1
|
Baerenfaenger M, Post MA, Zijlstra F, van Gool AJ, Lefeber DJ, Wessels HJCT. Maximizing Glycoproteomics Results through an Integrated Parallel Accumulation Serial Fragmentation Workflow. Anal Chem 2024; 96:8956-8964. [PMID: 38776126 PMCID: PMC11154686 DOI: 10.1021/acs.analchem.3c05874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 06/05/2024]
Abstract
Glycoproteins play important roles in numerous physiological processes and are often implicated in disease. Analysis of site-specific protein glycobiology through glycoproteomics has evolved rapidly in recent years thanks to hardware and software innovations. Particularly, the introduction of parallel accumulation serial fragmentation (PASEF) on hybrid trapped ion mobility time-of-flight mass spectrometry instruments combined deep proteome sequencing with separation of (near-)isobaric precursor ions or converging isotope envelopes through ion mobility separation. However, the reported use of PASEF in integrated glycoproteomics workflows to comprehensively capture the glycoproteome is still limited. To this end, we developed an integrated methodology using timsTOF Pro 2 to enhance N-glycopeptide identifications in complex mixtures. We systematically optimized the ion optics tuning, collision energies, mobility isolation width, and the use of dopant-enriched nitrogen gas (DEN). Thus, we obtained a marked increase in unique glycopeptide identification rates compared to standard proteomics settings, showcasing our results on a large set of glycopeptides. With short liquid chromatography gradients of 30 min, we increased the number of unique N-glycopeptide identifications in human plasma samples from around 100 identifications under standard proteomics conditions to up to 1500 with our optimized glycoproteomics approach, highlighting the need for tailored optimizations to obtain comprehensive data.
Collapse
Affiliation(s)
- Melissa Baerenfaenger
- Department
of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
- Division
of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular
and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, Netherlands
| | - Merel A. Post
- Department
of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| | - Fokje Zijlstra
- Translational
Metabolic Laboratory, Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| | - Alain J. van Gool
- Translational
Metabolic Laboratory, Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| | - Dirk J. Lefeber
- Department
of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
- Translational
Metabolic Laboratory, Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| | - Hans J. C. T. Wessels
- Translational
Metabolic Laboratory, Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| |
Collapse
|
2
|
Dong S, Chen L, Sauer A, Dittus L. LC/MS Assessment of Glycoform Clearance of A Biotherapeutic MAb in Rabbit Ocular Tissues. J Pharm Sci 2023; 112:2285-2291. [PMID: 37062414 DOI: 10.1016/j.xphs.2023.04.008] [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: 02/08/2023] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 04/18/2023]
Abstract
Many biotherapeutics such as monoclonal antibodies (mAbs) consist of various glycoforms, which can have different PK properties upon administration to animals and human. As a result, it is necessary to monitor the abundance of glycoforms and limit lot-to-lot variability during the manufacturing process. However, limited information is known about the clearance of mAb glycoforms from ocular space upon intravitreal injection. We present here an assessment of glycoform clearance of a biotherapeutic mAb (IgG1) from rabbit vitreous humor, aqueous humor and retina tissue using LC/MS. The results show that G0, G0F and G1F have similar T1/2, while mannose-5 has a longer T1/2 and is cleared slower in rabbit ocular space, which contradicted with what has been reported in the literature in which Mann5 was cleared faster systematically.
