1
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Hevér H, Xue A, Nagy K, Komka K, Vékey K, Drahos L, Révész Á. Can We Boost N-Glycopeptide Identification Confidence? Smart Collision Energy Choice Taking into Account Structure and Search Engine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:333-343. [PMID: 38286027 PMCID: PMC10853973 DOI: 10.1021/jasms.3c00375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/31/2024]
Abstract
High confidence and reproducibility are still challenges in bottom-up mass spectrometric N-glycopeptide identification. The collision energy used in the MS/MS measurements and the database search engine used to identify the species are perhaps the two most decisive factors. We investigated how the structural features of N-glycopeptides and the choice of the search engine influence the optimal collision energy, delivering the highest identification confidence. We carried out LC-MS/MS measurements using a series of collision energies on a large set of N-glycopeptides with both the glycan and peptide part varied and studied the behavior of Byonic, pGlyco, and GlycoQuest scores. We found that search engines show a range of behavior between peptide-centric and glycan-centric, which manifests itself already in the dependence of optimal collision energy on m/z. Using classical statistical and machine learning methods, we revealed that peptide hydrophobicity, glycan and peptide masses, and the number of mobile protons also have significant and search-engine-dependent influence, as opposed to a series of other parameters we probed. We envisioned an MS/MS workflow making a smart collision energy choice based on online available features such as the hydrophobicity (described by retention time) and glycan mass (potentially available from a scout MS/MS). Our assessment suggests that this workflow can lead to a significant gain (up to 100%) in the identification confidence, particularly for low-scoring hits close to the filtering limit, which has the potential to enhance reproducibility of N-glycopeptide analyses. Data are available via MassIVE (MSV000093110).
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Affiliation(s)
- Helga Hevér
- MS
Proteomics Research Group, HUN-REN Research
Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest H-1117, Hungary
| | - Andrea Xue
- MS
Proteomics Research Group, HUN-REN Research
Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest H-1117, Hungary
| | - Kinga Nagy
- MS
Proteomics Research Group, HUN-REN Research
Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest H-1117, Hungary
- Faculty
of Science, Institute of Chemistry, Hevesy György PhD School
of Chemistry, Eötvös Loránd
University, Pázmány
Péter sétány 1/A, Budapest H-1117, Hungary
| | - Kinga Komka
- Department
of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Károly Vékey
- MS
Proteomics Research Group, HUN-REN Research
Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest H-1117, Hungary
| | - László Drahos
- MS
Proteomics Research Group, HUN-REN Research
Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest H-1117, Hungary
| | - Ágnes Révész
- MS
Proteomics Research Group, HUN-REN Research
Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest H-1117, Hungary
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2
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Haga Y, Yamada M, Fujii R, Saichi N, Yokokawa T, Hama T, Hayakawa Y, Ueda K. Fast and Ultrasensitive Glycoform Analysis by Supercritical Fluid Chromatography–Tandem Mass Spectrometry. Anal Chem 2022; 94:15948-15955. [DOI: 10.1021/acs.analchem.2c01721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yoshimi Haga
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Masaki Yamada
- Global Application Development Center, Shimadzu Corporation, Nishinokyo Kuwabara-cho 1, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Risa Fujii
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Naomi Saichi
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Takashi Yokokawa
- Department of Pharmacy, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Toshihiro Hama
- Department of Pharmacy, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Yoshihiro Hayakawa
- Global Application Development Center, Shimadzu Corporation, Nishinokyo Kuwabara-cho 1, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
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3
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Fitzgerald CCJ, Bowen C, Elbourne M, Cawley A, McLeod MD. Energy-Resolved Fragmentation Aiding the Structure Elucidation of Steroid Biomarkers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1276-1281. [PMID: 35791638 DOI: 10.1021/jasms.2c00092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The identification and confirmation of steroid sulfate metabolites in biological samples are essential to various fields, including anti-doping analysis and clinical sciences. Ultra-high-performance liquid chromatography with tandem mass spectrometry (UHPLC-MS/MS) is the leading method for the detection of intact steroid conjugates in biofluids, but because of the inherent complexity of biological samples and the low concentration of many targets of interest, metabolite identification based solely on mass spectrometry remains a major challenge. The confirmation of new metabolites typically depends on a comparison with synthetically derived reference materials that encompass a range of possible conjugation sites and stereochemistries. Herein, energy-resolved collision-induced dissociation (CID) is used as part of UHPLC-HRMS/MS analysis to distinguish between regio- and stereo-isomeric steroid sulfate compounds. This wholly MS-based approach was employed to guide the synthesis of reference materials to unambiguously confirm the identity of an equine steroid sulfate biomarker of testosterone propionate administration.
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Affiliation(s)
- Christopher C J Fitzgerald
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Christopher Bowen
- Mass Spectrometry Business Unit, Shimadzu Scientific Instruments (Australasia), Rydalmere, New South Wales 2116, Australia
| | - Madysen Elbourne
- Centre for Forensic Science, University of Technology Sydney, Broadway, New South Wales 2007, Australia
| | - Adam Cawley
- Australian Racing Forensic Laboratory, Racing NSW, Sydney, New South Wales 2000, Australia
| | - Malcolm D McLeod
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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4
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Fitzgerald CCJ, McLeod MD. Synthesis of stable isotope labelled steroid bis(sulfate) conjugates and their behaviour in collision induced dissociation experiments. Org Biomol Chem 2022; 20:3311-3322. [PMID: 35354200 DOI: 10.1039/d2ob00375a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Steroid bis(sulfate) metabolites derived from the two-fold sulfation of unconjugated precursors represent an important yet understudied portion of the steroid profile. The investigation of these compounds in fields such as medicine or anti-doping science relies on mass spectrometry (MS) as the principal tool to identify and quantify biomarkers of interest and depends in turn on access to steroid reference materials and their stable isotope labelled (SIL) derivatives. A new [18O] stable isotope label for sulfate metabolites is reported, which allows for the selective, late-stage and 'one-pot' synthesis of a variety of SIL-steroid conjugates suitable as MS probes and internal standards. The method is applied to more comprehensively study the MS behaviour of steroid bis(sulfate) compounds through collision-induced dissociation (CID) experiments.
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Affiliation(s)
| | - Malcolm D McLeod
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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5
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Takashima S, Kurogochi M, Tsukimura W, Mori M, Osumi K, Sugawara SI, Amano J, Mizuno M, Takada Y, Matsuda A. Preparation and biological activities of anti-HER2 monoclonal antibodies with multi-branched complex-type N-glycans. Glycobiology 2021; 31:1401-1414. [PMID: 34192331 DOI: 10.1093/glycob/cwab064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/13/2022] Open
Abstract
Immunoglobulin G (IgG) has a conserved N-glycosylation site at Asn297 in the fragment crystallizable (Fc) region. Previous studies have shown that N-glycosylation of this site is a critical mediator of the antibody's effector functions, such as antibody-dependent cellular cytotoxicity. While the N-glycan structures attached to the IgG-Fc region are generally heterogenous, IgGs engineered to be homogenously glycosylated with functional N-glycans may improve the efficacy of antibodies. The major glycoforms of the N-glycans on the IgG-Fc region are bi-antennary complex-type N-glycans, while multi-branched complex-type N-glycans are not typically found. However, IgGs with tri-antennary complex-type N-glycans have been generated using the N-glycan remodeling technique, suggesting that more branched N-glycans might be artificially attached. At present, little is known about the properties of these IgGs. In this study, IgGs with multi-branched N-glycans on the Fc region were prepared by using a combination of the glycosynthase/oxazoline substrate-based N-glycan remodeling technique and successive reactions with glycosyltransferases. Among the IgGs produced by these methods, the largest N-glycan attached was a bisecting N-acetylglucosamine (GlcNAc) containing a sialylated penta-antennary structure. Concerning the Fc-mediated effector functions, the majority of IgGs with tri- and tetra-antennary N-glycans on their Fc region showed properties similar to IgGs with ordinary bi-antennary N-glycans.
