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Huo Z, Tu H, Ren J, Zhang X, Qi Y, Situ C, Li Y, Guo Y, Guo X, Zhu H. Lectin-Based SP3 Technology Enables N-Glycoproteomic Analysis of Mouse Oocytes. J Proteome Res 2024. [PMID: 38787631 DOI: 10.1021/acs.jproteome.4c00089] [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: 05/26/2024]
Abstract
N-glycosylation is one of the most universal and complex protein post-translational modifications (PTMs), and it is involved in many physiological and pathological activities. Owing to the low abundance of N-glycoproteins, enrichment of N-glycopeptides for mass spectrometry analysis usually requires a large amount of peptides. Additionally, oocyte protein N-glycosylation has not been systemically characterized due to the limited sample amount. Here, we developed a glycosylation enrichment method based on lectin and a single-pot, solid-phase-enhanced sample preparation (SP3) technology, termed lectin-based SP3 technology (LectinSP3). LectinSP3 immobilized lectin on the SP3 beads for N-glycopeptide enrichment. It could identify over 1100 N-glycosylation sites and 600 N-glycoproteins from 10 μg of mouse testis peptides. Furthermore, using the LectinSP3 method, we characterized the N-glycoproteome of 1000 mouse oocytes in three replicates and identified a total of 363 N-glycosylation sites from 215 N-glycoproteins. Bioinformatics analysis revealed that these oocyte N-glycoproteins were mainly enriched in cell adhesion, fertilization, and sperm-egg recognition. Overall, the LectinSP3 method has all procedures performed in one tube, using magnetic beads. It is suitable for analysis of a low amount of samples and is expected to be easily adaptable for automation. In addition, our mouse oocyte protein N-glycosylation profiling could help further characterize the regulation of oocyte functions.
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Affiliation(s)
- Zian Huo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Haixia Tu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
- Department of Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Jie Ren
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Xiangzheng Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Yaling Qi
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Chenghao Situ
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Yan Li
- Department of Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Hui Zhu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
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Tremblay TL, Alata W, Slinn J, Baumann E, Delaney CE, Moreno M, Haqqani AS, Stanimirovic DB, Hill JJ. The proteome of the blood-brain barrier in rat and mouse: highly specific identification of proteins on the luminal surface of brain microvessels by in vivo glycocapture. Fluids Barriers CNS 2024; 21:23. [PMID: 38433215 PMCID: PMC10910681 DOI: 10.1186/s12987-024-00523-x] [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: 10/11/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND The active transport of molecules into the brain from blood is regulated by receptors, transporters, and other cell surface proteins that are present on the luminal surface of endothelial cells at the blood-brain barrier (BBB). However, proteomic profiling of proteins present on the luminal endothelial cell surface of the BBB has proven challenging due to difficulty in labelling these proteins in a way that allows efficient purification of these relatively low abundance cell surface proteins. METHODS Here we describe a novel perfusion-based labelling workflow: in vivo glycocapture. This workflow relies on the oxidation of glycans present on the luminal vessel surface via perfusion of a mild oxidizing agent, followed by subsequent isolation of glycoproteins by covalent linkage of their oxidized glycans to hydrazide beads. Mass spectrometry-based identification of the isolated proteins enables high-confidence identification of endothelial cell surface proteins in rats and mice. RESULTS Using the developed workflow, 347 proteins were identified from the BBB in rat and 224 proteins in mouse, for a total of 395 proteins in both species combined. These proteins included many proteins with transporter activity (73 proteins), cell adhesion proteins (47 proteins), and transmembrane signal receptors (31 proteins). To identify proteins that are enriched in vessels relative to the entire brain, we established a vessel-enrichment score and showed that proteins with a high vessel-enrichment score are involved in vascular development functions, binding to integrins, and cell adhesion. Using publicly-available single-cell RNAseq data, we show that the proteins identified by in vivo glycocapture were more likely to be detected by scRNAseq in endothelial cells than in any other cell type. Furthermore, nearly 50% of the genes encoding cell-surface proteins that were detected by scRNAseq in endothelial cells were also identified by in vivo glycocapture. CONCLUSIONS The proteins identified by in vivo glycocapture in this work represent the most complete and specific profiling of proteins on the luminal BBB surface to date. The identified proteins reflect possible targets for the development of antibodies to improve the crossing of therapeutic proteins into the brain and will contribute to our further understanding of BBB transport mechanisms.
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Affiliation(s)
- Tammy-Lynn Tremblay
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Wael Alata
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
- Biology Program, New York University Abu Dhabi, Saadiyat Island Campus, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Jacqueline Slinn
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Ewa Baumann
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Christie E Delaney
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Maria Moreno
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Arsalan S Haqqani
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Danica B Stanimirovic
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Jennifer J Hill
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada.
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Tremblay TL, Fauteux F, Callaghan D, Hill JJ. Cell surface profiling of cultured cells by direct hydrazide capture of oxidized glycoproteins. MethodsX 2023; 11:102349. [PMID: 37680365 PMCID: PMC10480300 DOI: 10.1016/j.mex.2023.102349] [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: 06/08/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Glycoproteins are a particularly interesting subset of the cellular proteome as a high proportion of proteins present on the extracellular cell surface are glycosylated. These cell surface proteins are ideal targets for biologic drug therapies or for diagnostics tests. Here, we describe a modification of the well-described Cell Surface Capture (CSC) method for the selective isolation and identification of cell surface glycoproteins that contain N-linked carbohydrates. This modification, which we refer to as Direct Cell Surface Capture (D-CSC), is based on oxidation of cell surface glycans on intact cells, followed by direct conjugation of the oxidized oligosaccharides to a solid support using hydrazide chemistry, with no biotinylation step. As a proof-of-principle, we applied D-CSC to the analysis of cell surface membrane proteins of three adherent cancer cell lines (A549, OVCAR3, and U87MG) and compared our results to those published using the well-established Cell Surface Capture (CSC) method, demonstrating comparable selectivity for cell surface proteins. •A method enabling the identification of cell surface proteins from cells in culture is described.•Application of this method to profile the cell surface on three different cancer cell lines is included.
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Affiliation(s)
- Tammy-Lynn Tremblay
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A0R6, Canada
| | - François Fauteux
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A0R6, Canada
| | - Deborah Callaghan
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A0R6, Canada
| | - Jennifer J. Hill
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A0R6, Canada
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4
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Desai M, Singh A, Pham D, Chowdhury SR, Sun B. Discovery and Visualization of the Hidden Relationships among N-Glycosylation, Disulfide Bonds, and Membrane Topology. Int J Mol Sci 2023; 24:16182. [PMID: 38003370 PMCID: PMC10671238 DOI: 10.3390/ijms242216182] [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: 10/06/2023] [Revised: 11/02/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Membrane proteins (MPs) are functionally important but structurally complex. In particular, MPs often carry three structural features, i.e., transmembrane domains (TMs), disulfide bonds (SSs), and N-glycosylation (N-GLYCO). All three features have been intensively studied; however, how the three features potentially correlate has been less addressed in the literature. With the growing accuracy from computational prediction, we used publicly available information on SSs and N-GLYCO and analyzed the potential relationships among post-translational modifications (PTMs) and the predicted membrane topology in the human proteome. Our results suggested a very close relationship between SSs and N-GLYCO that behaved similarly, whereas a complementary relation between the TMs and the two PTMs was also revealed, in which the high SS and/or N-GLYCO presence is often accompanied by a low TM occurrence in a protein. Furthermore, the occurrence of SSs and N-GLYCO in a protein heavily relies on the protein length; however, TMs seem not to possess such length dependence. Finally, SSs exhibits larger potential dynamics than N-GLYCO, which is confined by the presence of sequons. The special classes of proteins possessing extreme or unique patterns of the three structural features are comprehensively identified, and their structural features and potential dynamics help to identify their susceptibility to different physiological and pathophysiological insults, which could help drug development and protein engineering.
