1
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Rauniyar N, Khetani J, Han X. Comparative analysis of Herceptin N-Linked glycosylation by HILIC-FLD and LC-MS/MS methods. J Pharm Biomed Anal 2024; 244:116123. [PMID: 38554555 DOI: 10.1016/j.jpba.2024.116123] [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: 12/20/2023] [Revised: 02/26/2024] [Accepted: 03/17/2024] [Indexed: 04/01/2024]
Abstract
Monoclonal antibodies like Herceptin play a pivotal role in modern therapeutics, with their glycosylation patterns significantly influencing their bioactivity. To characterize the N-glycan profile and their relative abundance in Herceptin, we employed two analytical methods: hydrophilic interaction chromatography with fluorescence detection (HILIC-FLD) for released glycans and liquid chromatography tandem mass spectrometry (LC-MS/MS) for glycopeptides. Our analysis included 21 European Union (EU)-Herceptin lots and 14 United States (US)-Herceptin lots. HILIC-FLD detected 25 glycan species, including positional isomers, revealing comparable chromatographic profiles for both EU and US lots. On the other hand, LC-MS/MS identified 26 glycoforms within the glycopeptide EEQYNSTYR. Both methods showed that a subset of glycans dominated the total abundance. Notably, EU-Herceptin lots with an expiration date of October 2022 exhibited increased levels of afucosylated and high mannose N-glycans. Our statistical comparisons showed that the difference in quantitative results between HILIC-FLD and LC-MS/MS is significant, indicating that the absolute quantitative values depend on the choice of the analytical method. However, despite these differences, both methods demonstrated a strong correlation in relative glycan proportions. This study contributes to the comprehensive analysis of Herceptin's glycosylation, offering insights into the influence of analytical methods on glycan quantification and providing valuable information for the biopharmaceutical industry.
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Affiliation(s)
- Navin Rauniyar
- Tanvex BioPharma USA, Inc, 10394 Pacific Center Ct, San Diego, CA 92121, USA.
| | - Joy Khetani
- Tanvex BioPharma USA, Inc, 10394 Pacific Center Ct, San Diego, CA 92121, USA
| | - Xuemei Han
- Tanvex BioPharma USA, Inc, 10394 Pacific Center Ct, San Diego, CA 92121, USA
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2
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DeBono NJ, Moh ESX, Packer NH. Experimentally Determined Diagnostic Ions for Identification of Peptide Glycotopes. J Proteome Res 2024; 23:2661-2673. [PMID: 38888225 DOI: 10.1021/acs.jproteome.3c00858] [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] [Indexed: 06/20/2024]
Abstract
The analysis of the structures of glycans present on glycoproteins is an essential component for determining glycoprotein function; however, detailed glycan structural assignment on glycopeptides from proteomics mass spectrometric data remains challenging. Glycoproteomic analysis by mass spectrometry currently can provide significant, yet incomplete, information about the glycans present, including the glycan monosaccharide composition and in some circumstances the site(s) of glycosylation. Advancements in mass spectrometric resolution, using high-mass accuracy instrumentation and tailored MS/MS fragmentation parameters, coupled with a dedicated definition of diagnostic fragmentation ions have enabled the determination of some glycan structural features, or glycotopes, expressed on glycopeptides. Here we present a collation of diagnostic glycan fragments produced by traditional positive-ion-mode reversed-phase LC-ESI MS/MS proteomic workflows and describe the specific fragmentation energy settings required to identify specific glycotopes presented on N- or O-linked glycopeptides in a typical proteomics MS/MS experiment.
