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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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Liew CY, Chen JL, Lin YT, Luo HS, Hung AT, Magoling BJA, Nguan HS, Lai CPK, Ni CK. Chromatograms and Mass Spectra of High-Mannose and Paucimannose N-Glycans for Rapid Isomeric Identifications. J Proteome Res 2024; 23:939-955. [PMID: 38364797 PMCID: PMC10913092 DOI: 10.1021/acs.jproteome.3c00640] [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: 10/03/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/18/2024]
Abstract
N-Linked glycosylation is one of the most essential post-translational modifications of proteins. However, N-glycan structural determination remains challenging because of the small differences in structures between isomers. In this study, we constructed a database containing collision-induced dissociation MSn mass spectra and chromatograms of high-performance liquid chromatography for the rapid identification of high-mannose and paucimannose N-glycan isomers. These N-glycans include isomers by breaking of arbitrary numbers of glycosidic bonds at arbitrary positions of canonical Man9GlcNAc2 N-glycans. In addition, some GlcMannGlcNAc2 N-glycan isomers were included in the database. This database is particularly useful for the identification of the N-glycans not in conventional N-glycan standards. This study demonstrated the application of the database to structural assignment for high-mannose N-glycans extracted from bovine whey proteins, soybean proteins, human mammary epithelial cells, and human breast carcinoma cells. We found many N-glycans that are not expected to be generated by conventional biosynthetic pathways of multicellular eukaryotes.
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Affiliation(s)
- Chia Yen Liew
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- International
Graduate Program of Molecular Science and Technology, National Taiwan University, Taipei 106216, Taiwan
- Molecular
Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 106216, Taiwan
| | - Jien-Lian Chen
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
| | - Yen-Ting Lin
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
| | - Hong-Sheng Luo
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Department
of Chemistry, National Taiwan Normal University, Taipei 116059, Taiwan
| | - An-Ti Hung
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Bryan John Abel Magoling
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Institute
of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106216, Taiwan
- Chemical
Biology and Molecular Biophysics Program, Taiwan International Graduate
Program, Academia Sinica, Taipei 115201, Taiwan
| | - Hock-Seng Nguan
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
| | - Charles Pin-Kuang Lai
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Chemical
Biology and Molecular Biophysics Program, Taiwan International Graduate
Program, Academia Sinica, Taipei 115201, Taiwan
- Genome
and Systems Biology Degree Program, National
Taiwan University and Academia Sinica, Taipei 106216, Taiwan
| | - Chi-Kung Ni
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Molecular
Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 106216, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300044, Taiwan
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Le MT, Holden DT, Manheim JM, Dziekonski ET, Iyer K, Graham Cooks R. Two-Dimensional Tandem Mass Spectrometry for Biopolymer Structural Analysis. Angew Chem Int Ed Engl 2024; 63:e202315904. [PMID: 38117612 DOI: 10.1002/anie.202315904] [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: 11/10/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 12/22/2023]
Abstract
Biopolymer analysis, including proteomics and glycomics, relies heavily on the use of mass spectrometry for structural elucidation, including sequence determination. Novel methods to improve sample workup, instrument performance, and data analysis continue to be developed to address shortcomings associated with sample preparation, analysis time, data quality, and data interpretation. Here, we present a new method that couples in-source collision-induced dissociation (IS-CID) with two-dimensional tandem mass spectrometry (2D MS/MS) as a way to simplify proteomics and glycomics workflows while also providing additional insight into analyte structures over traditional MS/MS experiments. Specifically, IS-CID is employed as a gas-phase digestion method, i.e., to break down intact full-length polysaccharide or peptide ions prior to mass analysis. The resulting mixtures of oligomeric ions are analyzed by 2D-MS/MS, a technique that allows association of product ions with their precursor ions without isolation of the latter. A novel data analysis strategy is introduced to leverage the second dimension of 2D MS/MS spectra, in which stairstep patterns, representing outputs of a molecule's MSn scans, are extracted for structural interconnectivity information on the oligomer. The results demonstrate the potential applicability of 2D MS/MS strategies to the modern omics workflow and structural analysis of various classes of biopolymers.