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Affiliation(s)
- Shou Takashima
- Laboratory of Glycobiology, The Noguchi Institute, Tokyo 173-0003, Japan
| | - Masaki Kurogochi
- Laboratory of Glyco-Organic Chemistry, The Noguchi Institute, Tokyo 173-0003, Japan
| | - Wataru Tsukimura
- Laboratory of Glycobiology, The Noguchi Institute, Tokyo 173-0003, Japan
| | - Masako Mori
- Laboratory of Glycobiology, The Noguchi Institute, Tokyo 173-0003, Japan
| | - Kenji Osumi
- Laboratory of Glyco-Organic Chemistry, The Noguchi Institute, Tokyo 173-0003, Japan
| | - Shu-Ichi Sugawara
- Laboratory of Glyco-Organic Chemistry, The Noguchi Institute, Tokyo 173-0003, Japan
| | - Junko Amano
- Laboratory of Glycobiology, The Noguchi Institute, Tokyo 173-0003, Japan
| | - Mamoru Mizuno
- Laboratory of Glyco-Organic Chemistry, The Noguchi Institute, Tokyo 173-0003, Japan
| | - Yoshio Takada
- Laboratory of Glycobiology, The Noguchi Institute, Tokyo 173-0003, Japan
| | - Akio Matsuda
- Laboratory of Glycobiology, The Noguchi Institute, Tokyo 173-0003, Japan.,Laboratory of Glyco-Organic Chemistry, The Noguchi Institute, Tokyo 173-0003, Japan
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6
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Cao C, Yu L, Zhang X, Dong X, Yuan J, Liang X. Calibration for quantitative Fc-glycosylation analysis of therapeutic IgG1-type monoclonal antibodies by using glycopeptide standards. Anal Chim Acta 2021; 1154:338306. [PMID: 33736796 DOI: 10.1016/j.aca.2021.338306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/25/2021] [Accepted: 02/07/2021] [Indexed: 11/28/2022]
Abstract
Fc-glycosylation has crucial impact on the efficacy and safety of IgG-type therapeutic monoclonal antibodies (mAbs). In order to enhance the performance of MS-based bottom-up quantitation strategy, a library of glycopeptide standards containing 26 common IgG1-type Fc-glycoforms has been constructed via modified two-dimensional hydrophilic interaction liquid chromatography (HILIC) purification. Taking advantage of the acquired glycopeptide standards, calibrated quantitation strategy for Fc-glycosylation analysis of mAbs was established and evaluated on the basis of three LC-MS-based methods, including HILIC-MRM (multiple reaction monitoring), HILIC-SIM (selected ion monitor) and RPLC-SIM. Molar concentrations of eleven individual Fc-glycoforms (0.03 ± 0.001-13.77 ± 0.64 nmol mg-1) as well as degree of fucosylation (75.44-97.04%), galactosylation (3.39-49.47%) and mannosylation (1.12-21.22%) in six IgG1-type mAbs were achieved. In addition, Fc-glycosylation site occupancy was also determined from 98.05% to 99.83%. Compared with traditional MS-based quantitation via peak area normalization, the quantitation accuracy and precision of the calibrated strategy had been remarkably improved, especially when combining with HILIC separation. In addition, the transferability of calibrated quantitation as assessed by using MRM-based method had also been significantly enhanced on different instruments from different laboratories. This calibrated quantitation strategy using glycopeptide standards as calibrators will be useful for Fc-glycosylation analysis of IgG1-type mAbs with multiple glycosylation sites.
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Affiliation(s)
- Cuiyan Cao
- 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; State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian, 116024, China
| | - Long Yu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Xiuli Zhang
- College of Pharmaceutical Science, Soochow University, Suzhou, 215123, China
| | - Xuefang Dong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jingli Yuan
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian, 116024, China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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7
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Separation based characterization methods for the N-glycosylation analysis of prostate-specific antigen. J Pharm Biomed Anal 2020; 194:113797. [PMID: 33288345 DOI: 10.1016/j.jpba.2020.113797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/13/2022]
Abstract
Prostate cancer has the highest malignancy rate diagnosed in men worldwide. Albeit, the gold standard serum prostate-specific antigen (PSA) assays reduced the mortality rate of the disease, the number of false positive diagnoses steeply increased. Therefore, there is an urgent need for complementary biomarkers to enhance the specificity and selectivity of current diagnostic methods. Information about PSA glycosylation can help to fulfill this gap as alterations of its carbohydrate moieties due to cancerous transformation may represent additional markers to distinguish malignant from benign tumors. However, development of suitable methods and instrumentations to investigate the N-glycosylation profile of PSA represents a challenge. In this paper, we critically review the current bioanalytical trends and strategies in the field of PSA glycobiomarker research focusing on separation based characterization methods.
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8
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Camperi J, Dai L, Guillarme D, Stella C. Development of a 3D-LC/MS Workflow for Fast, Automated, and Effective Characterization of Glycosylation Patterns of Biotherapeutic Products. Anal Chem 2020; 92:4357-4363. [DOI: 10.1021/acs.analchem.9b05193] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Julien Camperi
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Lu Dai
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU, Rue Michel-Servet, 1, 1206 Geneva, Switzerland
| | - Cinzia Stella
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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9
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Haga Y, Uemura M, Baba S, Inamura K, Takeuchi K, Nonomura N, Ueda K. Identification of Multisialylated LacdiNAc Structures as Highly Prostate Cancer Specific Glycan Signatures on PSA. Anal Chem 2019; 91:2247-2254. [PMID: 30669833 DOI: 10.1021/acs.analchem.8b04829] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Serum prostate-specific antigen (PSA) test is the current gold standard for screening and diagnosis of prostate cancer (PCa), while overdiagnosis and overtreatment are social problems. In order to improve the specificity and exclude a false positive diagnosis in PSA test, PCa-specific glycosylation subtypes of PSA were explored using in-depth quantitative profiling of PSA glycoforms based on mass spectrometric oxonium ion monitoring technology. As a result of analysis using sera from 15 PCa or 15 benign prostate hyperplasia (BPH) patients whose PSA levels were in the "gray zone" (4.0-10.0 ng/mL), 52 glycan structures on PSA were quantitatively observed. We found that abundance of multisialylated LacdiNAc (GalNAcβ1-4GlcNAc) structures were significantly upregulated in the PCa group compared to the BPH group. A couple of those glycoforms were then extracted and subjected to establish a novel PCa-specific diagnosis model (PSA G-index). When the diagnostic power was assessed using an independent validation sample set (15 PCa and 15 BPH patients in the PSA gray zone), an AUC of PSA G-index was 1.00, while that of total PSA or PSA f/T ratio was 0.50 or 0.60, respectively. Moreover, both PSA glycoforms showed significant correlation with Gleason scores. Lectin histochemical staining analysis also showed that PCa cells overexpressed glycoproteins containing LacdiNAc and sialic acids moieties. Thus, PSA G-index could serve as not only an effective secondary screening method to exclude false positive diagnosis in PSA screening, but also a potential grading biomarker for PCa.
