic proteins without the need for other approaches (capillary electrophoresis, MALDI-TOF). This workflow does not call for the use of highly specialized/custom hardware and software nor an extensive knowledge of glycan analysis. Most notably, we present the point of view of a contract research organization, with the constraints associated to the work in a regulated environment (GxP). Two salient points of this work are i) the use of mixed-mode chromatography as a fast and straightforward mean of profiling N-glycans sialylation as well as an orthogonal method to separate N-glycans co-eluting in the HILIC mode; and ii) the use of widepore HILIC/MS to analyze challenging N/O-glycosylation profiles at both the peptide and subunit levels. A particular attention was given to the sample preparations in terms of duration, specificity, versatility, and robustness, as well as the ease of data processing.
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Affiliation(s)
- Eric Largy
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium
| | - Fabrice Cantais
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium
| | - Géry Van Vyncht
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium
| | - Alain Beck
- Centre d'Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164, Saint-Julien-en-Genevois, France
| | - Arnaud Delobel
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium.
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15
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Xiao H, Wu R. Global and Site-Specific Analysis Revealing Unexpected and Extensive Protein S-GlcNAcylation in Human Cells. Anal Chem 2017; 89:3656-3663. [PMID: 28234450 DOI: 10.1021/acs.analchem.6b05064] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein glycosylation is highly diverse and essential for mammalian cell survival. Heterogeneous glycans may be bound to different amino acid residues, forming multiple types of protein glycosylation. In this work, unexpected protein S-GlcNAcylation on cysteine residues was observed to extensively exist in human cells through global and site-specific analysis of protein GlcNAcylation by mass spectrometry. Three independent experiments produced similar results of many cysteine residues bound to N-acetylglucosamine (GlcNAc). Among well-localized S-GlcNAcylation sites, several motifs with an acidic amino acid around the sites were identified, which strongly suggests that a particular type of enzyme is responsible for this modification. Clustering results show that glycoproteins modified with S-GlcNAc are mainly involved in cell-cell adhesion and gene expression. For the first time, we found that proteins were extensively bound to GlcNAc through the side chains of cysteine residues in human cells, and the current discovery further advances our understanding of protein glycosylation.
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Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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16
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Struwe WB, Stuckmann A, Behrens AJ, Pagel K, Crispin M. Global N-Glycan Site Occupancy of HIV-1 gp120 by Metabolic Engineering and High-Resolution Intact Mass Spectrometry. ACS Chem Biol 2017; 12:357-361. [PMID: 27984693 DOI: 10.1021/acschembio.6b00854] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A vital step in HIV vaccine development strategies has been the observation that some infected individuals generate broadly neutralizing antibodies that target the glycans on the surface of HIV-1 gp120. These antibodies target glycan epitopes on viral envelope spikes, and yet the positions and degree of occupancy of glycosylation sites is diverse. Therefore, there is a need to understand glycosylation occupancy on recombinant immunogens. The sheer number of potential glycosylation sites and degree of chemical heterogeneity impedes assessing the global sequon occupancy of gp120 glycoforms. Here, we trap the glycan processing of recombinant gp120 to generate homogeneous glycoforms, facilitating occupancy assessment by intact mass spectrometry. We show that gp120 monomers of the BG505 strain contain either fully occupied sequons or missing the equivalent of one and sometimes two glycans across the molecule. This biosynthetic engineering approach enables the analysis of therapeutically important glycoproteins otherwise recalcitrant to analysis by native mass spectrometry.