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Affiliation(s)
- Nicholas J DeBono
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Edward S X Moh
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Nicolle H Packer
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
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3
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Remoroza CA, Burke MC, Mak TD, Sheetlin SL, Mirokhin YA, Cooper BT, Goecker ZC, Lowenthal MS, Yang X, Wang G, Tchekhovskoi DV, Stein SE. Comparison of N-Glycopeptide to Released N-Glycan Abundances and the Influence of Glycopeptide Mass and Charge States on N-Linked Glycosylation of IgG Antibodies. J Proteome Res 2024; 23:1443-1457. [PMID: 38450643 PMCID: PMC10997438 DOI: 10.1021/acs.jproteome.3c00904] [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] [Indexed: 03/08/2024]
Abstract
We report the comparison of mass-spectral-based abundances of tryptic glycopeptides to fluorescence abundances of released labeled glycans and the effects of mass and charge state and in-source fragmentation on glycopeptide abundances. The primary glycoforms derived from Rituximab, NISTmAb, Evolocumab, and Infliximab were high-mannose and biantennary complex galactosylated and fucosylated N-glycans. Except for Evolocumab, in-source ions derived from the loss of HexNAc or HexNAc-Hex sugars are prominent for other therapeutic IgGs. After excluding in-source fragmentation of glycopeptide ions from the results, a linear correlation was observed between fluorescently labeled N-glycan and glycopeptide abundances over a dynamic range of 500. Different charge states of human IgG-derived glycopeptides containing a wider variety of abundant attached glycans were also investigated to examine the effects of the charge state on ion abundances. These revealed a linear dependence of glycopeptide abundance on the mass of the glycan with higher charge states favoring higher-mass glycans. Findings indicate that the mass spectrometry-based bottom-up approach can provide results as accurate as those of glycan release studies while revealing the origin of each attached glycan. These site-specific relative abundances are conveniently displayed and compared using previously described glycopeptide abundance distribution spectra "GADS" representations. Mass spectrometry data are available from the MAssIVE repository (MSV000093562).
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Affiliation(s)
| | | | | | | | | | - Brian T. Cooper
- Mass Spectrometry Data Center
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | | | - Mark S. Lowenthal
- Bioanalytical Science Group, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive Gaithersburg, MD 20899, US
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4
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Wang J, Yu A, Cho BG, Mechref Y. Assessing the hydrophobicity of glycopeptides using reversed-phase liquid chromatography and tandem mass spectrometry. J Chromatogr A 2023; 1706:464237. [PMID: 37523904 DOI: 10.1016/j.chroma.2023.464237] [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: 05/31/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023]
Abstract
Retention time is one of the most important parameters that has been widely used to demonstrate the separation results obtained from liquid chromatography (LC) platforms. However, retention time can shift when samples are tested with different instruments and laboratories, which hinders the identification process of analytes when comparing data collected from different LC systems. To address this problem, hydrophobicity index was introduced for retention time normalization of the glycopeptides separated by reversed-phase LC (RPLC). Tandem MS was used for the detection and identification of glycopeptides. In addition, the influence of different types of glycans on the hydrophobicity of peptide backbones was studied by comparing the retention time of glycopeptides with their non-glycosylated counterparts. The hydrophobicity of tryptic digested glycopeptides derived from model glycoproteins, including bovine fetuin, α1-acid glycoprotein, and haptoglobin from human plasma, were evaluated based on the hydrophobicity index of the standard peptides from a peptide retention time calibration mixture. The reduction of hydrophobicity of multiple peptide backbones was observed due to the hydrophilic glycan structures. By comparing the hydrophobicity index of glycopeptides collected from different time and instruments, the day-to-day and lab-to-lab comparisons suggested high reliability and reproducibility of this approach. The RSD% of hydrophobicity index from inter-lab experiments was 1.2%, while the RSD% of retention time was 5.1%. Then, the applications of this method were demonstrated on complex glycopeptide samples extracted from human blood serum. The hydrophobicity index can be applied to address the retention time shift when using different instruments, thereby boosting confidence of the characterization of glycopeptides.
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Affiliation(s)
- Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, United States
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, United States
| | - Byeong Gwan Cho
- Department of Chemistry and Biochemistry, Texas Tech University, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, United States.
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5
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Influence of ion-pairing reagents on the separation of intact glycoproteins using hydrophilic-interaction liquid chromatography - high-resolution mass spectrometry. J Chromatogr A 2023; 1688:463721. [PMID: 36565654 DOI: 10.1016/j.chroma.2022.463721] [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: 09/04/2022] [Revised: 12/04/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Hydrophilic-interaction liquid chromatography (HILIC) of intact proteins offers high-resolution separations of glycoforms of glycoproteins differing in the number of (neutral) glycans. However, to obtain efficient separations it is essential that the positively charged sites of the proteins are shielded by acidic (negative) ion-pair reagents (IPRs), so as to enhance the contribution of the hydroxyl groups of the (neutral) sugars in the glycoprotein. Here, we studied the influence of various IPRs that differ in physico-chemical properties, such as hydrophobicity and acidity, on the capillary-scale HILIC separation of intact (glyco)proteins. We evaluated the use of fluoroacetic acid (MFA), difluoroacetic acid (DFA), trifluoroacetic acid (TFA), and heptafluorobutyric acid (HFBA) as diluents for sample preparation, as solvents for sample loading on a reversed-phase trap prior to the HILIC separation, and as mobile-phase components for HILIC and HILIC-MS. To reduce the contribution of ion-exchange interaction with the (silica-based) stationary phase, we used an acrylamide-based monolithic column. We studied the influence of the different IPRs on each step of the separation of a mixture of proteins of different size and hydrophilicity and on the separation of the five glycoforms of ribonuclease B. The content of IPR in the sample was shown not to affect the separation and the MS detection. However, a low content of TFA and DFA in the mobile phase is favourable, as it reduces adduct formation and leads to higher signal intensity. The optimized HILIC conditions successfully resolved nine major glycoforms groups of a ∼40 kDa glycoprotein horseradish peroxidase (HRP), as an example of a complex glycoprotein.