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Affiliation(s)
- Yoshimi Haga
- Cancer Proteomics Group, Cancer Precision Medicine Center , Japanese Foundation for Cancer Research , Tokyo 135-8550 , Japan
| | - Motohide Uemura
- Department of Urology , Osaka University Graduate School of Medicine , Osaka 565-0871 , Japan
| | - Satoko Baba
- Pathology Project for Molecular Targets, The Cancer Institute , Japanese Foundation for Cancer Research , Tokyo 135-8550 , Japan
| | - Kentaro Inamura
- Division of Pathology, the Cancer Institute , Japanese Foundation for Cancer Research , Tokyo 135-8550 , Japan
| | - Kengo Takeuchi
- Pathology Project for Molecular Targets, The Cancer Institute , Japanese Foundation for Cancer Research , Tokyo 135-8550 , Japan.,Division of Pathology, the Cancer Institute , Japanese Foundation for Cancer Research , Tokyo 135-8550 , Japan
| | - Norio Nonomura
- Department of Urology , Osaka University Graduate School of Medicine , Osaka 565-0871 , Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center , Japanese Foundation for Cancer Research , Tokyo 135-8550 , Japan
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10
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Iwamoto N, Yokoyama K, Takanashi M, Yonezawa A, Matsubara K, Shimada T. Verification between Original and Biosimilar Therapeutic Antibody Infliximab Using nSMOL Coupled LC-MS Bioanalysis in Human Serum. Curr Pharm Biotechnol 2018; 19:495-505. [PMID: 29968534 PMCID: PMC6198460 DOI: 10.2174/1389201019666180703093517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/29/2018] [Accepted: 07/02/2018] [Indexed: 12/14/2022]
Abstract
Background: Infliximab (IFX) is a chimeric therapeutic monoclonal antibody targeting tumor necrosis factor alpha (TNFα)-mediated inflammatory immune diseases. However, despite of an initial good clinical response, decrease in response to long-term treatment is a common observation. Objective: Recent studies suggest that IFX level in circulation has a correlation with clinical bioavailabil-ity. Therefore, the management of IFX dosage for individual manifestation by IFX monitoring may be valuable for the improvement of therapeutic response and outcomes. Method: In order to develop a broad IFX therapeutic monitoring in human serum, we have developed the validated IFX bioanalysis for RemicadeTM and its biosimilar product using our nano-surface and molecu-lar-orientation limited proteolysis (nSMOL) technology coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). The nSMOL chemistry has a unique property of Fab-selective prote-olysis, and makes it possible a global bioanalysis for many monoclonal antibodies. Results: The quantitation range of IFX in serum was from 0.293 to 300 μg/ml with good linearity. Quan-titation verification at the concentrations of 0.293, 0.879, 14.1 and 240 μg/ml was within 1.56-7.53% of precision and 98.9-111% of accuracy using H-chain signature peptide SINSATHYAESVK. Moreover, cross-verified bioanalysis of Remicade quantitation using biosimilar standard, and its opposite combina-tion, obtained an identical and inter-comparative results. Conclusion: The nSMOL strategy has the potential as a practical therapeutic monitoring technology in IFX therapeutic applications.
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Affiliation(s)
- Noriko Iwamoto
- Leading Technology of Bioanalysis and Protein Chemistry, Shimadzu Corporation, Kyoto, Japan
| | - Kotoko Yokoyama
- Leading Technology of Bioanalysis and Protein Chemistry, Shimadzu Corporation, Kyoto, Japan
| | - Megumi Takanashi
- Leading Technology of Bioanalysis and Protein Chemistry, Shimadzu Corporation, Kyoto, Japan
| | - Atsushi Yonezawa
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan.,Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kazuo Matsubara
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan
| | - Takashi Shimada
- Leading Technology of Bioanalysis and Protein Chemistry, Shimadzu Corporation, Kyoto, Japan
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11
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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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12
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Narimatsu H, Kaji H, Vakhrushev SY, Clausen H, Zhang H, Noro E, Togayachi A, Nagai-Okatani C, Kuno A, Zou X, Cheng L, Tao SC, Sun Y. Current Technologies for Complex Glycoproteomics and Their Applications to Biology/Disease-Driven Glycoproteomics. J Proteome Res 2018; 17:4097-4112. [PMID: 30359034 DOI: 10.1021/acs.jproteome.8b00515] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glycoproteomics is an important recent advance in the field of glycoscience. In glycomics, glycan structures are comprehensively analyzed after glycans are released from glycoproteins. However, a major limitation of glycomics is the lack of insight into glycoprotein functions. The Biology/Disease-driven Human Proteome Project has a particular focus on biological and medical applications. Glycoproteomics technologies aimed at obtaining a comprehensive understanding of intact glycoproteins, i.e., the kind of glycan structures that are attached to particular amino acids and proteins, have been developed. This Review focuses on the recent progress of the technologies and their applications. First, the methods for large-scale identification of both N- and O-glycosylated proteins are summarized. Next, the progress of analytical methods for intact glycopeptides is outlined. MS/MS-based methods were developed for improving the sensitivity and speed of the mass spectrometer, in parallel with the software for complex spectrum assignment. In addition, a unique approach to identify intact glycopeptides using MS1-based accurate masses is introduced. Finally, as an advance of glycomics, two approaches to provide the spatial distribution of glycans in cells are described, i.e., MS imaging and lectin microarray. These methods allow rapid glycomic profiling of different types of biological samples and thus facilitate glycoproteomics.
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Affiliation(s)
- Hisashi Narimatsu
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Hiroyuki Kaji
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics , University of Copenhagen , Blegdamsvej 3 , Copenhagen 2200 , Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics , University of Copenhagen , Blegdamsvej 3 , Copenhagen 2200 , Denmark
| | - Hui Zhang
- Center for Biomarker Discovery and Translation , Johns Hopkins University , 400 North Broadway , Baltimore , Maryland 21205 , United States
| | - Erika Noro
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Akira Togayachi
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Chiaki Nagai-Okatani
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Atsushi Kuno
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Xia Zou
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan.,Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Li Cheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Yangyang Sun
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
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13
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Hammura K, Ishikawa A, H. V. RK, Miyoshi R, Yokoi Y, Tanaka M, Hinou H, Nishimura SI. Synthetic Glycopeptides Allow for the Quantitation of Scarce Nonfucosylated IgG Fc N-Glycans of Therapeutic Antibody. ACS Med Chem Lett 2018; 9:889-894. [PMID: 30258536 DOI: 10.1021/acsmedchemlett.8b00127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/10/2018] [Indexed: 01/01/2023] Open
Abstract
Glycans attached to the IgG Fc domain affect strongly biological activities such as antibody-dependent cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC) of therapeutic antibodies. However, molecular mechanism in the glycoform-dependent functional modulation of the IgGs remains elusive. The present study communicates that selected reaction monitoring (SRM)-based assay of tryptic IgG Fc glycopeptides is a promising approach for the characterization of antibodies when combined with structure-defined synthetic Fc peptides having a focused N-glycoform as a calibration standard. We describe a novel synthetic approach to the human IgG1 Fc peptide having a bisected decasaccharide and its nonbisected counterpart compound, the signatures of antibodies involving Fc domain with rare N-glycans expected to show much higher ADCC/CDC than abundant IgG N-glycans, and their application to the SRM-based quantitative glycoproteomics. Use of a key intermediate, phenyl (2-O-benzyl-4,6-O-benzylidine-β-d-mannopyranosyl)-(1 → 4)-3,6-di-O-benzyl-2-azido-2-deoxy-1-thio-β-d-glucopyranoside, derived from locust bean gum galactomannan, facilitated greatly the synthesis of a bisected nonasaccharide as a stable precursor of oxazoline derivative needed for the enzymatic trans-glycosylation with Fc nonapeptide carrying a GlcNAc at Asn297 residue, while the coupling reaction catalyzed by mutant endo-M-N175Q proceeded very slowly. Strikingly, SRM assay using the synthetic Fc glycopeptides as calibration standards uncovered the occurrence of the targeted IgG1 Fc fragment carrying a nonfucosylated and bisected (315 fmol, 0.20%) and its nonbisected counterpart (1154 fmol, 0.73%) in the tryptic digests from 158 pmol of anticancer antibody Herceptin (trastuzumab). The results suggest that aberrantly glycosylated IgG Fc variants may contribute to the total biological activities of the therapeutic antibodies.