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Affiliation(s)
- Manthan Desai
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (A.S.); (D.P.); (S.R.C.)
| | - Amritpal Singh
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (A.S.); (D.P.); (S.R.C.)
| | - David Pham
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (A.S.); (D.P.); (S.R.C.)
| | - Syed Rafid Chowdhury
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (A.S.); (D.P.); (S.R.C.)
| | - Bingyun Sun
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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5
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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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6
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Baboo S, Diedrich JK, Martínez-Bartolomé S, Wang X, Schiffner T, Groschel B, Schief WR, Paulson JC, Yates JR. DeGlyPHER: Highly sensitive site-specific analysis of N-linked glycans on proteins. Methods Enzymol 2022; 682:137-185. [PMID: 36948700 PMCID: PMC11032187 DOI: 10.1016/bs.mie.2022.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Traditional mass spectrometry-based glycoproteomic approaches have been widely used for site-specific N-glycoform analysis, but a large amount of starting material is needed to obtain sampling that is representative of the vast diversity of N-glycans on glycoproteins. These methods also often include a complicated workflow and very challenging data analysis. These limitations have prevented glycoproteomics from being adapted to high-throughput platforms, and the sensitivity of the analysis is currently inadequate for elucidating N-glycan heterogeneity in clinical samples. Heavily glycosylated spike proteins of enveloped viruses, recombinantly expressed as potential vaccines, are prime targets for glycoproteomic analysis. Since the immunogenicity of spike proteins may be impacted by their glycosylation patterns, site-specific analysis of N-glycoforms provides critical information for vaccine design. Using recombinantly expressed soluble HIV Env trimer, we describe DeGlyPHER, a modification of our previously reported sequential deglycosylation strategy to yield a "single-pot" process. DeGlyPHER is an ultrasensitive, simple, rapid, robust, and efficient approach for site-specific analysis of protein N-glycoforms, that we developed for analysis of limited quantities of glycoproteins.
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Affiliation(s)
- Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States.
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | | | - Xiaoning Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA, United States
| | - Bettina Groschel
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA, United States
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States.
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7
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Sun B, Lorang C, Qin S, Zhang Y, Liu K, Li G, Sun Z, Francke A, Utleg AG, Hu Z, Wang K, Moritz RL, Hood L. Mouse Organ-Specific Proteins and Functions. Cells 2021; 10:cells10123449. [PMID: 34943957 PMCID: PMC8700158 DOI: 10.3390/cells10123449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/29/2021] [Accepted: 12/04/2021] [Indexed: 11/19/2022] Open
Abstract
Organ-specific proteins (OSPs) possess great medical potential both in clinics and in biomedical research. Applications of them—such as alanine transaminase, aspartate transaminase, and troponins—in clinics have raised certain concerns of their organ specificity. The dynamics and diversity of protein expression in heterogeneous human populations are well known, yet their effects on OSPs are less addressed. Here, we used mice as a model and implemented a breadth study to examine the panorgan proteome for potential variations in organ specificity in different genetic backgrounds. Using reasonable resources, we generated panorgan proteomes of four in-bred mouse strains. The results revealed a large diversity that was more profound among OSPs than among proteomes overall. We defined a robustness score to quantify such variation and derived three sets of OSPs with different stringencies. In the meantime, we found that the enriched biological functions of OSPs are also organ-specific and are sensitive and useful to assess the quality of OSPs. We hope our breadth study can open doors to explore the molecular diversity and dynamics of organ specificity at the protein level.
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Affiliation(s)
- Bingyun Sun
- Departments of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada; (Y.Z.); (K.L.)
- Departments of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada
- Correspondence: (B.S.); (L.H.)
| | - Cynthia Lorang
- Institute for Systems Biology, Seattle, WA 98109, USA; (C.L.); (S.Q.); (G.L.); (Z.S.); (A.G.U.); (Z.H.); (K.W.); (R.L.M.)
| | - Shizhen Qin
- Institute for Systems Biology, Seattle, WA 98109, USA; (C.L.); (S.Q.); (G.L.); (Z.S.); (A.G.U.); (Z.H.); (K.W.); (R.L.M.)
| | - Yijuan Zhang
- Departments of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada; (Y.Z.); (K.L.)
| | - Ken Liu
- Departments of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada; (Y.Z.); (K.L.)
| | - Gray Li
- Institute for Systems Biology, Seattle, WA 98109, USA; (C.L.); (S.Q.); (G.L.); (Z.S.); (A.G.U.); (Z.H.); (K.W.); (R.L.M.)
| | - Zhi Sun
- Institute for Systems Biology, Seattle, WA 98109, USA; (C.L.); (S.Q.); (G.L.); (Z.S.); (A.G.U.); (Z.H.); (K.W.); (R.L.M.)
| | - Ashley Francke
- Departments of Computing Science, Simon Fraser University, Burnaby, BC V5A1S6, Canada;
| | - Angelita G. Utleg
- Institute for Systems Biology, Seattle, WA 98109, USA; (C.L.); (S.Q.); (G.L.); (Z.S.); (A.G.U.); (Z.H.); (K.W.); (R.L.M.)
| | - Zhiyuan Hu
- Institute for Systems Biology, Seattle, WA 98109, USA; (C.L.); (S.Q.); (G.L.); (Z.S.); (A.G.U.); (Z.H.); (K.W.); (R.L.M.)
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98109, USA; (C.L.); (S.Q.); (G.L.); (Z.S.); (A.G.U.); (Z.H.); (K.W.); (R.L.M.)
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, WA 98109, USA; (C.L.); (S.Q.); (G.L.); (Z.S.); (A.G.U.); (Z.H.); (K.W.); (R.L.M.)
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, USA; (C.L.); (S.Q.); (G.L.); (Z.S.); (A.G.U.); (Z.H.); (K.W.); (R.L.M.)
- Correspondence: (B.S.); (L.H.)
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Abstract
Mucin-domain glycoproteins comprise a class of proteins whose densely O-glycosylated mucin domains adopt a secondary structure with unique biophysical and biochemical properties. The canonical family of mucins is well-known to be involved in various diseases, especially cancer. Despite this, very little is known about the site-specific molecular structures and biological activities of mucins, in part because they are extremely challenging to study by mass spectrometry (MS). Here, we summarize recent advancements toward this goal, with a particular focus on mucin-domain glycoproteins as opposed to general O-glycoproteins. We summarize proteolytic digestion techniques, enrichment strategies, MS fragmentation, and intact analysis, as well as new bioinformatic platforms. In particular, we highlight mucin directed technologies such as mucin-selective proteases, tunable mucin platforms, and a mucinomics strategy to enrich mucin-domain glycoproteins from complex samples. Finally, we provide examples of targeted mucin-domain glycoproteomics that combine these techniques in comprehensive site-specific analyses of proteins. Overall, this Review summarizes the methods, challenges, and new opportunities associated with studying enigmatic mucin domains.
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Affiliation(s)
- Valentina Rangel-Angarita
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
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9
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Gutierrez-Reyes CD, Jiang P, Atashi M, Bennett A, Yu A, Peng W, Zhong J, Mechref Y. Advances in mass spectrometry-based glycoproteomics: An update covering the period 2017-2021. Electrophoresis 2021; 43:370-387. [PMID: 34614238 DOI: 10.1002/elps.202100188] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/30/2021] [Accepted: 09/25/2021] [Indexed: 12/23/2022]
Abstract
Protein glycosylation is one of the most common posttranslational modifications, and plays an essential role in a wide range of biological processes such as immune response, intercellular signaling, inflammation, host-pathogen interaction, and protein stability. Glycoproteomics is a proteomics subfield dedicated to identifying and characterizing the glycans and glycoproteins in a given cell or tissue. Aberrant glycosylation has been associated with various diseases such as Alzheimer's disease, viral infections, inflammation, immune deficiencies, congenital disorders, and cancers. However, glycoproteomic analysis remains challenging because of the low abundance, site-specific heterogeneity, and poor ionization efficiency of glycopeptides during LC-MS analyses. Therefore, the development of sensitive and accurate approaches to efficiently characterize protein glycosylation is crucial. Methods such as metabolic labeling, enrichment, and derivatization of glycopeptides, coupled with different mass spectrometry techniques and bioinformatics tools, have been developed to achieve sophisticated levels of quantitative and qualitative analyses of glycoproteins. This review attempts to update the recent developments in the field of glycoproteomics reported between 2017 and 2021.