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6
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Glycomic and Glycoproteomic Techniques in Neurodegenerative Disorders and Neurotrauma: Towards Personalized Markers. Cells 2022; 11:cells11030581. [PMID: 35159390 PMCID: PMC8834236 DOI: 10.3390/cells11030581] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/22/2022] [Accepted: 02/03/2022] [Indexed: 12/16/2022] Open
Abstract
The proteome represents all the proteins expressed by a genome, a cell, a tissue, or an organism at any given time under defined physiological or pathological circumstances. Proteomic analysis has provided unparalleled opportunities for the discovery of expression patterns of proteins in a biological system, yielding precise and inclusive data about the system. Advances in the proteomics field opened the door to wider knowledge of the mechanisms underlying various post-translational modifications (PTMs) of proteins, including glycosylation. As of yet, the role of most of these PTMs remains unidentified. In this state-of-the-art review, we present a synopsis of glycosylation processes and the pathophysiological conditions that might ensue secondary to glycosylation shortcomings. The dynamics of protein glycosylation, a crucial mechanism that allows gene and pathway regulation, is described. We also explain how-at a biomolecular level-mutations in glycosylation-related genes may lead to neuropsychiatric manifestations and neurodegenerative disorders. We then analyze the shortcomings of glycoproteomic studies, putting into perspective their downfalls and the different advanced enrichment techniques that emanated to overcome some of these challenges. Furthermore, we summarize studies tackling the association between glycosylation and neuropsychiatric disorders and explore glycoproteomic changes in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington disease, multiple sclerosis, and amyotrophic lateral sclerosis. We finally conclude with the role of glycomics in the area of traumatic brain injury (TBI) and provide perspectives on the clinical application of glycoproteomics as potential diagnostic tools and their application in personalized medicine.
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7
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Schulze S, Oltmanns A, Fufezan C, Krägenbring J, Mormann M, Pohlschröder M, Hippler M. SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides. Bioinformatics 2020; 36:5330-5336. [PMID: 33325487 DOI: 10.1093/bioinformatics/btaa1042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/26/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION Protein glycosylation is a complex post-translational modification with crucial cellular functions in all domains of life. Currently, large-scale glycoproteomics approaches rely on glycan database dependent algorithms and are thus unsuitable for discovery-driven analyses of glycoproteomes. RESULTS Therefore, we devised SugarPy, a glycan database independent Python module, and validated it on the glycoproteome of human breast milk. We further demonstrated its applicability by analyzing glycoproteomes with uncommon glycans stemming from the green alga Chlamydomonas reinhardtii and the archaeon Haloferax volcanii. SugarPy also facilitated the novel characterization of glycoproteins from the red alga Cyanidioschyzon merolae. AVAILABILITY The source code is freely available on GitHub (https://github.com/SugarPy/SugarPy), and its implementation in Python ensures support for all operating systems. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stefan Schulze
- University of Pennsylvania, Department of Biology, Leidy Laboratories, Philadelphia, USA.,University of Muenster, Institute of Plant Biology and Biotechnology, Muenster, Germany
| | - Anne Oltmanns
- University of Muenster, Institute of Plant Biology and Biotechnology, Muenster, Germany
| | - Christian Fufezan
- University of Muenster, Institute of Plant Biology and Biotechnology, Muenster, Germany.,Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Heidelberg, Germany
| | - Julia Krägenbring
- University of Muenster, Institute of Plant Biology and Biotechnology, Muenster, Germany.,University of Muenster, Institute for Hygiene, Muenster, Germany
| | - Michael Mormann
- University of Muenster, Institute for Hygiene, Muenster, Germany
| | - Mechthild Pohlschröder
- University of Pennsylvania, Department of Biology, Leidy Laboratories, Philadelphia, USA
| | - Michael Hippler
- University of Muenster, Institute of Plant Biology and Biotechnology, Muenster, Germany.,Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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8