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Affiliation(s)
- Kazuki Hammura
- Division of Drug Discovery Research, Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo 001-0021, Japan
| | - Akari Ishikawa
- Division of Drug Discovery Research, Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo 001-0021, Japan
| | - Ravi Kumar H. V.
- Division of Drug Discovery Research, Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo 001-0021, Japan
| | - Risho Miyoshi
- Medicinal Chemistry Pharmaceuticals, Co., Ltd.,
N9, W15, Chuo-ku, Sapporo 060-0009, Japan
| | - Yasuhiro Yokoi
- Division of Drug Discovery Research, Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo 001-0021, Japan
| | - Masakazu Tanaka
- Medicinal Chemistry Pharmaceuticals, Co., Ltd.,
N9, W15, Chuo-ku, Sapporo 060-0009, Japan
| | - Hiroshi Hinou
- Division of Drug Discovery Research, Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo 001-0021, Japan
- Medicinal Chemistry Pharmaceuticals, Co., Ltd.,
N9, W15, Chuo-ku, Sapporo 060-0009, Japan
| | - Shin-Ichiro Nishimura
- Division of Drug Discovery Research, Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo 001-0021, Japan
- Medicinal Chemistry Pharmaceuticals, Co., Ltd.,
N9, W15, Chuo-ku, Sapporo 060-0009, Japan
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14
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Madsen JA, Farutin V, Lin YY, Smith S, Capila I. Data-independent oxonium ion profiling of multi-glycosylated biotherapeutics. MAbs 2018; 10:968-978. [PMID: 30067433 PMCID: PMC6204843 DOI: 10.1080/19420862.2018.1494106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The characterization of glycosylation is required for many protein therapeutics. The emergence of antibody and antibody-like molecules with multiple glycan attachment sites has rendered glycan analysis increasingly more complicated. Reliance on site-specific glycopeptide analysis is therefore necessary to fully analyze multi-glycosylated biotherapeutics. Established glycopeptide methodologies have generally utilized a priori knowledge of the glycosylation states of the investigated protein(s), database searching of results generated from data-dependent liquid chromatography–tandem mass spectrometry workflows, and extracted ion quantitation of the individual identified species. However, the inherent complexity of glycosylation makes predicting all glycoforms on all glycosylation sites extremely challenging, if not impossible. That is, only the “knowns” are assessed. Here, we describe an agnostic methodology to qualitatively and quantitatively assess both “known” and “unknown” site-specific glycosylation for biotherapeutics that contain multiple glycosylation sites. The workflow uses data-independent, all ion fragmentation to generate glycan oxonium ions, which are then extracted across the entirety of the chromatographic timeline to produce a glycan-specific “fingerprint” of the glycoprotein sample. We utilized both HexNAc and sialic acid oxonium ion profiles to quickly assess the presence of Fab glycosylation in a therapeutic monoclonal antibody, as well as for high-throughput comparisons of multi-glycosylated protein drugs derived from different clones to a reference product. An automated method was created to rapidly assess oxonium profiles between samples, and to provide a quantitative assessment of similarity.
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Affiliation(s)
- James A Madsen
- a Pharmaceutical Sciences and Research , Momenta Pharmaceuticals , Cambridge , MA , USA
| | - Victor Farutin
- a Pharmaceutical Sciences and Research , Momenta Pharmaceuticals , Cambridge , MA , USA
| | - Yin Yin Lin
- a Pharmaceutical Sciences and Research , Momenta Pharmaceuticals , Cambridge , MA , USA
| | - Stephen Smith
- a Pharmaceutical Sciences and Research , Momenta Pharmaceuticals , Cambridge , MA , USA
| | - Ishan Capila
- a Pharmaceutical Sciences and Research , Momenta Pharmaceuticals , Cambridge , MA , USA
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15
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Rathore D, Faustino A, Schiel J, Pang E, Boyne M, Rogstad S. The role of mass spectrometry in the characterization of biologic protein products. Expert Rev Proteomics 2018; 15:431-449. [DOI: 10.1080/14789450.2018.1469982] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Deepali Rathore
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Anneliese Faustino
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - John Schiel
- Biomolecular Measurement Division, National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Eric Pang
- Office of Lifecycle Drug Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Michael Boyne
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
- COUR Pharmaceuticals Development Company, Northbrook, IL, USA
| | - Sarah Rogstad
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
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16
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Fulton KM, Li J, Tomas JM, Smith JC, Twine SM. Characterizing bacterial glycoproteins with LC-MS. Expert Rev Proteomics 2018; 15:203-216. [PMID: 29400572 DOI: 10.1080/14789450.2018.1435276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Though eukaryotic glycoproteins have been studied since their discovery in the 1930s, the first bacterial glycoprotein was not identified until the 1970s. As a result, their role in bacterial pathogenesis is still not well understood and they remain an understudied component of bacterial virulence. In recent years, mass spectrometry has emerged as a leading technology for the study of bacterial glycoproteins, largely due to its sensitivity and versatility. Areas covered: Identification and comprehensive characterization of bacterial glycoproteins usually requires multiple complementary mass spectrometry approaches, including intact protein analysis, top-down analysis, and bottom-up methods used in combination with specialized liquid chromatography. This review provides an overview of liquid chromatography separation technologies, as well as current and emerging mass spectrometry approaches used specifically for bacterial glycoprotein identification and characterization. Expert commentary: Bacterial glycoproteins may have significant clinical utility as a result of their unique structures and exposure on the surface of the cells. Better understanding of these glycoconjugates is an essential first step towards that goal. These often unique structures, and by extension the key enzymes involved in their synthesis, represent promising targets for novel antimicrobials, while unique carbohydrate structures may be used as antigens in vaccines or as biomarkers.