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Affiliation(s)
| | - Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Andrew Bennett
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Jieqiang Zhong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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10
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Balli OI, Uversky VN, Durdagi S, Coskuner-Weber O. Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective. Proteins 2021; 90:322-339. [PMID: 34549826 DOI: 10.1002/prot.26242] [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: 06/23/2021] [Revised: 08/24/2021] [Accepted: 09/07/2021] [Indexed: 11/08/2022]
Abstract
Experimenters face challenges and limitations while analyzing glycoproteins due to their high flexibility, stereochemistry, anisotropic effects, and hydration phenomena. Computational studies complement experiments and have been used in characterization of the structural properties of glycoproteins. However, recent investigations revealed that computational studies face significant challenges as well. Here, we introduce and discuss some of these challenges and weaknesses in the investigations of glycoproteins. We also present requirements of future developments in computational biochemistry and computational biology areas that could be necessary for providing more accurate structural property analyses of glycoproteins using computational tools. Further theoretical strategies that need to be and can be developed are discussed herein.
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Affiliation(s)
- Oyku Irem Balli
- Molecular Biotechnology, Turkish-German University, Istanbul, Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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11
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Zhao Q, Zhang Z, Li J, Xu F, Zhang B, Liu M, Liu Y, Chen H, Yang J, Zhang J. Lysine Acetylome Study of Human Hepatocellular Carcinoma Tissues for Biomarkers and Therapeutic Targets Discovery. Front Genet 2020; 11:572663. [PMID: 33093847 PMCID: PMC7527632 DOI: 10.3389/fgene.2020.572663] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
Lysine acetylation is a vital post-translational modification (PTM) of proteins, which plays an important role in cancer development. In healthy human liver tissues, multiple non-histone proteins were identified with acetylation modification, however, the role of acetylated proteins in hepatocellular carcinoma (HCC) development remains largely unknown. Here we performed a quantitative acetylome study of tumor and normal liver tissues from HCC patients. Overall, 598 lysine acetylation sites in 325 proteins were quantified, and almost 59% of their acetylation levels were significantly changed. The differentially acetylated proteins mainly consisted of non-histone proteins located in mitochondria and cytoplasm, which accounted for 42% and 24%, respectively. Bioinformatics analysis showed that differentially acetylated proteins were enriched in metabolism, oxidative stress, and signal transduction processes. In tumor tissues, 278 lysine sites in 189 proteins showed decreased acetylation levels, which occupied 98% of differentially acetylated proteins. Moreover, we collected twenty pairs of tumor and normal liver tissues from HCC male patients, and found that expression levels of SIRT1 (p = 0.002), SIRT2 (p = 0.01), and SIRT4 (p = 0.045) were significantly up-regulated in tumor tissues. Over-expression of possibly accounted for the widespread deacetylation of non-histone proteins identified in HCC tumor tissues, which could serve as promising predictors of HCC. Taken together, our work illustrates abundant differentially acetylated proteins in HCC tumor tissues, and offered insights into the role of lysine acetylation in HCC development. It provided potential biomarker and drug target candidates for clinical HCC diagnosis and treatment.
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Affiliation(s)
- Qianwei Zhao
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory for Pharmacology of Liver Diseases, Zhengzhou University, Zhengzhou, China
| | - Zhendong Zhang
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jinxia Li
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Fang Xu
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Bingxia Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Mengduan Liu
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yixian Liu
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Huiping Chen
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Junxia Yang
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jintao Zhang
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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12
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Magnetic metal-organic frameworks containing abundant carboxylic groups for highly effective enrichment of glycopeptides in breast cancer serum. Talanta 2019; 204:446-454. [DOI: 10.1016/j.talanta.2019.06.037] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/03/2019] [Accepted: 06/09/2019] [Indexed: 12/14/2022]
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13
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Sun S, Hu Y, Ao M, Shah P, Chen J, Yang W, Jia X, Tian Y, Thomas S, Zhang H. N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping. Clin Proteomics 2019; 16:35. [PMID: 31516400 PMCID: PMC6731604 DOI: 10.1186/s12014-019-9254-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND N-linked glycoprotein is a highly interesting class of proteins for clinical and biological research. The large-scale characterization of N-linked glycoproteins accomplished by mass spectrometry-based glycoproteomics has provided valuable insights into the interdependence of glycoprotein structure and protein function. However, these studies focused mainly on the analysis of specific sample type, and lack the integration of glycoproteomic data from different tissues, body fluids or cell types. METHODS In this study, we collected the human glycosite-containing peptides identified through their de-glycosylated forms by mass spectrometry from over 100 publications and unpublished datasets generated from our laboratory. A database resource termed N-GlycositeAtlas was created and further used for the distribution analyses of glycoproteins among different human cells, tissues and body fluids. Finally, a web interface of N-GlycositeAtlas was created to maximize the utility and value of the database. RESULTS The N-GlycositeAtlas database contains more than 30,000 glycosite-containing peptides (representing > 14,000 N-glycosylation sites) from more than 7200 N-glycoproteins from different biological sources including human-derived tissues, body fluids and cell lines from over 100 studies. CONCLUSIONS The entire human N-glycoproteome database as well as 22 sub-databases associated with individual tissues or body fluids can be downloaded from the N-GlycositeAtlas website at http://nglycositeatlas.biomarkercenter.org.
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Affiliation(s)
- Shisheng Sun
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
- College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Minghui Ao
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Punit Shah
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Jing Chen
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Weiming Yang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Xingwang Jia
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Yuan Tian
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Stefani Thomas
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
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14
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Chen Z, Huang J, Li L. Recent advances in mass spectrometry (MS)-based glycoproteomics in complex biological samples. Trends Analyt Chem 2019; 118:880-892. [PMID: 31579312 PMCID: PMC6774629 DOI: 10.1016/j.trac.2018.10.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein glycosylation plays a key role in various biological processes and disease-related pathological progression. Mass spectrometry (MS)-based glycoproteomics is a powerful approach that provides a system-wide profiling of the glycoproteome in a high-throughput manner. There have been numerous significant technological advances in this field, including improved glycopeptide enrichment, hybrid fragmentation techniques, emerging specialized software packages, and effective quantitation strategies, as well as more dedicated workflows. With increasingly sophisticated glycoproteomics tools on hand, researchers have extensively adapted this approach to explore different biological systems both in terms of in-depth glycoproteome profiling and comparative glycoproteome analysis. Quantitative glycoproteomics enables researchers to discover novel glycosylation-based biomarkers in various diseases with potential to offer better sensitivity and specificity for disease diagnosis. In this review, we present recent methodological developments in MS-based glycoproteomics and highlight its utility and applications in answering various questions in complex biological systems.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
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15
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Expanding our understanding of the role of microbial glycoproteomes through high-throughput mass spectrometry approaches. Glycoconj J 2019; 36:259-266. [DOI: 10.1007/s10719-019-09875-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/18/2019] [Accepted: 05/24/2019] [Indexed: 01/14/2023]
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16
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Sun N, Wang Z, Wang J, Chen H, Wu H, Shen S, Deng C. Hydrophilic tripeptide combined with magnetic titania as a multipurpose platform for universal enrichment of phospho- and glycopeptides. J Chromatogr A 2019; 1595:1-10. [DOI: 10.1016/j.chroma.2019.02.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 12/11/2022]
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17
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Capture and Analysis of Cell Surface N-Glycans by Hydrazide-Modified Magnetic Beads and CE-LIF. Chromatographia 2019. [DOI: 10.1007/s10337-019-03742-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Zhang L, Ma S, Chen Y, Wang Y, Ou J, Uyama H, Ye M. Facile Fabrication of Biomimetic Chitosan Membrane with Honeycomb-Like Structure for Enrichment of Glycosylated Peptides. Anal Chem 2019; 91:2985-2993. [PMID: 30673210 DOI: 10.1021/acs.analchem.8b05215] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the study of glycoproteomics with mass spectrometry, certain pretreatments of samples are required for eliminating the interference of nonglycopeptides and improving the efficiency of glycopeptides detection. Although hydrophilic interaction chromatography (HILIC) has been developed for enrichment of glycosylated peptides, a plethora of hydrophilic materials always suffered from large steric hindrance, great cost, and difficulty with modifications of high-density hydrophilic groups. In this work, a 1 mm thick biomimetic honeycomb chitosan membrane (BHCM) with honeycomb-like accessible macropores was directly prepared by the freeze-casting method as an adsorbent for HILIC. The N-glycopeptides from trypsin digests of immunoglobulin G (IgG), mixture of IgG and bovine serum albumin (BSA), and serum proteins were enriched using this material and compared with a commercial material ZIC-HILIC. The biomimetic membrane could identify as many as 32 N-glycopeptides from the IgG digest, exhibiting high sensitivity (about 50 fmol) and a wide scope for glycopeptide enrichment. A molar ratio of IgG trypsin digest to bovine serum albumin trypsin digest as low as 1/500 verified the outstanding specificity and efficiency for glycopeptide enrichment. In addition, 270 unique N-glycosylation sites of 400 unique glycopeptides from 146 glycosylated proteins were identified from the triplicate analysis of 2 μL human serum. Furthermore, 48 unique O-glycosylation sites of 278 unique O-glycopeptides were identified from the triplicate analysis of 30 μg deglycosylated fetuin digest. These results indicated that the chitosan-based membrane prepared in this work had great potential for pretreatment of samples in glycoproteomics.