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Zhao J, Peng W, Dong X, Mechref Y. Analysis of NIST Monoclonal Antibody Reference Material Glycosylation Using the LC-MS/MS-Based Glycoproteomic Approach. J Proteome Res 2020; 20:818-830. [PMID: 33196194 DOI: 10.1021/acs.jproteome.0c00659] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-based therapeutics such as mAbs have become emerging drugs in modern medicine. Most of the approved therapeutic proteins are glycoproteins. Glycosylation is an essential critical quality attribute (CQA) due to the influence that glycoforms have on the safety, efficacy, and pharmacokinetics/pharmacodynamics (PK/PD) of biotherapeutics. Here, we applied an LC-MS/MS-based glycoproteomics approach to characterize Fc glycans of an NISTmAb reference material (RM) 8671 (sample B) and a β-1,4-galactosidase-treated NISTmAb (sample A). Overall, 48 glycan compositions were identified and quantified. The glycan structure with the highest abundance was FA2, with a relative abundance of 52% in sample A and 38% in sample B. Over 50% of the identified glycans presented at levels smaller than 0.1%. Important glycan attributes were further derived using the quantitative results. The galactosylation level of modified NISTmAb was found to decrease by ∼10% when compared to the galactosylation level of NISTmAb. There was no significant difference between the two samples in the levels of sialylation, fucosylation, and high mannose. Moreover, unglycosylated peptides were also observed at a level of 1-2%.
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Affiliation(s)
- Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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9
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Yu F, Haynes SE, Teo GC, Avtonomov DM, Polasky DA, Nesvizhskii AI. Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant. Mol Cell Proteomics 2020; 19:1575-1585. [PMID: 32616513 PMCID: PMC7996969 DOI: 10.1074/mcp.tir120.002048] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/21/2020] [Indexed: 01/01/2023] Open
Abstract
Ion mobility brings an additional dimension of separation to LC-MS, improving identification of peptides and proteins in complex mixtures. A recently introduced timsTOF mass spectrometer (Bruker) couples trapped ion mobility separation to TOF mass analysis. With the parallel accumulation serial fragmentation (PASEF) method, the timsTOF platform achieves promising results, yet analysis of the data generated on this platform represents a major bottleneck. Currently, MaxQuant and PEAKS are most used to analyze these data. However, because of the high complexity of timsTOF PASEF data, both require substantial time to perform even standard tryptic searches. Advanced searches (e.g. with many variable modifications, semi- or non-enzymatic searches, or open searches for post-translational modification discovery) are practically impossible. We have extended our fast peptide identification tool MSFragger to support timsTOF PASEF data, and developed a label-free quantification tool, IonQuant, for fast and accurate 4-D feature extraction and quantification. Using a HeLa data set published by Meier et al. (2018), we demonstrate that MSFragger identifies significantly (∼30%) more unique peptides than MaxQuant (1.6.10.43), and performs comparably or better than PEAKS X+ (∼10% more peptides). IonQuant outperforms both in terms of number of quantified proteins while maintaining good quantification precision and accuracy. Runtime tests show that MSFragger and IonQuant can fully process a typical two-hour PASEF run in under 70 min on a typical desktop (6 CPU cores, 32 GB RAM), significantly faster than other tools. Finally, through semi-enzymatic searching, we significantly increase the number of identified peptides. Within these semi-tryptic identifications, we report evidence of gas-phase fragmentation before MS/MS analysis.
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Affiliation(s)
- Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sarah E Haynes
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Dmitry M Avtonomov
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
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10
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Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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11
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Abstract
In humans, the thyroid hormones T3 and T4 are synthesized in the thyroid gland in a process that crucially involves the iodoglycoprotein thyroglobulin. The overall structure of thyroglobulin is conserved in all vertebrates. Upon thyroglobulin delivery from thyrocytes to the follicular lumen of the thyroid gland via the secretory pathway, multiple tyrosine residues can become iodinated to form mono-iodotyrosine (MIT) and/or di-iodotyrosine (DIT); however, selective tyrosine residues lead to preferential formation of T4 and T3 at distinct sites. T4 formation involves oxidative coupling between two DIT side chains, and de novo T3 formation involves coupling between an MIT donor and a DIT acceptor. Thyroid hormone synthesis is stimulated by TSH activating its receptor (TSHR), which upregulates the activity of many thyroid gene products involved in hormonogenesis. Additionally, TSH regulates post-translational changes in thyroglobulin that selectively enhance its capacity for T3 formation - this process is important in iodide deficiency and in Graves disease. 167 different mutations, many of which are newly discovered, are now known to exist in TG (encoding human thyroglobulin) that can lead to defective thyroid hormone synthesis, resulting in congenital hypothyroidism.