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Affiliation(s)
- Weston B. Struwe
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Alexandra Stuckmann
- Free University Berlin, Department of Chemistry
and Biochemistry, Takustrasse
3, 14195 Berlin, Germany
| | - Anna-Janina Behrens
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Kevin Pagel
- Free University Berlin, Department of Chemistry
and Biochemistry, Takustrasse
3, 14195 Berlin, Germany
| | - Max Crispin
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
- Department
of Immunology and Microbial Science, The Scripps Research Institute, La
Jolla, California 92037, United States
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17
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Kailemia MJ, Park D, Lebrilla CB. Glycans and glycoproteins as specific biomarkers for cancer. Anal Bioanal Chem 2017; 409:395-410. [PMID: 27590322 PMCID: PMC5203967 DOI: 10.1007/s00216-016-9880-6] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/28/2016] [Accepted: 08/12/2016] [Indexed: 12/12/2022]
Abstract
Protein glycosylation and other post-translational modifications are involved in potentially all aspects of human growth and development. Defective glycosylation has adverse effects on human physiological conditions and accompanies many chronic and infectious diseases. Altered glycosylation can occur at the onset and/or during tumor progression. Identifying these changes at early disease stages may aid in making decisions regarding treatments, as early intervention can greatly enhance survival. This review highlights some of the efforts being made to identify N- and O-glycosylation profile shifts in cancer using mass spectrometry. The analysis of single or panels of potential glycoprotein cancer markers are covered. Other emerging technologies such as global glycan release and site-specific glycosylation analysis and quantitation are also discussed. Graphical Abstract Steps involved in the biomarker discovery.
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Affiliation(s)
- Muchena J Kailemia
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Dayoung Park
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
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18
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Banazadeh A, Veillon L, Wooding KM, Zabet-Moghaddam M, Mechref Y. Recent advances in mass spectrometric analysis of glycoproteins. Electrophoresis 2016; 38:162-189. [PMID: 27757981 DOI: 10.1002/elps.201600357] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 12/13/2022]
Abstract
Glycosylation is one of the most common posttranslational modifications of proteins that plays essential roles in various biological processes, including protein folding, host-pathogen interaction, immune response, and inflammation and aberrant protein glycosylation is a well-known event in various disease states including cancer. As a result, it is critical to develop rapid and sensitive methods for the analysis of abnormal glycoproteins associated with diseases. Mass spectrometry (MS) in conjunction with different separation methods, such as capillary electrophoresis (CE), ion mobility (IM), and high performance liquid chromatography (HPLC) has become a popular tool for glycoprotein analysis, providing highly informative fragments for structural identification of glycoproteins. This review provides an overview of the developments and accomplishments in the field of glycomics and glycoproteomics reported between 2014 and 2016.
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Affiliation(s)
- Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Lucas Veillon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Kerry M Wooding
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.,Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, USA
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19
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Planinc A, Bones J, Dejaegher B, Van Antwerpen P, Delporte C. Glycan characterization of biopharmaceuticals: Updates and perspectives. Anal Chim Acta 2016; 921:13-27. [PMID: 27126786 DOI: 10.1016/j.aca.2016.03.049] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/21/2016] [Accepted: 03/29/2016] [Indexed: 02/01/2023]
Abstract
Therapeutic proteins are rapidly becoming the most promising class of pharmaceuticals on the market due to their successful treatment of a vast array of serious diseases, such as cancers and immune disorders. Therapeutic proteins are produced using recombinant DNA technology. More than 60% of therapeutic proteins are posttranslationally modified following biosynthesis by the addition of N- or O-linked glycans. Glycosylation is the most common posttranslational modifications of proteins. However, it is also the most demanding and complex posttranslational modification from the analytical point of view. Moreover, research has shown that glycosylation significantly impacts stability, half-life, mechanism of action and safety of a therapeutic protein. Considering the exponential growth of biotherapeutics, this present review of the literature (2009-2015) focuses on the characterization of protein glycosylation, which has witnessed an improvement in methodology. Furthermore, it discusses current issues in the fields of production and characterization of therapeutic proteins. This review also highlights the problem of non-standard requirements for the approval of biosimilars with regard to their glycosylation and discusses recent developments and perspectives for improved glycan characterization.