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Affiliation(s)
- Luwei Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education , Northwest University , Xi'an , Shaanxi 710127 , China.,CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Shujuan Ma
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education , Northwest University , Xi'an , Shaanxi 710127 , China.,CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Yao Chen
- 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
| | - Yan Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education , Northwest University , Xi'an , Shaanxi 710127 , China.,CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Junjie Ou
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Hiroshi Uyama
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education , Northwest University , Xi'an , Shaanxi 710127 , China.,Department of Applied Chemistry, Graduate School of Engineering , Osaka University , Suita 565-0871 , Japan
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
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19
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Yu A, Zhao J, Peng W, Banazadeh A, Williamson SD, Goli M, Huang Y, Mechref Y. Advances in mass spectrometry-based glycoproteomics. Electrophoresis 2018; 39:3104-3122. [PMID: 30203847 PMCID: PMC6375712 DOI: 10.1002/elps.201800272] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/03/2018] [Accepted: 09/03/2018] [Indexed: 12/13/2022]
Abstract
Protein glycosylation, an important PTM, plays an essential role in a wide range of biological processes such as immune response, intercellular signaling, inflammation, and host-pathogen interaction. Aberrant glycosylation has been correlated with various diseases. However, studying protein glycosylation remains challenging because of low abundance, microheterogeneities of glycosylation sites, and poor ionization efficiency of glycopeptides. Therefore, the development of sensitive and accurate approaches to characterize protein glycosylation is crucial. The identification and characterization of protein glycosylation by MS is referred to as the field of glycoproteomics. Methods such as enrichment, metabolic labeling, and derivatization of glycopeptides in conjunction with different MS techniques and bioinformatics tools, have been developed to achieve an unequivocal quantitative and qualitative characterization of glycoproteins. This review summarizes the recent developments in the field of glycoproteomics over the past 6 years (2012 to 2018).
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Affiliation(s)
- Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Seth D. Williamson
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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20
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Smith J, Mittermayr S, Váradi C, Bones J. Quantitative glycomics using liquid phase separations coupled to mass spectrometry. Analyst 2018; 142:700-720. [PMID: 28170017 DOI: 10.1039/c6an02715f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Post-translational modification of proteins by the attachment of glycans is governed by a variety of highly specific enzymes and is associated with fundamental impacts on the parent protein's physical, chemical and biological properties. The inherent connection between cellular physiology and specific glycosylation patterns has been shown to offer potential for diagnostic and prognostic monitoring of altered glycosylation in the disease state. Conversely, glycoprotein based biopharmaceuticals have emerged as dominant therapeutic strategies in the treatment of intricate diseases. Glycosylation present on these biopharmaceuticals represents a major critical quality attribute with impacts on both pharmacokinetics and pharmacodynamics. The structural variety of glycans, based upon their non-template driven assembly, poses a significant analytical challenge for both qualitative and quantitative analysis. Labile monosaccharide constituents, isomeric species and often low sample availability from biological sources necessitates meticulous sample handling, ultra-high-resolution analytical separation and sensitive detection techniques, respectively. In this article a critical review of analytical quantitation approaches using liquid phase separations coupled to mass spectrometry for released glycans of biopharmaceutical and biomedical significance is presented. Considerations associated with sample derivatisation strategies, ionisation, relative quantitation through isotopic as well as isobaric labelling, metabolic/enzymatic incorporation and targeted analysis are all thoroughly discussed.
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Affiliation(s)
- Josh Smith
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland. and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590, Ireland
| | - Stefan Mittermayr
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland.
| | - Csaba Váradi
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland.
| | - Jonathan Bones
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland. and School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1 W8, Ireland
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21
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Cao L, Diedrich JK, Ma Y, Wang N, Pauthner M, Park SKR, Delahunty CM, McLellan JS, Burton DR, Yates JR, Paulson JC. Global site-specific analysis of glycoprotein N-glycan processing. Nat Protoc 2018; 13:1196-1212. [PMID: 29725121 PMCID: PMC5941933 DOI: 10.1038/nprot.2018.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
N-glycans contribute to the folding, stability and functions of the proteins they decorate. They are produced by transfer of the glycan precursor to the sequon Asn-X-Thr/Ser, followed by enzymatic trimming to a high-mannose-type core and sequential addition of monosaccharides to generate complex-type and hybrid glycans. This process, mediated by the concerted action of multiple enzymes, produces a mixture of related glycoforms at each glycosite, making analysis of glycosylation difficult. To address this analytical challenge, we developed a robust semiquantitative mass spectrometry (MS)-based method that determines the degree of glycan occupancy at each glycosite and the proportion of N-glycans processed from high-mannose type to complex type. It is applicable to virtually any glycoprotein, and a complete analysis can be conducted with 30 μg of protein. Here, we provide a detailed description of the method that includes procedures for (i) proteolytic digestion of glycoprotein(s) with specific and nonspecific proteases; (ii) denaturation of proteases by heating; (iii) sequential treatment of the glycopeptide mixture with two endoglycosidases, Endo H and PNGase F, to create unique mass signatures for the three glycosylation states; (iv) LC-MS/MS analysis; and (v) data analysis for identification and quantitation of peptides for the three glycosylation states. Full coverage of site-specific glycosylation of glycoproteins is achieved, with up to thousands of high-confidence spectra hits for each glycosite. The protocol can be performed by an experienced technician or student/postdoc with basic skills for proteomics experiments and takes ∼7 d to complete.
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Affiliation(s)
- Liwei Cao
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery and IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Yuanhui Ma
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Nianshuang Wang
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Matthias Pauthner
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery and IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Sung-Kyu Robin Park
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Claire M Delahunty
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Jason S McLellan
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Dennis R Burton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery and IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery and IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
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22
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Zhang D, Wang M, Guo Z, Guo P, Chen X, Wang J. Specific Isolation of Glycoproteins with Mesoporous Zirconia-Polyoxometalate Hybrid. Proteomics 2018; 18:e1700381. [DOI: 10.1002/pmic.201700381] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 01/01/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Dandan Zhang
- Research Center for Analytical Sciences; Northeastern University; Shenyang P. R. China
| | - Mengmeng Wang
- Research Center for Analytical Sciences; Northeastern University; Shenyang P. R. China
| | - Zhiyong Guo
- Research Center for Analytical Sciences; Northeastern University; Shenyang P. R. China
| | - Pengfei Guo
- Research Center for Analytical Sciences; Northeastern University; Shenyang P. R. China
| | - Xuwei Chen
- Research Center for Analytical Sciences; Northeastern University; Shenyang P. R. China
| | - Jianhua Wang
- Research Center for Analytical Sciences; Northeastern University; Shenyang P. R. China
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23
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Biotin-transfer from a trifunctional crosslinker for identification of cell surface receptors of soluble protein ligands. Sci Rep 2017; 7:46574. [PMID: 28422167 PMCID: PMC5396193 DOI: 10.1038/srep46574] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/17/2017] [Indexed: 11/09/2022] Open
Abstract
Here we describe a novel crosslinker and its application as a biotin-transfer reagent to identify cell surface receptors of soluble protein ligands on live cells. This crosslinker contains three functional groups: an aldehyde-reactive aminooxy group, a sulfhydryl, and a biotin (ASB). It is readily synthesized via a 3-step addition reaction using standard solid-phase peptide synthesis methods and commercially available intermediates, allowing access to laboratories without specialized synthetic chemistry capabilities. For the biotin-transfer method, ASB is linked to a protein ligand through the sulfhydryl group in a two-step process that allows the introduction of a disulfide bond between the ligand and the crosslinker. Incubation of the labelled ligand with oxidized live cells leads to the formation of crosslinks with aldehyde-containing glycans on the cell surface receptor. Subsequent reduction of the disulfide bond results in biotin transfer from the ligand to the cell surface receptor. Protein biotinylation that is mediated by ligand binding to its receptor is differentiated from background biotinylation events by comparison with a similarly labelled control protein using comparative proteomic mass spectrometry to quantify streptavidin-bound proteins. Using this method, we successfully identified the cell surface receptors of a peptide hormone, a monoclonal antibody, and a single-domain antibody-Fc fusion construct.