Collapse
Affiliation(s)
- Shiyu Dong
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc. Ridgefield, CT, USA
| | - Linzhi Chen
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc. Ridgefield, CT, USA.
| | - Achim Sauer
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG. Birkendorfer Str. 65, 88397 Biberach an der Riß, Germany
| | - Lars Dittus
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG. Birkendorfer Str. 65, 88397 Biberach an der Riß, Germany
| |
Collapse
|
3
|
Liu S, Wang H, Jiang X, Ji Y, Wang Z, Zhang Y, Wang P, Xiao H. Integrated N-glycoproteomics Analysis of Human Saliva for Lung Cancer. J Proteome Res 2022; 21:1589-1602. [PMID: 35715216 DOI: 10.1021/acs.jproteome.1c00701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aberrant protein N-glycosylation is a cancer hallmark, which has great potential for cancer detection. However, large-scale and in-depth analysis of N-glycosylation remains challenging because of its high heterogeneity, complexity, and low abundance. Human saliva is an attractive diagnostic body fluid, while few efforts explored its N-glycoproteome for lung cancer. Here, we utilized a zwitterionic-hydrophilic interaction chromatography-based strategy to specifically enrich salivary glycopeptides. Through quantitative proteomics analysis, 1492 and 1234 intact N-glycopeptides were confidently identified from pooled saliva samples of 10 subjects in the nonsmall-cell lung cancer group and 10 subjects in the normal control group. Accordingly, 575 and 404 N-glycosites were revealed for the lung cancer group and normal control group. In particular, 154 N-glycosites and 259 site-specific glycoforms were significantly dysregulated in the lung cancer group. Several N-glycosites located at the same glycoprotein and glycans attached to the same N-glycosites were observed with differential expressions, including haptoglobin, Mucin-5B, lactotransferrin, and α-1-acid glycoprotein 1. These N-glycoproteins were mainly related to inflammatory responses, infectious diseases, and cancers. Our study achieved comprehensive characterization of salivary N-glycoproteome, and dysregulated site-specific glycoforms hold promise for noninvasive detection of lung cancer.
Collapse
Affiliation(s)
- Sha Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoteng Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yin Ji
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Pharmaceutical Co., Ltd., Nanjing 210042, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Peng Wang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Pharmaceutical Co., Ltd., Nanjing 210042, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
4
|
Heffner KM, Wang Q, Hizal DB, Can Ö, Betenbaugh MJ. Glycoengineering of Mammalian Expression Systems on a Cellular Level. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021. [PMID: 29532110 DOI: 10.1007/10_2017_57] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mammalian expression systems such as Chinese hamster ovary (CHO), mouse myeloma (NS0), and human embryonic kidney (HEK) cells serve a critical role in the biotechnology industry as the production host of choice for recombinant protein therapeutics. Most of the recombinant biologics are glycoproteins that contain complex oligosaccharide or glycan attachments representing a principal component of product quality. Both N-glycans and O-glycans are present in these mammalian cells, but the engineering of N-linked glycosylation is of critical interest in industry and many efforts have been directed to improve this pathway. This is because altering the N-glycan composition can change the product quality of recombinant biotherapeutics in mammalian hosts. In addition, sialylation and fucosylation represent components of the glycosylation pathway that affect circulatory half-life and antibody-dependent cellular cytotoxicity, respectively. In this chapter, we first offer an overview of the glycosylation, sialylation, and fucosylation networks in mammalian cells, specifically CHO cells, which are extensively used in antibody production. Next, genetic engineering technologies used in CHO cells to modulate glycosylation pathways are described. We provide examples of their use in CHO cell engineering approaches to highlight these technologies further. Specifically, we describe efforts to overexpress glycosyltransferases and sialyltransfereases, and efforts to decrease sialidase cleavage and fucosylation. Finally, this chapter covers new strategies and future directions of CHO cell glycoengineering, such as the application of glycoproteomics, glycomics, and the integration of 'omics' approaches to identify, quantify, and characterize the glycosylated proteins in CHO cells. Graphical Abstract.