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Affiliation(s)
- Kelly M Fulton
- a Human Health Therapeutics Portfolio , National Research Council Canada , Ottawa , Canada
| | - Jianjun Li
- a Human Health Therapeutics Portfolio , National Research Council Canada , Ottawa , Canada
| | - Juan M Tomas
- b Departament de Microbiologia, Facultat de Biologia , Universitat de Barcelona , Barcelona , Spain
| | - Jeffrey C Smith
- c Department of Chemistry , Carleton University , Ottawa , Canada
| | - Susan M Twine
- a Human Health Therapeutics Portfolio , National Research Council Canada , Ottawa , Canada
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17
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Lee JH, Reier J, Heffner KM, Barton C, Spencer D, Schmelzer AE, Venkat R. Production and characterization of active recombinant human factor II with consistent sialylation. Biotechnol Bioeng 2017; 114:1991-2000. [DOI: 10.1002/bit.26317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 04/04/2017] [Accepted: 04/17/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Jeong H. Lee
- Biopharmaceutical Development; MedImmune; 1 MedImmune Way Gaithersburg 20878 Maryland
| | - Jason Reier
- Biopharmaceutical Development; MedImmune; 1 MedImmune Way Gaithersburg 20878 Maryland
| | - Kelley M. Heffner
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; Baltimore Maryland
| | | | - David Spencer
- Ipsen Biopharm Limited; Wrexham Industrial Estate, Wrexham United Kingdom
| | - Albert E. Schmelzer
- Biopharmaceutical Development; MedImmune; 1 MedImmune Way Gaithersburg 20878 Maryland
| | - Raghavan Venkat
- Biopharmaceutical Development; MedImmune; 1 MedImmune Way Gaithersburg 20878 Maryland
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18
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Bora de Oliveira K, Spencer D, Barton C, Agarwal N. Site-specific monitoring of N-Glycosylation profiles of a CTLA4-Fc-fusion protein from the secretory pathway to the extracellular environment. Biotechnol Bioeng 2017; 114:1550-1560. [PMID: 28186328 DOI: 10.1002/bit.26266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/31/2017] [Accepted: 02/06/2017] [Indexed: 01/18/2023]
Abstract
Glycosylation often plays a key role in the safety and efficacy of therapeutic proteins to patients, thus underlying the need for consistent control of this important post-translational modification during biologics production. In this study, we profiled the site-specific evolution of N-glycans on a CTLA4-Fc-fusion protein, from the intracellular secretory pathway to the conditioned medium (CM) in fed-batch cell culture. For this, we developed an approach that combined sub-cellular fractionation with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses. The study revealed that there was a significant amount of heterogeneity in the glycans displayed amongst the three distinct N-glycosylation sites. Furthermore, 54-60% of the intracellular protein was characterized by Man8 and Man9 glycans on day 10, when the cell density peaks, indicative of a significant bottleneck between the endoplasmic reticulum (ER) and the cis-Golgi. At longer culture duration, the accumulation of intracellular protein with bi-antennary-fucosylated GlcNAc-terminated residues identified the formation of another bottleneck in the medial and trans-Golgi compartments, which subsequently led to a decrease in sialylated species in the secreted protein. Glucose deprivation caused a reduction in the Man8 and Man9 glycans in favor of Man5 glycans and bi-antennary-fucosylated GlcNAc-terminated residues in the organellar pool of the Fc-fusion protein. However, transient deprivation of glucose did not lead to major differences in the glycan profile of proteins secreted into the CM. The approach developed here allows us to probe the secretory pathway and sheds light on the site-specific intracellular processing of glycans during fed-batch cell culture, thus serving as an initial step towards their rational control. Biotechnol. Bioeng. 2017;114: 1550-1560. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
| | - David Spencer
- MedImmune LLC., One MedImmune Way, Gaithersburg, Maryland 20878
| | | | - Nitin Agarwal
- MedImmune LLC., One MedImmune Way, Gaithersburg, Maryland 20878
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19
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D’Atri V, Fekete S, Beck A, Lauber M, Guillarme D. Hydrophilic Interaction Chromatography Hyphenated with Mass Spectrometry: A Powerful Analytical Tool for the Comparison of Originator and Biosimilar Therapeutic Monoclonal Antibodies at the Middle-up Level of Analysis. Anal Chem 2017; 89:2086-2092. [DOI: 10.1021/acs.analchem.6b04726] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Valentina D’Atri
- School
of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Szabolcs Fekete
- School
of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Alain Beck
- Center of Immunology
Pierre Fabre, 5 Avenue Napoléon
III, BP 60497, Saint-Julien-en-Genevois, France
| | - Matthew Lauber
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757-3696, United States
| | - Davy Guillarme
- School
of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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20
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Analysis of therapeutic monoclonal antibody glycoforms by mass spectrometry for pharmacokinetics study. Talanta 2017; 165:664-670. [PMID: 28153314 DOI: 10.1016/j.talanta.2017.01.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/28/2016] [Accepted: 01/06/2017] [Indexed: 02/02/2023]
Abstract
Monoclonal antibodies (mAbs), are one of the most important protein drugs have attracted increasing attention. However, the pharmacokinetics of mAbs has not been fully investigated due to the complexity of protein drugs. Traditonal immuno-based approaches can not recognize the proteoforms of mAbs because of the long development cycles, prohibitive cost, and interactions between different proteins. Therefore, reliable qualitative and quantitative analysis of the proteoforms of mAbs in biological samples is of crucial importance. Herein, a novel method was developed for absolute quantitation of mAbs and their glycoforms in complex biological samples such as serum and tissues. With the combination of HILIC enrichment and parallel reaction monitoring by high resolution mass spectrometry, most of the glycoforms can be accurately quantified at the fmol level through the use of the model mAb of bevacizumab. More importantly, the structural confirmation can be achieved simultaneously without the need for additional experiments. This strategy can be readily applied to the pharmacokinetic study of glycosylation modification and biomarker discovery for clinical applications.
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21
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Kanie Y, Kanie O. Addressing the glycan complexity by using mass spectrometry: In the pursuit of decoding glycologic. ACTA ACUST UNITED AC 2017. [DOI: 10.7243/2052-9341-5-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Production process reproducibility and product quality consistency of transient gene expression in HEK293 cells with anti-PD1 antibody as the model protein. Appl Microbiol Biotechnol 2016; 101:1889-1898. [PMID: 27853858 DOI: 10.1007/s00253-016-7973-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/19/2016] [Accepted: 10/26/2016] [Indexed: 10/20/2022]
Abstract
Demonstration of reproducibility and consistency of process and product quality is one of the most crucial issues in using transient gene expression (TGE) technology for biopharmaceutical development. In this study, we challenged the production consistency of TGE by expressing nine batches of recombinant IgG antibody in human embryonic kidney 293 cells to evaluate reproducibility including viable cell density, viability, apoptotic status, and antibody yield in cell culture supernatant. Product quality including isoelectric point, binding affinity, secondary structure, and thermal stability was assessed as well. In addition, major glycan forms of antibody from different batches of production were compared to demonstrate glycosylation consistency. Glycan compositions of the antibody harvested at different time periods were also measured to illustrate N-glycan distribution over the culture time. From the results, it has been demonstrated that different TGE batches are reproducible from lot to lot in overall cell growth, product yield, and product qualities including isoelectric point, binding affinity, secondary structure, and thermal stability. Furthermore, major N-glycan compositions are consistent among different TGE batches and conserved during cell culture time.
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23
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Murakami T, Iwamuro Y, Ishimaru R, Chinaka S, Sugimura N, Takayama N. Differentiation of AB-FUBINACA positional isomers by the abundance of product ions using electron ionization-triple quadrupole mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1016-1022. [PMID: 27441731 DOI: 10.1002/jms.3814] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 07/07/2016] [Accepted: 07/16/2016] [Indexed: 06/06/2023]
Abstract
Mass spectrometric differentiation of structural isomers is important for the analysis of forensic samples. Presently, there is no mass spectrometric method for differentiating halogen positional isomers of cannabimimetic compounds. We describe here a novel and practical method for differentiating one of these compounds, N-(1-amino-3-methyl-1-oxobutan-2-yl)-1-(4-fluorobenzyl)-1H-indazole-3-carboxamide (AB-FUBINACA (para)), and its fluoro positional (ortho and meta) isomers in the phenyl ring by electron ionization-triple quadrupole mass spectrometry. It was found that the three isomers differed in the relative abundance of the ion at m/z 109 and 253 in the product ion spectra, while the detected product ions were identical. The logarithmic values of the abundance ratio of the ions at m/z 109 to 253 (ln(A109 /A253 )) were in the order meta < ortho < para and increased linearly with collision energy. The differences in abundances were attributed to differences in the dissociation reactivity between the indazole moiety and the fluorobenzyl group because of the halogen-positional effect on the phenyl ring. Our methodology, which is based on the abundance of the product ions in mass spectra, should be applicable to determination of the structures of other newly encountered designer drugs. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Takaya Murakami
- Forensic Science Laboratory, Ishikawa Prefectural Police H.Q., 1-1 Kuratsuki, Kanazawa, Ishikawa, 920-8553, Japan.