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24
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Abstract
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.
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Affiliation(s)
- Krishnan K. Palaniappan
- Verily Life Sciences, 269 East Grand Ave., South San Francisco, California 94080, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
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25
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Li X, Xiong Y, Qing G, Jiang G, Li X, Sun T, Liang X. Bioinspired Saccharide-Saccharide Interaction and Smart Polymer for Specific Enrichment of Sialylated Glycopeptides. ACS APPLIED MATERIALS & INTERFACES 2016; 8:13294-13302. [PMID: 27172767 DOI: 10.1021/acsami.6b03104] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Abnormal sialylation of proteins is highly associated with many major diseases, such as cancers and neurodegenerative diseases. However, this study is challenging owing to the difficulty in enriching trace sialylated glycopeptides (SGs) from highly complex biosamples. The key to solving this problem relies strongly on the design of novel SG receptors to capture the sialic acid (SA) moieties in a specific and tunable manner. Inspired by the saccharide-saccharide interactions in life systems, here we introduce saccharide-based SG receptors into this study. Allose (a monosaccharide) displays specific and pH-sensitive binding toward SAs. Integrating allose units into a polyacrylamide chain generates a saccharide-responsive smart copolymer (SRSC). Such design significantly improves the selectivity of SA binding; meanwhile, this binding can be intelligently triggered in a large extent by solution polarity and pH. As a result, SRSC exhibits high-performance enrichment capacity toward SGs, even under 500-fold interference of bovine serum albumins digests, which is notably higher than conventional materials. In real biosamples of HeLa cell lysates, 180 sialylated glycosylation sites (SGSs) have been identified using SRSC. This is apparently superior to those obtained by SA-binding lectins including WGA (18 SGSs) and SNA (22 SGSs). Furthermore, lactose displays good chemoselectivity toward diverse disaccharides, which indicated the good potential of lactose-based material in glycan discrimination. Subsequently, the lactose-based SRSC facilitates the stepwise isolation of O-linked or N-linked SGs with the same peptide sequence but varied glycans by CH3CN/H2O gradients. This study opens a new avenue for next generation of glycopeptide enrichment materials.
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Affiliation(s)
- Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yuting Xiong
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Guangyan Qing
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Ge Jiang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xianqin Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, P. R. China
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26
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Chen R, Zou H, Figeys D. Detergent-Assisted Glycoprotein Capture: A Versatile Tool for In-Depth N-Glycoproteome Analysis. J Proteome Res 2016; 15:2080-6. [PMID: 27147131 DOI: 10.1021/acs.jproteome.6b00056] [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] [Indexed: 11/30/2022]
Abstract
Large-scale N-glycoproteome studies have been hindered by poor solubility of hydrophobic membrane proteins and the complexity of proteome samples. Herein, we developed a detergent-assisted glycoprotein capture method to reduce these issues by conducting hydrazide chemistry-based glycoprotein capture in the presence of strong detergents such as sodium dodecyl sulfate and Triton X-100. The strong detergents helped to solubilize hydrophobic membrane proteins and then increased the access of hydrazide groups to oxidized glycoproteins, thus increasing the coverage of the N-glycoproteome. Compared with the conventional glycopeptide capture method, the detergent-assisted glycoprotein capture approach nearly doubled the number of N-glycosylation sites identified from HEK 293T cells with improved specificity. Application of this approach in the larger scale N-glycoproteomics analysis of the HEK 293T cell membrane led to the identification of 2253 unique N-glycosites from 953 proteins. Furthermore, the application of this approach to human serum resulted in the identification of 850 N-glycosylation sites without any immunodepletion or fractionation. Overall, the detergent-assisted glycoprotein capture method simplified the capture process, and it increased the number of sites observed on both hydrophobic membrane proteins and hydrophilic secreted proteins.
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Affiliation(s)
- Rui Chen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology and Department of Chemistry and Biomolecular Sciences, University of Ottawa , 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Hanfa Zou
- Key Lab of Separation Science for Analytical Chemistry, National Chromatography R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Science , Dalian 116023, China
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology and Department of Chemistry and Biomolecular Sciences, University of Ottawa , 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
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27
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Identification, Quantification, and Site Localization of Protein Posttranslational Modifications via Mass Spectrometry-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:345-382. [PMID: 27975226 DOI: 10.1007/978-3-319-41448-5_17] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Posttranslational modifications (PTMs) are important biochemical processes for regulating various signaling pathways and determining specific cell fate. Mass spectrometry (MS)-based proteomics has been developed extensively in the past decade and is becoming the standard approach for systematic characterization of different PTMs on a global scale. In this chapter, we will explain the biological importance of various PTMs, summarize key innovations in PTMs enrichment strategies, high-performance liquid chromatography (HPLC)-based fractionation approaches, mass spectrometry detection methods, and lastly bioinformatic tools for PTMs related data analysis. With great effort in recent years by the proteomics community, highly efficient enriching methods and comprehensive resources have been developed. This chapter will specifically focus on five major types of PTMs; phosphorylation, glycosylation, ubiquitination/sumosylation, acetylation, and methylation.
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Huang J, Wan H, Yao Y, Li J, Cheng K, Mao J, Chen J, Wang Y, Qin H, Zhang W, Ye M, Zou H. Highly Efficient Release of Glycopeptides from Hydrazide Beads by Hydroxylamine Assisted PNGase F Deglycosylation for N-Glycoproteome Analysis. Anal Chem 2015; 87:10199-204. [DOI: 10.1021/acs.analchem.5b02669] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Junfeng Huang
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- University of Chinese Academy of Sciences, Beijing, China, 100049
| | - Hao Wan
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- Shanghai
Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Yating Yao
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- University of Chinese Academy of Sciences, Beijing, China, 100049
| | - Jinan Li
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- University of Chinese Academy of Sciences, Beijing, China, 100049
| | - Kai Cheng
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
| | - Jiawei Mao
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- University of Chinese Academy of Sciences, Beijing, China, 100049
| | - Jin Chen
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- University of Chinese Academy of Sciences, Beijing, China, 100049
| | - Yan Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- University of Chinese Academy of Sciences, Beijing, China, 100049
| | - Hongqiang Qin
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
| | - Weibing Zhang
- Shanghai
Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Mingliang Ye
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
| | - Hanfa Zou
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
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29
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Yan Q, Tang S, Tan Z, Han X, Zhou C, Kang J, Wang M. Proteomic Analysis of Isolated Plasma Membrane Fractions from the Mammary Gland in Lactating Cows. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:7388-7398. [PMID: 26237224 DOI: 10.1021/acs.jafc.5b02231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The mammary gland of dairy cows is a formidable lipid-synthesizing machine for lactation. This unique function depends on the activities of plasma membrane (PM) proteins in mammary cells. Little information is known about the expression profiles of PM proteins and their functions during the lactating process. This study investigated the proteome map of PM fractions of mammary gland in lactating cows using 1D-Gel-LC-MS/MS and identified 872 nonredundant proteins with 141 unknown proteins, wherein 215 were PM-associated proteins. Most of the PM-associated proteins were binding, transport, and catalytic proteins such as annexin proteins, heat shock proteins, integrins, RAS oncogene family members, and S100 calcium binding proteins. The PM-associated pathways such as caveolae-mediated endocytosis, leukocyte extravasation, aldosterone signaling in epithelial cells, and remodeling of epithelial adherens junctions were also significantly over-represented. Proteomic analysis revealed the characteristics and predicted functions of PM proteins isolated from the lactating bovine mammary gland. These results further provide experimental evidence for the presence of many proteins predicted in the annotated bovine genome. The data generated here also provide a reference for the PM-related functional research in the mammary gland of lactating cows.