Collapse
Affiliation(s)
- Kelley M Heffner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Qiong Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Deniz Baycin Hizal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Özge Can
- Department of Medical Engineering, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
5
|
Kim KH, Lee SY, Kim DG, Lee SY, Kim JY, Yoo JS. Absolute Quantification of N-Glycosylation of Alpha-Fetoprotein Using Parallel Reaction Monitoring with Stable Isotope-Labeled N-Glycopeptide as an Internal Standard. Anal Chem 2020; 92:12588-12595. [DOI: 10.1021/acs.analchem.0c02563] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kwang Hoe Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju 28119, Republic of Korea
| | - Sang Yoon Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju 28119, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Dong Geun Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju 28119, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Soo-Youn Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju 28119, Republic of Korea
| | - Jong Shin Yoo
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju 28119, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| |
Collapse
|
6
|
Yang W, Ao M, Song A, Xu Y, Sokoll L, Zhang H. Mass Spectrometric Mapping of Glycoproteins Modified by Tn-Antigen Using Solid-Phase Capture and Enzymatic Release. Anal Chem 2020; 92:9230-9238. [PMID: 32510927 DOI: 10.1021/acs.analchem.0c01564] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Tn-antigen (Tn), a single N-acetylgalactosamine (GalNAc) monosaccharide attached to protein Ser/Thr residues, is found on most cancer yet rarely detected in adult normal tissues as reported in previous studies, featuring it as one of the most distinctive signatures of cancer. Although it is important in cancer, Tn modified glycoproteins are not entirely clear owing to the lack of a suitable method. Knowing the Tn-glycosylated proteins and glycosylation sites are essential to the prevention, diagnosis, and therapy of cancer associated with the expression of Tn. Here, we introduce a method named EXoO-Tn for large-scale mapping of Tn-glycosylated proteins and glycosylation sites. EXoO-Tn utilizes solid-phase immobilization of proteolytic peptides of proteins, which modifies Tn by glycosyltransferase C1GalT1 with isotopically labeled UDP-Gal(13C6), to tag and convert Tn to Gal(13C6)-Tn, which gives rise to a unique glycan mass. The exquisite Gal(13C6) modified Tn are then recognized by a human-gut-bacterial enzyme, OpeRATOR, and released at the N-termini of the Gal(13C6)-Tn-occupied Ser/Thr residues from immobilized peptides to yield site-containing glycopeptides. The effectiveness of EXoO-Tn was benchmarked by analyzing Jurkat cells, where 947 Tn-glycosylation sites from 480 glycoproteins were mapped. The EXoO-Tn was further applied to the analysis of pancreatic cancer sera, where Tn-glycoproteins were identified. Given the significance of Tn in cancer, EXoO-Tn is anticipated to have broad translational and clinical utilities.
Collapse
Affiliation(s)
- Weiming Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Minghui Ao
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Angellina Song
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Yuanwei Xu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Lori Sokoll
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| |
Collapse
|
7
|
Li H, Li L, Cheng K, Ning Z, Mayne J, Zhang X, Walker K, Chen R, Twine S, Li J, Figeys D. Chemoenzymatic Method for Glycoproteomic N-Glycan Type Quantitation. Anal Chem 2019; 92:1618-1627. [DOI: 10.1021/acs.analchem.9b04937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Henghui Li
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Leyuan Li
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Kai Cheng
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Zhibin Ning
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Janice Mayne
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Xu Zhang
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Krystal Walker
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Rui Chen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Susan Twine
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Jianjun Li
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Daniel Figeys
- SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology and Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto M5G 1M1, Canada
| |
Collapse
|
8
|
Abstract
Chinese hamster ovary (CHO) cells represent the predominant platform in biopharmaceutical industry for the production of recombinant biotherapeutic proteins, especially glycoproteins. These glycoproteins include oligosaccharide or glycan attachments that represent one of the principal components dictating product quality. Especially important are the N-glycan attachments present on many recombinant glycoproteins of commercial interest. Furthermore, altering the glycan composition can be used to modulate the production quality of a recombinant biotherapeutic from CHO and other mammalian hosts. This review first describes the glycosylation network in mammalian cells and compares the glycosylation patterns between CHO and human cells. Next genetic strategies used in CHO cells to modulate the sialylation patterns through overexpression of sialyltransfereases and other glycosyltransferases are summarized. In addition, other approaches to alter sialylation including manipulation of sialic acid biosynthetic pathways and inhibition of sialidases are described. Finally, this review also covers other strategies such as the glycosylation site insertion and manipulation of glycan heterogeneity to produce desired glycoforms for diverse biotechnology applications.