| | - Yoshiaki Iwamuro
- Forensic Science Laboratory, Ishikawa Prefectural Police H.Q., 1-1 Kuratsuki, Kanazawa, Ishikawa, 920-8553, Japan
| | - Reiko Ishimaru
- Forensic Science Laboratory, Ishikawa Prefectural Police H.Q., 1-1 Kuratsuki, Kanazawa, Ishikawa, 920-8553, Japan
| | - Satoshi Chinaka
- Forensic Science Laboratory, Ishikawa Prefectural Police H.Q., 1-1 Kuratsuki, Kanazawa, Ishikawa, 920-8553, Japan
| | - Natsuhiko Sugimura
- Materials Characterization Central Laboratory, Waseda University, 3-4-1 Ohkubo, Shinjyuku, Tokyo, 169-8555, Japan
| | - Nariaki Takayama
- Forensic Science Laboratory, Ishikawa Prefectural Police H.Q., 1-1 Kuratsuki, Kanazawa, Ishikawa, 920-8553, Japan
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24
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Sanda M, Goldman R. Data Independent Analysis of IgG Glycoforms in Samples of Unfractionated Human Plasma. Anal Chem 2016; 88:10118-10125. [PMID: 27649061 PMCID: PMC5803558 DOI: 10.1021/acs.analchem.6b02554] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Glycosylation regulates functional responses mediated by the interaction of IgG with their receptors. Multiple analytical methods have been designed for the determination of the IgG N-glycan microheterogeneity, including MS methods for the analysis of site specific glycoforms of IgG. However, measurement of low abundant glycoforms remains challenging in complex samples like serum without enrichment of the IgG. We present a workflow for quantitative analysis of site specific glycoforms of IgG based on data independent acquisition (DIA) of Y-ions generated under "minimal" fragmentation conditions. The adjusted collision induced dissociation (CID) conditions generate specific Y-ions in the yield of up to 60% precursor ion intensity. These selective fragments, measured in high resolution, improve specificity of detection compared to the typically quantified B-ions which have higher overall intensity but lower signal-to-noise ratios. Under optimized conditions, we achieve label-free quantification of the majority of previously reported glycoforms of IgG (26 glycoforms of IgG1, 22 glycoforms of IgG 2/3, and 19 glycoforms of IgG4) directly in unfractionated samples of human plasma and we detect traces of previously unreported glycoforms of IgG1, including doubly fucosylated glycoforms. The SWATH data independent quantification of IgG glycoforms in pooled plasma samples of patients with liver cirrhosis detects reliably the expected changes in the quantity of major glycoforms compared to healthy controls. Our results show that optimized CID fragmentation enables DIA of IgG glycoforms and suggest that such workflow may enable quantitative analyses of the glycoproteome in complex matrixes.
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Affiliation(s)
- Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia 20057, United States
| | - Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia 20057, United States
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia 20057, United States
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25
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Jacobs JF, Wevers RA, Lefeber DJ, van Scherpenzeel M. Fast, robust and high-resolution glycosylation profiling of intact monoclonal IgG antibodies using nanoLC-chip-QTOF. Clin Chim Acta 2016; 461:90-7. [DOI: 10.1016/j.cca.2016.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 12/31/2022]
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26
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Integrated GlycoProteome Analyzer (I-GPA) for Automated Identification and Quantitation of Site-Specific N-Glycosylation. Sci Rep 2016; 6:21175. [PMID: 26883985 PMCID: PMC4756296 DOI: 10.1038/srep21175] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 01/19/2016] [Indexed: 01/01/2023] Open
Abstract
Human glycoproteins exhibit enormous heterogeneity at each N-glycosite, but few studies have attempted to globally characterize the site-specific structural features. We have developed Integrated GlycoProteome Analyzer (I-GPA) including mapping system for complex N-glycoproteomes, which combines methods for tandem mass spectrometry with a database search and algorithmic suite. Using an N-glycopeptide database that we constructed, we created novel scoring algorithms with decoy glycopeptides, where 95 N-glycopeptides from standard α1-acid glycoprotein were identified with 0% false positives, giving the same results as manual validation. Additionally automated label-free quantitation method was first developed that utilizes the combined intensity of top three isotope peaks at three highest MS spectral points. The efficiency of I-GPA was demonstrated by automatically identifying 619 site-specific N-glycopeptides with FDR ≤ 1%, and simultaneously quantifying 598 N-glycopeptides, from human plasma samples that are known to contain highly glycosylated proteins. Thus, I-GPA platform could make a major breakthrough in high-throughput mapping of complex N-glycoproteomes, which can be applied to biomarker discovery and ongoing global human proteome project.
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27
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Cong Y, Zhang Z, Zhang S, Hu L, Gu J. Quantitative MS analysis of therapeutic mAbs and their glycosylation for pharmacokinetics study. Proteomics Clin Appl 2015; 10:303-14. [DOI: 10.1002/prca.201500098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/24/2015] [Accepted: 11/03/2015] [Indexed: 02/04/2023]
Affiliation(s)
- Yuting Cong
- Research Center for Drug Metabolism; School of Life Sciences; Jilin University; Changchun China
- 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
| | - 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
| | - Shen 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
| | - Lianghai Hu
- Research Center for Drug Metabolism; School of Life Sciences; Jilin University; Changchun China
| | - Jingkai Gu
- Research Center for Drug Metabolism; School of Life Sciences; Jilin University; Changchun China
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28
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Defaus S, Gupta P, Andreu D, Gutiérrez-Gallego R. Mammalian protein glycosylation--structure versus function. Analyst 2015; 139:2944-67. [PMID: 24779027 DOI: 10.1039/c3an02245e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Carbohydrates fulfil many common as well as extremely important functions in nature. They show a variety of molecular displays--e.g., free mono-, oligo-, and polysaccharides, glycolipids, proteoglycans, glycoproteins, etc.--with particular roles and localizations in living organisms. Structure-specific peculiarities are so many and diverse that it becomes virtually impossible to cover them all from an analytical perspective. Hence this manuscript, focused on mammalian glycosylation, rather than a complete list of analytical descriptors or recognized functions for carbohydrate structures, comprehensively reviews three central issues in current glycoscience, namely (i) structural analysis of glycoprotein glycans, covering both classical and novel approaches for teasing out the structural puzzle as well as potential pitfalls of these processes; (ii) an overview of functions attributed to carbohydrates, covering from monosaccharide to complex, well-defined epitopes and full glycans, including post-glycosylational modifications, and (iii) recent technical advances allowing structural identification of glycoprotein glycans with simultaneous assignation of biological functions.
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Affiliation(s)
- S Defaus
- Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona Biomedical Research Park, 08003 Barcelona, Spain.
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29
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Chen CH, Lin YP, Lin JL, Li ST, Ren CT, Wu CY, Chen CH. Rapid Identification of Terminal Sialic Acid Linkage Isomers by Pseudo-MS3Mass Spectrometry. Isr J Chem 2015. [DOI: 10.1002/ijch.201400141] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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30
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Ahn YH, Kim JY, Yoo JS. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods. MASS SPECTROMETRY REVIEWS 2015; 34:148-65. [PMID: 24889823 PMCID: PMC4340049 DOI: 10.1002/mas.21428] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/20/2013] [Indexed: 05/12/2023]
Abstract
Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies.