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Affiliation(s)
- MyPhuong T Le
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | - Dylan T Holden
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | - Jeremy M Manheim
- Merck & Co., Inc., Analytical Research and Development, Rahway, NJ 07065, USA
| | - Eric T Dziekonski
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | - Kiran Iyer
- Merck & Co., Inc., Analytical Research and Development, Rahway, NJ 07065, USA
| | - R Graham Cooks
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
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Pan S, Manabe N, Ohno S, Komatsu S, Fujimura T, Yamaguchi Y. Each N-glycan on human IgA and J-chain uniquely affects oligomericity and stability. Biochim Biophys Acta Gen Subj 2024; 1868:130536. [PMID: 38070292 DOI: 10.1016/j.bbagen.2023.130536] [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: 10/28/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Immunoglobulin A (IgA) plays a pivotal role in various immune responses, especially that of mucosal immunity. IgA is usually assembled into dimers with the contribution of J-chains. There are two N-glycosylation sites in human IgA1-Fc and one in the J-chain. There is no consensus as yet on the functional role of the N-glycosylation. METHODS To gain a better understanding of their role, we designed a series of IgA1-Fc mutants, which were expressed in the absence or presence of the J-chain. RESULTS IgA1-Fc without the J-chain, was predominantly expressed as a monomer, and in its presence dimers and some polymers appeared. N263 (Fc Cα2), N459 (Fc tailpiece) and N49 (J-chain) were shown to be site-specifically modified with N-glycans by mass spectrometry analysis. Mutant IgA1-Fc N459Q failed to form a proper dimer in the presence of the J-chain, instead higher-order aggregates appeared. Fluorescence experiments suggest that the N459-glycans cover a hydrophobic surface at the Fc tailpiece that prevents other Fc molecules from approaching the dimeric IgA. A thermofluor assay revealed that the N-glycans at N263 (Fc) and N49 (J-chain) both contribute in different ways to the thermal stability of the Fc-J-chain complex. NMR analysis of 13C-labeled Fc suggests that the N459-glycan is relatively flexible while the N263-glycan is more rigid. CONCLUSIONS We conclude that the N459-glycan of IgA1-Fc is essential for dimer formation and prevention of higher-order aggregates while those at N263 (Fc) and N49 (J-chain) stabilize the Fc-J-chain complex. GENERAL SIGNIFICANCE Site-specific role for N-glycan in molecular assembly is addressed.
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Affiliation(s)
- Shunli Pan
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Noriyoshi Manabe
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Shiho Ohno
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Sachiko Komatsu
- Division of Bioanalytical Chemistry, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Tsutomu Fujimura
- Division of Bioanalytical Chemistry, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Yoshiki Yamaguchi
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan.
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Liew CY, Luo HS, Yang TY, Hung AT, Magoling BJA, Lai CPK, Ni CK. Identification of the High Mannose N-Glycan Isomers Undescribed by Conventional Multicellular Eukaryotic Biosynthetic Pathways. Anal Chem 2023. [PMID: 37235553 DOI: 10.1021/acs.analchem.2c05599] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
N-linked glycosylation is one of the most important post-translational modifications of proteins. Current knowledge of multicellular eukaryote N-glycan biosynthesis suggests high mannose N-glycans are generated in the endoplasmic reticulum and Golgi apparatus through conserved biosynthetic pathways. According to conventional biosynthetic pathways, four Man7GlcNAc2 isomers, three Man6GlcNAc2 isomers, and one Man5GlcNAc2 isomer are generated during this process. In this study, we applied our latest mass spectrometry method, logically derived sequence tandem mass spectrometry (LODES/MSn), to re-examine high mannose N-glycans extracted from various multicellular eukaryotes which are not glycosylation mutants. LODES/MSn identified many high mannose N-glycan isomers previously unreported in plantae, animalia, cancer cells, and fungi. A database consisting of retention time and CID MSn mass spectra was constructed for all possible MannGlcNAc2 (n = 5, 6, 7) isomers that include the isomers by removing arbitrary numbers and positions of mannose from canonical N-glycan, Man9GlcNAc2. Many N-glycans in this database are not found in current N-glycan mass spectrum libraries. The database is useful for rapid high mannose N-glycan isomeric identification.