Collapse
Affiliation(s)
- Qiong Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., 220 Maryland Hall, Baltimore, MD, 21218, USA
| | - Bojiao Yin
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., 220 Maryland Hall, Baltimore, MD, 21218, USA
| | - Cheng-Yu Chung
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., 220 Maryland Hall, Baltimore, MD, 21218, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., 220 Maryland Hall, Baltimore, MD, 21218, USA.
| |
Collapse
|
9
|
Liquid chromatography-tandem mass spectrometry-based fragmentation analysis of glycopeptides. Glycoconj J 2016; 33:261-72. [PMID: 26780731 DOI: 10.1007/s10719-016-9649-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/23/2015] [Accepted: 01/04/2016] [Indexed: 02/08/2023]
Abstract
The use of liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS(n)) for the glycoproteomic characterization of glycopeptides is a growing field of research. The N- and O-glycosylated peptides (N- and O-glycopeptides) analyzed typically originate from protease-digested glycoproteins where many of them are expected to be biomedically important. Examples of LC-MS(2) and MS(3) fragmentation strategies used to pursue glycan structure, peptide identity and attachment-site identification analyses of glycopeptides are described in this review. MS(2) spectra, using the CID and HCD fragmentation techniques of a complex biantennary N-glycopeptide and a core 1 O-glycopeptide, representing two examples of commonly studied glycopeptide types, are presented. A few practical tips for accomplishing glycopeptide analysis using reversed-phase LC-MS(n) shotgun proteomics settings, together with references to the latest glycoproteomic studies, are presented.
Collapse
|
10
|
Characterization of N-glycosylation and amino acid sequence features of immunoglobulins from swine. Glycoconj J 2015; 33:79-91. [DOI: 10.1007/s10719-015-9637-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 11/02/2015] [Accepted: 11/03/2015] [Indexed: 12/29/2022]
|
11
|
Pabst M, Küster SK, Wahl F, Krismer J, Dittrich PS, Zenobi R. A Microarray-Matrix-assisted Laser Desorption/Ionization-Mass Spectrometry Approach for Site-specific Protein N-glycosylation Analysis, as Demonstrated for Human Serum Immunoglobulin M (IgM). Mol Cell Proteomics 2015; 14:1645-56. [PMID: 25802287 DOI: 10.1074/mcp.o114.046748] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Indexed: 12/31/2022] Open
Abstract
We demonstrate a new approach for the site-specific identification and characterization of protein N-glycosylation. It is based on a nano-liquid chromatography microarray-matrix assisted laser desorption/ionization-MS platform, which employs droplet microfluidics for on-plate nanoliter reactions. A chromatographic separation of a proteolytic digest is deposited at a high frequency on the microarray. In this way, a short separation run is archived into thousands of nanoliter reaction cavities, and chromatographic peaks are spread over multiple array spots. After fractionation, each other spot is treated with PNGaseF to generate two correlated traces within one run, one with treated spots where glycans are enzymatically released from the peptides, and one containing the intact glycopeptides. Mining for distinct glycosites is performed by searching for the predicted deglycosylated peptides in the treated trace. An identified peptide then leads directly to the position of the "intact" glycopeptide clusters, which are located in the adjacent spots. Furthermore, the deglycosylated peptide can be sequenced efficiently in a simple collision-induced dissociation-MS experiment. We applied the microarray approach to a detailed site-specific glycosylation analysis of human serum IgM. By scanning the treated spots with low-resolution matrix assisted laser desorption/ionization-time-of-flight-MS, we observed all five deglycosylated peptides, including the one originating from the secretory chain. A detailed glycopeptide characterization was then accomplished on the adjacent, untreated spots with high mass resolution and high mass accuracy using a matrix assisted laser desorption ionization-Fourier transform-MS. We present the first detailed and comprehensive mass spectrometric analysis on the glycopeptide level for human polyclonal IgM with high mass accuracy. Besides complex type glycans on Asn 395, 332, 171, and on the J chain, we observed oligomannosidic glycans on Asn 563, Asn 402 and minor amounts of oligomannosidic glycans on the glycosite Asn 171. Furthermore, hybrid type glycans were found on Asn 402, Asn 171 and in traces Asn 332.