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Affiliation(s)
- Ana Planinc
- Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Universite Libre de Bruxelles (ULB), Brussels, Belgium
| | - Jonathan Bones
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Bieke Dejaegher
- Laboratory of Instrumental Analysis and Bioelectrochemistry, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, B-1050 Brussels, Belgium; Department of Analytical Chemistry and Pharmaceutical Technology (FABI), Center for Pharmaceutical Research (CePhaR), Faculty of Medicines and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Pierre Van Antwerpen
- Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Universite Libre de Bruxelles (ULB), Brussels, Belgium
| | - Cédric Delporte
- Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Universite Libre de Bruxelles (ULB), Brussels, Belgium.
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20
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A case for protein-level and site-level specificity in glycoproteomic studies of disease. Glycoconj J 2016; 33:377-85. [PMID: 27007620 DOI: 10.1007/s10719-016-9663-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 02/16/2016] [Accepted: 03/09/2016] [Indexed: 12/12/2022]
Abstract
Abnormal glycosylation of proteins is known to be either resultant or causative of a variety of diseases. This makes glycoproteins appealing targets as potential biomarkers and focal points of molecular studies on the development and progression of human ailment. To date, a majority of efforts in disease glycoproteomics have tended to center on either determining the concentration of a given glycoprotein, or on profiling the total population of glycans released from a mixture of glycoproteins. While these approaches have demonstrated some diagnostic potential, they are inherently insensitive to the fine molecular detail which distinguishes unique and possibly disease relevant glycoforms of specific proteins. As a consequence, such analyses can be of limited sensitivity, specificity, and accuracy because they do not comprehensively consider the glycosylation status of any particular glycoprotein, or of any particular glycosylation site. Therefore, significant opportunities exist to improve glycoproteomic inquiry into disease by engaging in these studies at the level of individual glycoproteins and their exact loci of glycosylation. In this concise review, the rationale for glycoprotein and glycosylation site specificity is developed in the context of human disease glycoproteomics with an emphasis on N-glycosylation. Recent examples highlighting disease-related perturbations in glycosylation will be presented, including those involving alterations in the overall glycosylation of a specific protein, alterations in the occupancy of a given glycosylation site, and alterations in the compositional heterogeneity of glycans occurring at a given glycosylation site. Each will be discussed with particular emphasis on how protein-specific and site-specific approaches can contribute to improved discrimination between glycoproteomes and glycoproteins associated with healthy and unhealthy states.
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21
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Zacchi LF, Schulz BL. N-glycoprotein macroheterogeneity: biological implications and proteomic characterization. Glycoconj J 2015; 33:359-76. [DOI: 10.1007/s10719-015-9641-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/04/2015] [Accepted: 11/20/2015] [Indexed: 10/22/2022]
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22
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Zhu Z, Desaire H. Carbohydrates on Proteins: Site-Specific Glycosylation Analysis by Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:463-483. [PMID: 26070719 DOI: 10.1146/annurev-anchem-071114-040240] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Glycosylation on proteins adds complexity and versatility to these biologically vital macromolecules. To unveil the structure-function relationship of glycoproteins, glycopeptide-centric analysis using mass spectrometry (MS) has become a method of choice because the glycan is preserved on the glycosylation site and site-specific glycosylation profiles of proteins can be readily determined. However, glycopeptide analysis is still challenging given that glycopeptides are usually low in abundance and relatively difficult to detect and the resulting data require expertise to analyze. Viewing the urgent need to address these challenges, emerging methods and techniques are being developed with the goal of analyzing glycopeptides in a sensitive, comprehensive, and high-throughput manner. In this review, we discuss recent advances in glycoprotein and glycopeptide analysis, with topics covering sample preparation, analytical separation, MS and tandem MS techniques, as well as data interpretation and automation.