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Affiliation(s)
- Chia Yen Liew
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- International Graduate Program of Molecular Science and Technology, National Taiwan University (NTU-MST), Taipei 10617, Taiwan
- Molecular Science and Technology (MST), Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 10617, Taiwan
| | - Hong-Sheng Luo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Ting-Yi Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - An-Ti Hung
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Bryan John Abel Magoling
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
| | - Charles Pin-Kuang Lai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Molecular Science and Technology (MST), Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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Pohl T, Gervais A, Dirksen E, D'Alessio V, Bechtold-Peters K, Burkitt W, Cao L, Greven S, Lennard A, Li X, Lössner C, Niu B, Reusch D, O'Riordan T, Shearer J, Spencer D, Xu W, Yi L. Technical considerations for the implementation of the Multi-Attribute-Method by mass spectrometry in a Quality Control laboratory. Eur J Pharm Biopharm 2023:S0939-6411(23)00112-1. [PMID: 37146738 DOI: 10.1016/j.ejpb.2023.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023]
Abstract
Multi-attribute methods employing mass spectrometry are applied throughout the biopharmaceutical industry for product and process characterization purposes but are not yet widely accepted as a method for batch release and stability testing under good manufacturing practice (GMP) due to limited experience and level of comfort with the technical, compliance and regulatory aspects of its implementation at quality control (QC) laboratories. Here, current literature related to the development and application of the multi-attribute method by peptide mapping liquid chromatography mass spectrometry (MAM) is compiled with the aim of providing guidance for the implementation of MAM in a QC laboratory. This article, focusing on technical considerations, is the first part of a two-tiered publication, whereby the second part will focus on GMP compliance and regulatory aspects. This publication has been prepared by a group of industry experts representing 14 globally acting major biotechnology companies under the umbrella of the European Federation of Pharmaceutical Industries and Associations (EFPIA) Manufacturing & Quality Expert Group (MQEG).
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Affiliation(s)
- Thomas Pohl
- Biologics Analytical Development, Novartis Pharma AG, Klybeckstrasse 141, CH-4057 Basel, Switzerland
| | - Annick Gervais
- Analytical Development Sciences for Biologicals, UCB, Chemin du Foriest, 1420 Braine L'Alleud, Belgium
| | - Eef Dirksen
- Analytical Development and Quality Control, Byondis, Microweg 22, 6545 CM, Nijmegen, The Netherlands
| | - Valerio D'Alessio
- Analytical Development Biotech, Merck Serono S.p.A., Via Luigi Einaudi, 11, 00012 Guidonia Montecelio - Rome, Italy
| | - Karoline Bechtold-Peters
- Biologics Drug Product Development, Novartis Pharma AG, Klybeckstrasse 141, CH-4057 Basel, Switzerland
| | - Will Burkitt
- Biological Characterisation Product Development Sciences, UCB, 216 Bath Road, Slough, SL1 3WE, UK
| | - Li Cao
- Strategic External Development, GSK, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, USA
| | - Simone Greven
- Pharmaceuticals, Biological Development, Bayer AG, Friedrich-Ebert-Strasse 217-333, 42117 Wuppertal, Germany
| | - Andrew Lennard
- Amgen, 4 Uxbridge Business Park, Sanderson Road, Uxbridge, UB8 1DH, UK
| | - Xue Li
- Biologics Development, Bristol Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08901, USA
| | - Christopher Lössner
- Analytical Dev. Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Ben Niu
- Biotherapeutics, Bristol Myers Squibb, 4224 Campus Point Court, San Diego, California 92121, USA
| | - Dietmar Reusch
- Pharma Technical Development, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Tomás O'Riordan
- Eli Lilly Kinsale Limited, Dunderrow, Kinsale, Co. Cork, P17NY71, Ireland
| | - Justin Shearer
- Analytical Development, GSK, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, USA
| | - David Spencer
- BioPharmaceutical Development, Ipsen Biopharm Limited, 9 Ash Road, Wrexham Industrial Estate, Wrexham, LL13 9UF, UK
| | - Wei Xu
- Analytical Sciences, BioPharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, Maryland 20878, USA
| | - Linda Yi
- Analytical Development, Biogen, 5000 Davis Drive, Research Triangle Park, North Carolina 27709, USA
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