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Affiliation(s)
- Qiongxian Yan
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
| | - Shaoxun Tang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
| | - Zhiliang Tan
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
| | - Xuefeng Han
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
| | - Chuanshe Zhou
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
| | - Jinhe Kang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
| | - Min Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
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30
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Kim EJ. The Utilities of Chemical Reactions and Molecular Tools for O-GlcNAc Proteomic Studies. Chembiochem 2015; 16:1397-409. [PMID: 26096757 DOI: 10.1002/cbic.201500183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 11/05/2022]
Abstract
The post-translational modification of nuclear and cytoplasmic proteins with O-linked β-N-acetylglucosamine (O-GlcNAc) is involved in a wide variety of cellular processes and is associated with the pathological progression of chronic diseases. Considering its emerging biological significance, systematic identification, site mapping, and quantification of O-GlcNAc proteins are essential and have led to the development of several approaches for O-GlcNAc protein profiling. This minireview mainly focuses on the various useful chemical reactions and molecular tools with detailed reaction mechanisms widely adopted for O-GlcNAc protein/peptide enrichment and its quantification for comprehensive O-GlcNAc protein profiling.
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Affiliation(s)
- Eun Ju Kim
- Department of Science Education-Chemistry Major, Daegu University, Gyeongsan-si, GyeongBuk 712-714 (Republic of Korea). ,
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31
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Huang J, Qin H, Sun Z, Huang G, Mao J, Cheng K, Zhang Z, Wan H, Yao Y, Dong J, Zhu J, Wang F, Ye M, Zou H. A peptide N-terminal protection strategy for comprehensive glycoproteome analysis using hydrazide chemistry based method. Sci Rep 2015; 5:10164. [PMID: 25959593 PMCID: PMC4426672 DOI: 10.1038/srep10164] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/01/2015] [Indexed: 01/01/2023] Open
Abstract
Enrichment of glycopeptides by hydrazide chemistry (HC) is a popular method for glycoproteomics analysis. However, possible side reactions of peptide backbones during the glycan oxidation in this method have not been comprehensively studied. Here, we developed a proteomics approach to locate such side reactions and found several types of the side reactions that could seriously compromise the performance of glycoproteomics analysis. Particularly, the HC method failed to identify N-terminal Ser/Thr glycopeptides because the oxidation of vicinal amino alcohol on these peptides generates aldehyde groups and after they are covalently coupled to HC beads, these peptides cannot be released by PNGase F for identification. To overcome this drawback, we apply a peptide N-terminal protection strategy in which primary amine groups on peptides are chemically blocked via dimethyl labeling, thus the vicinal amino alcohols on peptide N-termini are eliminated. Our results showed that this strategy successfully prevented the oxidation of peptide N-termini and significantly improved the coverage of glycoproteome.
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Affiliation(s)
- Junfeng Huang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Zhen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guang Huang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kai Cheng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhang Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Wan
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology
| | - Yating Yao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Jun Zhu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Hanfa Zou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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32
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Hill JJ, Tremblay TL, Fauteux F, Li J, Wang E, Aguilar-Mahecha A, Basik M, O'Connor-McCourt M. Glycoproteomic comparison of clinical triple-negative and luminal breast tumors. J Proteome Res 2015; 14:1376-88. [PMID: 25658377 DOI: 10.1021/pr500987r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Triple-negative (TN) breast cancer accounts for ∼ 15% of breast cancers and is characterized by a high likelihood of relapse and a lack of targeted therapies. In contrast, luminal-type tumors that express the estrogen and progesterone receptors (ER+/PR+) and lack expression of human epidermal growth factor receptor 2 (Her2-) are treated with targeted hormonal therapy and carry a better prognosis. To identify potential targets for the development of future therapeutics aimed specifically at TN breast cancers, we have used a hydrazide-based glycoproteomic workflow to compare protein expression in clinical tumors from nine TN (Her2-/ER-/PR-) and nine luminal (Her2-/ER+/PR+) patients. Using a label-free LC-MS based approach, we identified and quantified 2264 proteins. Of these, 90 proteins were more highly expressed and 86 proteins were underexpressed in the TN tumors relative to the luminal tumors. The expression level of four of these potential targets was verified in the original set of tumors by Western blot and correlated well with our mass-spectrometry-based quantification. Furthermore, 30% of the proteins differentially expressed between luminal and TN tumors were validated in a larger cohort of 406 TN and 469 luminal tumors through corresponding differences in their mRNA expression in publically available microarray data. A group of 29 of these differentially expressed proteins was shown to correctly classify 88% of TN and luminal tumors using microarray data of their associated mRNA levels. Interestingly, even within a group of TN breast cancer patients, the expression levels of these same mRNAs were able to significantly predict patient survival, suggesting that these proteins play a role in the aggressiveness seen in TN tumors. This study provides a comprehensive list of potential targets for the development of diagnostic and therapeutic agents specifically aimed at treating TN breast cancer and demonstrates the utility of using publicly available microarray data to further prioritize potential targets.
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Affiliation(s)
- Jennifer J Hill
- Human Health Therapeutics, National Research Council Canada , 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
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33
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Huang J, Wang F, Ye M, Zou H. Enrichment and separation techniques for large-scale proteomics analysis of the protein post-translational modifications. J Chromatogr A 2014; 1372C:1-17. [DOI: 10.1016/j.chroma.2014.10.107] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 12/16/2022]
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34
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Zhang L, Jiang H, Yao J, Wang Y, Fang C, Yang P, Lu H. Highly specific enrichment of N-linked glycopeptides based on hydrazide functionalized soluble nanopolymers. Chem Commun (Camb) 2014; 50:1027-9. [PMID: 24309553 DOI: 10.1039/c3cc47347c] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, for the first time, hydrazide functionalized PAMAM was designed and synthesized for efficient and selective enrichment of N-linked glycopeptides from complex biological samples using FASP (filter-aided sample preparation) mode.
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Affiliation(s)
- Lijuan Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
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35
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Qiao X, Qin X, She D, Wang R, Zhang X, Zhang L, Zhang Y. Mass spectrometry-based tag and its application to high efficient peptide analysis – A review. Talanta 2014; 126:91-102. [DOI: 10.1016/j.talanta.2014.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/27/2014] [Accepted: 03/10/2014] [Indexed: 12/16/2022]
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36
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Abstract
Cell surface proteins, including extracellular matrix proteins, participate in all major cellular processes and functions, such as growth, differentiation, and proliferation. A comprehensive characterization of these proteins provides rich information for biomarker discovery, cell-type identification, and drug-target selection, as well as helping to advance our understanding of cellular biology and physiology. Surface proteins, however, pose significant analytical challenges, because of their inherently low abundance, high hydrophobicity, and heavy post-translational modifications. Taking advantage of the prevalent glycosylation on surface proteins, we introduce here a high-throughput glycopeptide-capture approach that integrates the advantages of several existing N-glycoproteomics means. Our method can enrich the glycopeptides derived from surface proteins and remove their glycans for facile proteomics using LC-MS. The resolved N-glycoproteome comprises the information of protein identity and quantity as well as their sites of glycosylation. This method has been applied to a series of studies in areas including cancer, stem cells, and drug toxicity. The limitation of the method lies in the low abundance of surface membrane proteins, such that a relatively large quantity of samples is required for this analysis compared to studies centered on cytosolic proteins.
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Affiliation(s)
| | - Bingyun Sun
- Department of Chemistry, Simon Fraser University;
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37
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Sun B, Hood L. Protein-centric N-glycoproteomics analysis of membrane and plasma membrane proteins. J Proteome Res 2014; 13:2705-14. [PMID: 24754784 PMCID: PMC4053080 DOI: 10.1021/pr500187g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The advent of proteomics technology
has transformed our understanding
of biological membranes. The challenges for studying membrane proteins
have inspired the development of many analytical and bioanalytical
tools, and the techniques of glycoproteomics have emerged as an effective
means to enrich and characterize membrane and plasma-membrane proteomes.
This Review summarizes the development of various glycoproteomics
techniques to overcome the hurdles formed by the unique structures
and behaviors of membrane proteins with a focus on N-glycoproteomics.