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Affiliation(s)
- Yeong Hee Ahn
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
| | - Jin Young Kim
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
| | - Jong Shin Yoo
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
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31
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Goldman R, Sanda M. Targeted methods for quantitative analysis of protein glycosylation. Proteomics Clin Appl 2015; 9:17-32. [PMID: 25522218 DOI: 10.1002/prca.201400152] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/15/2014] [Accepted: 12/11/2014] [Indexed: 12/17/2022]
Abstract
Quantification of proteins by LC-MS/MS-MRM has become a standard method with broad projected clinical applicability. MRM quantification of protein modifications is, however, far less utilized, especially in the case of glycoproteins. This review summarizes current methods for quantitative analysis of protein glycosylation with a focus on MRM methods. We describe advantages of this quantitative approach, analytical parameters that need to be optimized to achieve reliable measurements, and point out the limitations. Differences between major classes of N- and O-glycopeptides are described and class-specific glycopeptide assays are demonstrated.
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Affiliation(s)
- Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC, USA; Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA
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32
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Quantitative analysis of immunoglobulin subclasses and subclass specific glycosylation by LC-MS-MRM in liver disease. J Proteomics 2015; 116:24-33. [PMID: 25582524 DOI: 10.1016/j.jprot.2014.12.020] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/13/2014] [Accepted: 12/09/2014] [Indexed: 12/23/2022]
Abstract
UNLABELLED Aberrant glycosylation of IgGs has been linked to human diseases, including liver disease. In this study, we have quantified plasma immunoglobulins in cirrhosis (CIR) and hepatocellular carcinoma (HCC) and employed a novel LC-MS-MRM assay to quantify glycoforms of IgG subclasses 1-4. Glycan oxonium ions and peptide-GlcNAc fragment ions were utilized to quantify the IgG glycoforms purified by affinity chromatography with normalization to the unique peptide for each IgG subclass. Our results indicate that HCC patients have increased circulating IgG1, IgG3, IgA1, and IgM compared to healthy controls; comparison of HCC and CIR patients shows that HCC patients have significantly higher concentration of IgG1 and IgM but lower concentration of IgG2. An increase in galactose-deficient core fucosylated glycoforms was consistently observed in CIR and HCC patients. The FA2G0 and FA2BG0 glycoforms increase approximately 2-fold in all IgG subclasses accompanied by a decrease in the FA2G2 glycoform. Fucosylation changes are less pronounced but we have detected increased degree of fucosylation in the IgG1 and IgG3 glycoforms. In conclusion, we have optimized a sensitive and selective LC-MS-MRM method for the quantification of immunoglobulin subclasses and their site specific glycoforms, demonstrating that both quantities and glycoforms of immunoglobulins change significantly in liver disease progression to HCC. BIOLOGICAL SIGNIFICANCE We have demonstrated that both quantities and glycoforms of immunoglobulin subclasses change significantly in liver disease progression to HCC through quantitative study of immunoglobulin subclasses and their site specific glycoforms using a sensitive and selective LC-MS-MRM method. Redistribution of the glycoforms of specific immunoglobulin subclasses could have important implications for receptor mediated responses affecting the progression of liver disease.
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33
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Lazar IM, Deng J, Ikenishi F, Lazar AC. Exploring the glycoproteomics landscape with advanced MS technologies. Electrophoresis 2014; 36:225-37. [PMID: 25311661 DOI: 10.1002/elps.201400400] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/28/2014] [Accepted: 09/29/2014] [Indexed: 12/13/2022]
Abstract
The advance of glycoproteomic technologies has offered unique insights into the importance of glycosylation in determining the functional roles of a protein within a cell. Biologically active glycoproteins include the categories of enzymes, hormones, proteins involved in cell proliferation, cell membrane proteins involved in cell-cell recognition, and communication events or secreted proteins, just to name a few. The recent progress in analytical instrumentation, methodologies, and computational approaches has enabled a detailed exploration of glycan structure, connectivity, and heterogeneity, underscoring the staggering complexity of the glycome repertoire in a cell. A variety of approaches involving the use of spectroscopy, MS, separation, microfluidic, and microarray technologies have been used alone or in combination to tackle the glycoproteome challenge, the research results of these efforts being captured in an overwhelming number of annual publications. This work is aimed at reviewing the major developments and accomplishments in the field of glycoproteomics, with focus on the most recent advancements (2012-2014) that involve the use of capillary separations and MS detection.
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Affiliation(s)
- Iulia M Lazar
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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34
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Hoffmann W, Hofmann J, Pagel K. Energy-resolved ion mobility-mass spectrometry--a concept to improve the separation of isomeric carbohydrates. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:471-479. [PMID: 24385395 DOI: 10.1007/s13361-013-0780-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 11/01/2013] [Accepted: 11/04/2013] [Indexed: 06/03/2023]
Abstract
Recent works using ion mobility-mass spectrometry (IM-MS) have highlighted the power of this instrumental configuration to tackle one of the greatest challenges in glycomics and glycoproteomics: the existence of isobaric isomers. For a successful separation of species with identical mass but different structure via IM-MS, it is crucial to have sufficient IM resolution. In commercially available IM-MS instruments, however, this resolution is limited by the design of the instrument and usually cannot be increased at-will without extensive modifications. Here, we present a systematic approach to improve the resolving capability of IM-MS instruments using so-called energy-resolved ion mobility-mass spectrometry. The technique utilizes the fact that individual components in an isobaric mixture fragment at considerably different energies when activated in the gas phase via collision-induced dissociation (CID). As a result, certain components can be suppressed selectively at increased CID activation energy. Using a mixture of four isobaric carbohydrates, we show that each of the individual sugars can be resolved and unambiguously identified even when their drift times differ by as little as 3%. However, the presented results also indicate that a certain difference in the gas-phase stability of the individual components is crucial for a successful separation via energy-resolved IM-MS.
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Affiliation(s)
- Waldemar Hoffmann
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
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35
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Kailemia MJ, Ruhaak LR, Lebrilla CB, Amster IJ. Oligosaccharide analysis by mass spectrometry: a review of recent developments. Anal Chem 2014; 86:196-212. [PMID: 24313268 PMCID: PMC3924431 DOI: 10.1021/ac403969n] [Citation(s) in RCA: 266] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - L. Renee Ruhaak
- Department of Chemistry, University of California at Davis, Davis, CA 95616
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36
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Barton C, Spencer D, Levitskaya S, Feng J, Harris R, Schenerman MA. Heterogeneity of IgGs: Role of Production, Processing, and Storage on Structure and Function. ACS SYMPOSIUM SERIES 2014. [DOI: 10.1021/bk-2014-1176.ch003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Chris Barton
- Analytical Biotechnology, MedImmune, Gaithersburg, Maryland 20878, United States
- Genentech, Inc., South San Francisco, California 94080, United States
| | - David Spencer
- Analytical Biotechnology, MedImmune, Gaithersburg, Maryland 20878, United States
- Genentech, Inc., South San Francisco, California 94080, United States
| | - Sophia Levitskaya
- Analytical Biotechnology, MedImmune, Gaithersburg, Maryland 20878, United States
- Genentech, Inc., South San Francisco, California 94080, United States
| | - Jinhua Feng
- Analytical Biotechnology, MedImmune, Gaithersburg, Maryland 20878, United States
- Genentech, Inc., South San Francisco, California 94080, United States
| | - Reed Harris
- Analytical Biotechnology, MedImmune, Gaithersburg, Maryland 20878, United States
- Genentech, Inc., South San Francisco, California 94080, United States
| | - Mark A. Schenerman
- Analytical Biotechnology, MedImmune, Gaithersburg, Maryland 20878, United States
- Genentech, Inc., South San Francisco, California 94080, United States
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37
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Ueda K. Glycoproteomic strategies: From discovery to clinical application of cancer carbohydrate biomarkers. Proteomics Clin Appl 2013; 7:607-17. [PMID: 23640819 DOI: 10.1002/prca.201200123] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
Carbohydrate antigens are the most frequently and traditionally used biomarkers for cancer, such as CA19-9, CA125, DUPAN-II, AFP-L3, and many others. The diagnostic potential of them was simply based on the cancer-specific alterations of glycan structures on particular glycoproteins in serum/plasma. In spite of the facts that glycosylation disorders are feasible for cancer biomarkers and glycomic analysis technologies to explore them have been rapidly developed, it remains difficult to sensitively screen glycan structure changes on cancer-associated glycoproteins from clinical specimens. Moreover, a lot of additional issues should be appropriately addressed for the clinical application of newly identified glycosylation biomarkers, including analytical throughput, quantitative confirmation of structural changes, and biological explanation for the alterations. In the last decade, significant improvement of mass spectrometric techniques is being made in the aspects of both hardware spec and preanalytical purification procedures for glycoprotein analysis. Here we review potential approaches to perform comprehensive analysis of glycoproteomic biomarker screening from serum/plasma and to realize high-throughput validation of site-specific oligosaccharide variations. The power and problems of mass spectrometric applications on the clinical use of carbohydrate biomarkers are also discussed in this review.