Collapse
Affiliation(s)
- Martin Pabst
- From the ‡Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Simon Karl Küster
- From the ‡Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Fabian Wahl
- §Sigma-Aldrich Chemie GmbH, Industriestrasse 25, 9471 Buchs (SG), Switzerland
| | - Jasmin Krismer
- From the ‡Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Petra S Dittrich
- From the ‡Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Renato Zenobi
- From the ‡Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland;
| |
Collapse
|
12
|
Zhou L, Qian Y, Zhang X, Ruan Y, Ren S, Gu J. Elucidation of differences in N-glycosylation between different molecular weight forms of recombinant CLEC-2 by LC MALDI tandem MS. Carbohydr Res 2015; 402:180-8. [DOI: 10.1016/j.carres.2014.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/17/2014] [Accepted: 07/07/2014] [Indexed: 10/25/2022]
|
13
|
Yang W, Shah P, Toghi Eshghi S, Yang S, Sun S, Ao M, Rubin A, Jackson JB, Zhang H. Glycoform analysis of recombinant and human immunodeficiency virus envelope protein gp120 via higher energy collisional dissociation and spectral-aligning strategy. Anal Chem 2014; 86:6959-67. [PMID: 24941220 PMCID: PMC4215848 DOI: 10.1021/ac500876p] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
![]()
Envelope
protein gp120 of human immunodeficiency virus (HIV) is
armored with a dense glycan shield, which plays critical roles in
envelope folding, immune-evasion, infectivity, and immunogenicity.
Site-specific glycosylation profiling of recombinant gp120 is very
challenging. Therefore, glycoproteomic analysis of native viral gp120
is still formidable to date. This challenge promoted us to employ
a Q-Exactive mass spectrometer to identify low abundant glycopeptides
from virion-associated gp120. To search the HCD-MS data for glycopeptides,
a novel spectral-aligning strategy was developed. This strategy depends
on the observation that glycopeptides and the corresponding deglycosylated
peptides share very similar MS/MS pattern in terms of b- and y-ions
that do not contain the site of glycosylation. Moreover, glycopeptides
with an identical peptide backbone show nearly resembling spectra
regardless of the attached glycan structures. For the recombinant
gp120, this “copy–paste” spectral pattern of
glycopeptides facilitated identification of 2224 spectra using only
18 spectral templates, and after precursor mass correction, 1268 (57%)
spectra were assigned to 460 unique glycopeptides accommodating 19
N-linked and one O-linked glycosylation sites (glycosites). Strikingly,
we were able to observe five N- and one O-linked glycosites in native
gp120. We further revealed that except for Asn276 in the C2 region,
glycans were processed to contain both high mannose and hybrid/complex
glycans; an additional four N-linked glycosites were decorated with
high mannose type. Core 1 O-linked glycan Gal1GalNAc1 was seen for the O-linked glycosite at Thr499. This direct
observation of site-specific glycosylation of virion-derived gp120
has implications in HIV glycobiology and vaccine design.
Collapse
Affiliation(s)
- Weiming Yang
- Department of Pathology, School of Medicine, Johns Hopkins University , 1550 Orleans Street , Baltimore, Maryland 21205, United States
| | | | | | | | | | | | | | | | | |
Collapse
|