Example contributions of N-glycoproteomics to the understanding of
membrane biology are provided, and the areas that require future technical
breakthroughs are discussed.
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Affiliation(s)
- Bingyun Sun
- Department of Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A1S6, Canada
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38
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Zhang Y, Ma W, Li D, Yu M, Guo J, Wang C. Benzoboroxole-functionalized magnetic core/shell microspheres for highly specific enrichment of glycoproteins under physiological conditions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:1379-1386. [PMID: 24307573 DOI: 10.1002/smll.201302841] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Indexed: 06/02/2023]
Abstract
Efficient enrichment of specific glycoproteins from complex biological samples is of great importance towards the discovery of disease biomarkers in biological systems. Recently, phenylboronic acid-based functional materials have been widely used for enrichment of glycoproteins. However, such enrichment was mainly carried out under alkaline conditions, which is different to the status of glycoproteins in neutral physiological conditions and may cause some unpredictable degradation. In this study, on-demand neutral enrichment of glycoproteins from crude biological samples is accomplished by utilizing the reversible interaction between the cis-diols of glycoproteins and benzoboroxole-functionalized magnetic composite microspheres (Fe3O4/PAA-AOPB). The Fe3O4/PAA-AOPB composite microspheres are deliberately designed and constructed with a high-magnetic-response magnetic supraparticle (MSP) core and a crosslinked poly(acrylic acid) (PAA) shell anchoring abundant benzoboroxole functional groups on the surface. These nanocomposites possessed many merits, such as large enrichment capacity (93.9 mg/g, protein/beads), low non-specific adsorption, quick enrichment process (10 min) and magnetic separation speed (20 s), and high recovery efficiency. Furthermore, the as-prepared Fe3O4/PAA-AOPB microspheres display high selectivity to glycoproteins even in the E. coli lysate or fetal bovine serum, showing great potential in the identify of low-abundance glycoproteins as biomarkers in real complex biological systems for clinical diagnoses.
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Affiliation(s)
- Yuting Zhang
- State Key Laboratory of Molecular, Engineering of Polymers, Department of Macromolecular Science and Laboratory of Advanced Materials, Fudan University, Shanghai, 200433, People's Republic of China
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39
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Chen W, Smeekens JM, Wu R. A universal chemical enrichment method for mapping the yeast N-glycoproteome by mass spectrometry (MS). Mol Cell Proteomics 2014; 13:1563-72. [PMID: 24692641 DOI: 10.1074/mcp.m113.036251] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycosylation is one of the most common and important protein modifications in biological systems. Many glycoproteins naturally occur at low abundances, which makes comprehensive analysis extremely difficult. Additionally, glycans are highly heterogeneous, which further complicates analysis in complex samples. Lectin enrichment has been commonly used, but each lectin is inherently specific to one or several carbohydrates, and thus no single or collection of lectin(s) can bind to all glycans. Here we have employed a boronic acid-based chemical method to universally enrich glycopeptides. The reaction between boronic acids and sugars has been extensively investigated, and it is well known that the interaction between boronic acid and diols is one of the strongest reversible covalent bond interactions in an aqueous environment. This strong covalent interaction provides a great opportunity to catch glycopeptides and glycoproteins by boronic acid, whereas the reversible property allows their release without side effects. More importantly, the boronic acid-diol recognition is universal, which provides great capability and potential for comprehensively mapping glycosylation sites in complex biological samples. By combining boronic acid enrichment with PNGase F treatment in heavy-oxygen water and MS, we have identified 816 N-glycosylation sites in 332 yeast proteins, among which 675 sites were well-localized with greater than 99% confidence. The results demonstrated that the boronic acid-based chemical method can effectively enrich glycopeptides for comprehensive analysis of protein glycosylation. A general trend seen within the large data set was that there were fewer glycosylation sites toward the C termini of proteins. Of the 332 glycoproteins identified in yeast, 194 were membrane proteins. Many proteins get glycosylated in the high-mannose N-glycan biosynthetic and GPI anchor biosynthetic pathways. Compared with lectin enrichment, the current method is more cost-efficient, generic, and effective. This method can be extensively applied to different complex samples for the comprehensive analysis of protein glycosylation.
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Affiliation(s)
- Weixuan Chen
- From the ‡School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Johanna M Smeekens
- From the ‡School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- From the ‡School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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40
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Zhu J, Sun Z, Cheng K, Chen R, Ye M, Xu B, Sun D, Wang L, Liu J, Wang F, Zou H. Comprehensive Mapping of Protein N-Glycosylation in Human Liver by Combining Hydrophilic Interaction Chromatography and Hydrazide Chemistry. J Proteome Res 2014; 13:1713-21. [DOI: 10.1021/pr401200h] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jun Zhu
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Zhen Sun
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Kai Cheng
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Rui Chen
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Mingliang Ye
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Bo Xu
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Deguang Sun
- The Second Affiliated Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116027, China
| | - Liming Wang
- The Second Affiliated Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116027, China
| | - Jing Liu
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Fangjun Wang
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Hanfa Zou
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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41
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Li QK, Gabrielson E, Askin F, Chan DW, Zhang H. Glycoproteomics using fluid-based specimens in the discovery of lung cancer protein biomarkers: promise and challenge. Proteomics Clin Appl 2014; 7:55-69. [PMID: 23112109 DOI: 10.1002/prca.201200105] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 12/29/2022]
Abstract
Lung cancer is the leading cancer in the United States and worldwide. In spite of the rapid progression in personalized treatments, the overall survival rate of lung cancer patients is still suboptimal. Over the past decade, tremendous efforts have been focused on the discovery of protein biomarkers to facilitate the early detection and monitoring of lung cancer progression during treatment. In addition to tumor tissues and cancer cell lines, a variety of biological material has been studied. Particularly in recent years, studies using fluid-based specimen or so-called "fluid-biopsy" specimens have progressed rapidly. Fluid specimens are relatively easier to collect than tumor tissue, and they can be repeatedly sampled during the disease progression. Glycoproteins are the major content of fluid specimens and have long been recognized to play fundamental roles in many physiological and pathological processes. In this review, we focus the discussion on recent advances of glycoproteomics, particularly in the identification of potential glyco protein biomarkers using fluid-based specimens in lung cancer. The purpose of this review is to summarize current strategies, achievements, and perspectives in the field. This insight will highlight the discovery of tumor-associated glycoprotein biomarkers in lung cancer and their potential clinical applications.
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Affiliation(s)
- Qing Kay Li
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD 21224, USA.
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Jurisicova A, Jurisica I, Kislinger T. Advances in ovarian cancer proteomics: the quest for biomarkers and improved therapeutic interventions. Expert Rev Proteomics 2014; 5:551-60. [DOI: 10.1586/14789450.5.4.551] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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43
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Hu J, Ma R, Liu F, Chen Y, Ju H. Mercaptophenylboronic acid modified gold nanoparticle@silica bubbles for buoyant separation and specific enrichment of glycopeptides. RSC Adv 2014. [DOI: 10.1039/c4ra03769c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A buoyant separation method was proposed for specific enrichment of glycopeptides using mercaptophenylboronic acid modified gold nanoparticles @silica bubbles.
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Affiliation(s)
- Junjie Hu
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093, P.R. China
| | - Rongna Ma
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093, P.R. China
| | - Fei Liu
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093, P.R. China
| | - Yunlong Chen
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093, P.R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093, P.R. China
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Yang G, Cui T, Wang Y, Sun S, Ma T, Wang T, Chen Q, Li Z. Selective isolation and analysis of glycoprotein fractions and their glycomes from hepatocellular carcinoma sera. Proteomics 2013; 13:1481-98. [PMID: 23436760 DOI: 10.1002/pmic.201200259] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 01/29/2013] [Accepted: 02/12/2013] [Indexed: 01/20/2023]
Abstract
As one of the most important post-translational modifications, the discovery, isolation, and identification of glycoproteins are becoming increasingly important. In this study, a Con A-magnetic particle conjugate-based method was utilized to selectively isolate the glycoproteins and their glycomes from the healthy donor and hepatocellular carcinoma (HCC) case sera. The isolated glycoproteins and their N-linked glycans were identified by LC-ESI-MS/MS and MALDI-TOF/TOF-MS, respectively. A total of 93 glycoproteins from the healthy donors and 85 glycoproteins from the HCC cases were identified. There were 34 different glycoproteins shown between the healthy donors (21/34) and the HCC cases (13/34). Twenty-eight glycans from the healthy donors and 30 glycans from the HCC cases were detected and there were 22 different glycans shown between the healthy donors (10/22) and HCC cases (12/22). Among these glycoproteins, 50 were known to be N-linked glycoproteins and three novel glycopeptides from two predicted potential glycoproteins were discovered. Moreover, lectin blotting, Western blotting and lectin/glyco-antibody microarrays were applied to definitely elucidate the change of selective protein expressions and their glycosylation levels, the results indicated that the differences of the identified glycoproteins between the healthy donors and HCC cases were caused by the change of both protein expression and their glycosylation levels.