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Affiliation(s)
- Koji Ueda
- Laboratory for Biomarker Development, Center for Genomic Medicine, RIKEN, Minato-ku, Tokyo, Japan.
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38
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Beck A, Reichert JM. Approval of the first biosimilar antibodies in Europe: a major landmark for the biopharmaceutical industry. MAbs 2013; 5:621-3. [PMID: 23924791 PMCID: PMC3851211 DOI: 10.4161/mabs.25864] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In a defining moment for the European Medicines Agency (EMA) and the biopharmaceutical industry, on June 27, 2013 EMA's Committee for Medicinal Products for Human Use adopted a positive opinion for two biosimilar infliximab products (Celltrion's Remsima® and Hospira's Inflectra®), and recommended that they be approved for marketing in the European Union (EU). The European Commission's decision on an application is typically issued 67 d after an opinion is provided; thus, decisions are expected in early September 2013. If approved, the products will comprise the first biosimilar antibody made available to patients in a highly regulated market, although launch may be delayed due to an extension of the reference product's (Remicade®) patent in the EU.
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Affiliation(s)
- Alain Beck
- Centre d'Immunologie Pierre Fabre; Saint-Julien-en-Genevois, France
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39
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Chandler KB, Pompach P, Goldman R, Edwards N. Exploring site-specific N-glycosylation microheterogeneity of haptoglobin using glycopeptide CID tandem mass spectra and glycan database search. J Proteome Res 2013; 12:3652-66. [PMID: 23829323 DOI: 10.1021/pr400196s] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Glycosylation is a common protein modification with a significant role in many vital cellular processes and human diseases, making the characterization of protein-attached glycan structures important for understanding cell biology and disease processes. Direct analysis of protein N-glycosylation by tandem mass spectrometry of glycopeptides promises site-specific elucidation of N-glycan microheterogeneity, something that detached N-glycan and deglycosylated peptide analyses cannot provide. However, successful implementation of direct N-glycopeptide analysis by tandem mass spectrometry remains a challenge. In this work, we consider algorithmic techniques for the analysis of LC-MS/MS data acquired from glycopeptide-enriched fractions of enzymatic digests of purified proteins. We implement a computational strategy that takes advantage of the properties of CID fragmentation spectra of N-glycopeptides, matching the MS/MS spectra to peptide-glycan pairs from protein sequences and glycan structure databases. Significantly, we also propose a novel false discovery rate estimation technique to estimate and manage the number of false identifications. We use a human glycoprotein standard, haptoglobin, digested with trypsin and GluC, enriched for glycopeptides using HILIC chromatography, and analyzed by LC-MS/MS to demonstrate our algorithmic strategy and evaluate its performance. Our software, GlycoPeptideSearch (GPS), assigned glycopeptide identifications to 246 of the spectra at a false discovery rate of 5.58%, identifying 42 distinct haptoglobin peptide-glycan pairs at each of the four haptoglobin N-linked glycosylation sites. We further demonstrate the effectiveness of this approach by analyzing plasma-derived haptoglobin, identifying 136 N-linked glycopeptide spectra at a false discovery rate of 0.4%, representing 15 distinct glycopeptides on at least three of the four N-linked glycosylation sites. The software, GlycoPeptideSearch, is available for download from http://edwardslab.bmcb.georgetown.edu/GPS .
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Affiliation(s)
- Kevin Brown Chandler
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
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40
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Chandler K, Goldman R. Glycoprotein disease markers and single protein-omics. Mol Cell Proteomics 2013; 12:836-45. [PMID: 23399550 PMCID: PMC3617330 DOI: 10.1074/mcp.r112.026930] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/07/2013] [Indexed: 12/14/2022] Open
Abstract
Glycoproteins are well represented among biomarkers for inflammatory and cancer diseases. Secreted and membrane-associated glycoproteins make excellent targets for noninvasive detection. In this review, we discuss clinically applicable markers of cancer diseases and methods for their analysis. High throughput discovery continues to supply marker candidates with unusual glycan structures, altered glycoprotein abundance, or distribution of site-specific glycoforms. Improved analytical methods are needed to unlock the potential of these discoveries in validated clinical assays. A new generation of targeted quantitative assays is expected to advance the use of glycoproteins in early detection of diseases, molecular disease classification, and monitoring of therapeutic interventions.
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Affiliation(s)
- Kevin Chandler
- From the Departments of ‡Biochemistry and Molecular and Cellular Biology and
| | - Radoslav Goldman
- From the Departments of ‡Biochemistry and Molecular and Cellular Biology and
- ¶Oncology, Georgetown University, Washington, D.C. 20057
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41
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Zauner G, Selman MHJ, Bondt A, Rombouts Y, Blank D, Deelder AM, Wuhrer M. Glycoproteomic analysis of antibodies. Mol Cell Proteomics 2013; 12:856-65. [PMID: 23325769 PMCID: PMC3617332 DOI: 10.1074/mcp.r112.026005] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Antibody glycosylation has been shown to change with various processes. This review presents mass spectrometric approaches for antibody glycosylation analysis at the level of released glycans, glycopeptides, and intact protein. With regard to IgG fragment crystallizable glycosylation, mass spectrometry has shown its potential for subclass-specific, high-throughput analysis. In contrast, because of the vast heterogeneity of peptide moieties, fragment antigen binding glycosylation analysis of polyclonal IgG relies entirely on glycan release. Next to IgG, IgA has gained some attention, and studies of its O- and N-glycosylation have revealed disease-associated glycosylation changes. Glycoproteomic analyses of IgM and IgE are lagging behind but should complete our picture of glycosylation's influence on antibody function.
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Affiliation(s)
- Gerhild Zauner
- Biomolecular Mass Spectrometry Unit, Postbus 9600, 2300RC Leiden University Medical Center, Leiden, The Netherlands
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42
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Beck A, Wagner-Rousset E, Ayoub D, Van Dorsselaer A, Sanglier-Cianférani S. Characterization of Therapeutic Antibodies and Related Products. Anal Chem 2012; 85:715-36. [DOI: 10.1021/ac3032355] [Citation(s) in RCA: 445] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alain Beck
- Centre d’Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164 Saint-Julien-en-Genevois,
France
| | - Elsa Wagner-Rousset
- Centre d’Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164 Saint-Julien-en-Genevois,
France
| | - Daniel Ayoub
- Centre d’Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164 Saint-Julien-en-Genevois,
France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie
de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087, Strasbourg, France and CNRS, UMR7178, 67037 Strasbourg, France
| | - Sarah Sanglier-Cianférani
- Laboratoire de Spectrométrie
de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087, Strasbourg, France and CNRS, UMR7178, 67037 Strasbourg, France
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