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Affiliation(s)
- Zhikai Zhu
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas 66047;
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23
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Xu Y, Bailey UM, Schulz BL. Automated measurement of site-specific N
-glycosylation occupancy with SWATH-MS. Proteomics 2015; 15:2177-86. [DOI: 10.1002/pmic.201400465] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/08/2015] [Accepted: 02/27/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Ying Xu
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
| | - Ulla-Maja Bailey
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
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Smeekens JM, Chen W, Wu R. Mass spectrometric analysis of the cell surface N-glycoproteome by combining metabolic labeling and click chemistry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:604-614. [PMID: 25425172 DOI: 10.1007/s13361-014-1016-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/02/2014] [Accepted: 10/03/2014] [Indexed: 06/04/2023]
Abstract
Cell surface N-glycoproteins play extraordinarily important roles in cell-cell communication, cell-matrix interactions, and cellular response to environmental cues. Global analysis is exceptionally challenging because many N-glycoproteins are present at low abundances and effective separation is difficult to achieve. Here, we have developed a novel strategy integrating metabolic labeling, copper-free click chemistry, and mass spectrometry (MS)-based proteomics methods to analyze cell surface N-glycoproteins comprehensively and site-specifically. A sugar analog containing an azido group, N-azidoacetylgalactosamine, was fed to cells to label glycoproteins. Glycoproteins with the functional group on the cell surface were then bound to dibenzocyclooctyne-sulfo-biotin via copper-free click chemistry under physiological conditions. After protein extraction and digestion, glycopeptides with the biotin tag were enriched by NeutrAvidin conjugated beads. Enriched glycopeptides were deglycosylated with peptide-N-glycosidase F in heavy-oxygen water, and in the process of glycan removal, asparagine was converted to aspartic acid and tagged with 18O for MS analysis. With this strategy, 144 unique N-glycopeptides containing 152 N-glycosylation sites were identified in 110 proteins in HEK293T cells. As expected, 95% of identified glycoproteins were membrane proteins, which were highly enriched. Many sites were located on important receptors, transporters, and cluster of differentiation proteins. The experimental results demonstrated that the current method is very effective for the comprehensive and site-specific identification of the cell surface N-glycoproteome and can be extensively applied to other cell surface protein studies.
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Affiliation(s)
- Johanna M Smeekens
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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26
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Zhu Z, Su X, Go EP, Desaire H. New glycoproteomics software, GlycoPep Evaluator, generates decoy glycopeptides de novo and enables accurate false discovery rate analysis for small data sets. Anal Chem 2014; 86:9212-9. [PMID: 25137014 PMCID: PMC4165450 DOI: 10.1021/ac502176n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Glycoproteins
are biologically significant large molecules that
participate in numerous cellular activities. In order to obtain site-specific
protein glycosylation information, intact glycopeptides, with the
glycan attached to the peptide sequence, are characterized by tandem
mass spectrometry (MS/MS) methods such as collision-induced dissociation
(CID) and electron transfer dissociation (ETD). While several emerging
automated tools are developed, no consensus is present in the field
about the best way to determine the reliability of the tools and/or
provide the false discovery rate (FDR). A common approach to calculate
FDRs for glycopeptide analysis, adopted from the target-decoy strategy
in proteomics, employs a decoy database that is created based on the
target protein sequence database. Nonetheless, this approach is not
optimal in measuring the confidence of N-linked glycopeptide
matches, because the glycopeptide data set is considerably smaller
compared to that of peptides, and the requirement of a consensus sequence
for N-glycosylation further limits the number of
possible decoy glycopeptides tested in a database search. To address
the need to accurately determine FDRs for automated glycopeptide assignments,
we developed GlycoPep Evaluator (GPE), a tool that helps to measure
FDRs in identifying glycopeptides without using a decoy database.
GPE generates decoy glycopeptides de novo for every target glycopeptide,
in a 1:20 target-to-decoy ratio. The decoys, along with target glycopeptides,
are scored against the ETD data, from which FDRs can be calculated
accurately based on the number of decoy matches and the ratio of the
number of targets to decoys, for small data sets. GPE is freely accessible
for download and can work with any search engine that interprets ETD
data of N-linked glycopeptides. The software is provided
at https://desairegroup.ku.edu/research.
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Affiliation(s)
- Zhikai Zhu
- Department of Chemistry, University of Kansas , Lawrence, Kansas 66047, United States
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