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Affiliation(s)
- Ganglong Yang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, PR China
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Identification of N-glycosylation in hepatocellular carcinoma patients' serum with a comparative proteomic approach. PLoS One 2013; 8:e77161. [PMID: 24143209 PMCID: PMC3797089 DOI: 10.1371/journal.pone.0077161] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/09/2013] [Indexed: 11/19/2022] Open
Abstract
Aim This study is to explore the different expressions of serum N-glycoproteins and glycosylation sites between hepatocellular carcinoma (HCC) patients and healthy controls. Method We combined high abundant proteins depletion and hydrophilic affinity method to enrich the glycoproteins. Through liquid chromatography-tandem mass spectrometry (LC-MS/MS), we extensively surveyed different expressions of glycosylation sites and glycoproteins between the two groups. Result This approach identified 152 glycosylation sites and 54 glycoproteins expressed differently between HCC patients and healthy controls. With the absolute values of Pearson coefficients of at least 0.8, eight proteins were identified significantly up or down regulated in HCC serum. Those proteins are supposed to be involved in several biological processes, cellular components and molecular functions of hepatocarcinogenesis. Several of them had been reported abnormally regulated in several kinds of malignant tumors, and may be promising biomarkers of HCC. Conclusion Our work provides a systematic and quantitative method of glycoproteomics and demonstrates some key changes in clinical HCC serum. These proteomic signatures may help to unveil the underlying mechanisms of hepatocarcinogenesis and may be useful for the exploration of candidate biomarkers.
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46
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Lattová E, Perreault H. The usefulness of hydrazine derivatives for mass spectrometric analysis of carbohydrates. MASS SPECTROMETRY REVIEWS 2013; 32:366-385. [PMID: 23345114 DOI: 10.1002/mas.21367] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 10/12/2012] [Accepted: 10/12/2012] [Indexed: 06/01/2023]
Abstract
Over the last years, extensive studies have evaluated glycans from different biological samples and validated the importance of glycosylation as one of the most important post-translational modifications of proteins. Although a number of new methods for carbohydrate analysis have been published and there has been significant progress in their identification, the development of new approaches to study these biomolecules and understand their role in living systems are still vivid challenges that intrigue glycobiologists. In the last decade, the success in analyses of oligosaccharides has been driven mainly by the development of innovative, highly sensitive mass spectrometry techniques. For enhanced mass spectrometry detection, carbohydrate molecules are often derivatized. Besides, the type of labeling can influence the fragmentation pattern and make the structural analysis less complicated. In this regard, in 2003 we introduced the low scale, simple non-reductive tagging of glycans employing phenylhydrazine (PHN) as the derivatizing reagent. PHN-labeled glycans showed increased detection and as reported previously they can be analyzed by HPLC, ESI, or MALDI immediately after derivatization. Under tandem mass spectrometry conditions, PHN-derivatives produced useful data for the structural elucidation of oligosaccharides. This approach of analysis has helped to reveal new isomeric structures for glycans of known/unknown composition and has been successfully applied for the profiling of N-glycans obtained from serum samples and cancer cells. The efficacy of this labeling has also been evaluated for different substituted hydrazine reagents. This review summarizes all types of reducing-end labeling based on hydrazone-linkage that have been used for mass spectrometric analyses of oligosaccharides. This review is also aimed at correcting some past misconceptions or interpretations reported in the literature.
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Affiliation(s)
- Erika Lattová
- Chemistry Department, University of Manitoba, 144 Dysart Road, Winnipeg, MB, Canada R3T 2N2.
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Cao L, Yu L, Guo Z, Li X, Xue X, Liang X. Application of a strong anion exchange material in electrostatic repulsion–hydrophilic interaction chromatography for selective enrichment of glycopeptides. J Chromatogr A 2013; 1299:18-24. [DOI: 10.1016/j.chroma.2013.05.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/15/2013] [Accepted: 05/15/2013] [Indexed: 12/13/2022]
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48
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Chen SH, Chen CR, Chen SH, Li DT, Hsu JL. Improved N(α)-acetylated peptide enrichment following dimethyl labeling and SCX. J Proteome Res 2013; 12:3277-87. [PMID: 23745983 DOI: 10.1021/pr400127j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein N-terminal acetylation is one of the most common modifications occurring co- and post-translationally on either eukaryote or prokaryote proteins. However, compared to other protein modifications, the physiological role of protein N-terminal acetylation is relatively unclear. To explore the biological functions of protein N-terminal acetylation, a robust and large-scale method for qualitative and quantitative analysis of this modification is required. Enrichment of N(α)-acetylated peptides or depletion of the free N-terminal and internal tryptic peptides prior to analysis by mass spectrometry are necessary based on current technologies. This study demonstrated a simple strong cation exchange (SCX) fractionation method to selectively enrich N(α)-acetylated tryptic peptides via dimethyl labeling without the need for tedious protective labeling and depleting procedures. This method was introduced for the comprehensive analysis of N-terminal acetylated proteins from HepG2 cells. Several hundred N-terminal acetylation sites were readily identified in a single SCX flow-through fraction. Moreover, the N(α)-acetylated peptides of some protein isoforms were simultaneously observed in the SCX flow-through fraction, which indicated that this approach can be utilized to discriminate protein isoforms with very similar full sequences but different N-terminal sequences, such as β-actin/γ-actin, ERK1/ERK2, α-centractin/β-centractin, and ADP/ATP translocase 2 and 3. Compared to other methods, this method is relatively simple and can be directly implemented in a two-dimensional separation (SCX-RP)-mass spectrometry scheme for quantitative N-terminal proteomics using stable-isotope dimethyl labeling.
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Affiliation(s)
- Sin-Hong Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
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Strum JS, Nwosu CC, Hua S, Kronewitter SR, Seipert RR, Bachelor RJ, An HJ, Lebrilla CB. Automated assignments of N- and O-site specific glycosylation with extensive glycan heterogeneity of glycoprotein mixtures. Anal Chem 2013; 85:5666-75. [PMID: 23662732 DOI: 10.1021/ac4006556] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Site-specific glycosylation (SSG) of glycoproteins remains a considerable challenge and limits further progress in the areas of proteomics and glycomics. Effective methods require new approaches in sample preparation, detection, and data analysis. While the field has advanced in sample preparation and detection, automated data analysis remains an important goal. A new bioinformatics approach implemented in software called GP Finder automatically distinguishes correct assignments from random matches and complements experimental techniques that are optimal for glycopeptides, including nonspecific proteolysis and high mass resolution liquid chromatography/tandem mass spectrometry (LC/MS/MS). SSG for multiple N- and O-glycosylation sites, including extensive glycan heterogeneity, was annotated for single proteins and protein mixtures with a 5% false-discovery rate, generating hundreds of nonrandom glycopeptide matches and demonstrating the proof-of-concept for a self-consistency scoring algorithm shown to be compliant with the target-decoy approach (TDA). The approach was further applied to a mixture of N-glycoproteins from unprocessed human milk and O-glycoproteins from very-low-density-lipoprotein (vLDL) particles.
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Affiliation(s)
- John S Strum
- Department of Chemistry, University of California, Davis, California 95616, USA
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50
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Zhao X, Ma C, Han H, Jiang J, Tian F, Wang J, Ying W, Qian X. Comparison and optimization of strategies for a more profound profiling of the sialylated N-glycoproteomics in human plasma using metal oxide enrichment. Anal Bioanal Chem 2013; 405:5519-29. [DOI: 10.1007/s00216-013-6971-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/02/2013] [Accepted: 04/03/2013] [Indexed: 11/28/2022]
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