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Affiliation(s)
- Cintia E Citterio
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología/Cátedra de Genética, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Héctor M Targovnik
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología/Cátedra de Genética, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Peter Arvan
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor, MI, USA.
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Yu A, Zhao J, Peng W, Banazadeh A, Williamson SD, Goli M, Huang Y, Mechref Y. Advances in mass spectrometry-based glycoproteomics. Electrophoresis 2018; 39:3104-3122. [PMID: 30203847 PMCID: PMC6375712 DOI: 10.1002/elps.201800272] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/03/2018] [Accepted: 09/03/2018] [Indexed: 12/13/2022]
Abstract
Protein glycosylation, an important PTM, plays an essential role in a wide range of biological processes such as immune response, intercellular signaling, inflammation, and host-pathogen interaction. Aberrant glycosylation has been correlated with various diseases. However, studying protein glycosylation remains challenging because of low abundance, microheterogeneities of glycosylation sites, and poor ionization efficiency of glycopeptides. Therefore, the development of sensitive and accurate approaches to characterize protein glycosylation is crucial. The identification and characterization of protein glycosylation by MS is referred to as the field of glycoproteomics. Methods such as enrichment, metabolic labeling, and derivatization of glycopeptides in conjunction with different MS techniques and bioinformatics tools, have been developed to achieve an unequivocal quantitative and qualitative characterization of glycoproteins. This review summarizes the recent developments in the field of glycoproteomics over the past 6 years (2012 to 2018).
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Affiliation(s)
- Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Seth D. Williamson
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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13
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Zhang Q, Li Z, Wang Y, Zheng Q, Li J. Mass spectrometry for protein sialoglycosylation. MASS SPECTROMETRY REVIEWS 2018; 37:652-680. [PMID: 29228471 DOI: 10.1002/mas.21555] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/17/2017] [Indexed: 06/07/2023]
Abstract
Sialic acids are a family of structurally unique and negatively charged nine-carbon sugars, normally found at the terminal positions of glycan chains on glycoproteins and glycolipids. The glycosylation of proteins is a universal post-translational modification in eukaryotic species and regulates essential biological functions, in which the most common sialic acid is N-acetyl-neuraminic acid (2-keto-5-acetamido-3,5-dideoxy-D-glycero-D-galactononulopyranos-1-onic acid) (Neu5NAc). Because of the properties of sialic acids under general mass spectrometry (MS) conditions, such as instability, ionization discrimination, and mixed adducts, the use of MS in the analysis of protein sialoglycosylation is still challenging. The present review is focused on the application of MS related methodologies to the study of both N- and O-linked sialoglycans. We reviewed MS-based strategies for characterizing sialylation by analyzing intact glycoproteins, proteolytic digested glycopeptides, and released glycans. The review concludes with future perspectives in the field.
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Affiliation(s)
- Qiwei Zhang
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Institute for Interdisciplinary Research, Institute of Environment and Health, School of Chemical and Environmental Engineering, Jianghan University, Wuhan, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Zack Li
- School of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Yawei Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Qi Zheng
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Institute for Interdisciplinary Research, Institute of Environment and Health, School of Chemical and Environmental Engineering, Jianghan University, Wuhan, China
| | - Jianjun Li
- National Research Council Canada, Ottawa, Ontario, Canada
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14
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Wang S, Li X, Li T, Wang H, Zhang X, Lou J, Xing Q, Hu X, Bao Z. The GRP94 gene of Yesso scallop (Patinopecten yessoensis): Characterization and expression regulation in response to thermal and bacterial stresses. FISH & SHELLFISH IMMUNOLOGY 2018; 80:443-451. [PMID: 29894740 DOI: 10.1016/j.fsi.2018.06.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/09/2018] [Indexed: 06/08/2023]
Abstract
The 94-kDa glucose-regulated protein (GRP94) belonging to the HSP90 family is an endoplasmic reticulum (ER) chaperone. It plays critical roles in ER quality control, and has been implicated as a specialized immune chaperone to regulate both innate and adaptive immunity. In this study, we identified and characterized a GRP94 gene (PyGRP94) from Yesso scallop (Patinopecten yessoensis). The protein sequence of PyGRP94 is highly conserved with its homologs in vertebrates, with a signal sequence in N-terminal, an ER retrieval signal sequence in C-terminal and a HATPase_c domain. Expression analysis suggests that PyGRP94 transcripts in early embryos are maternally derived and the zygotic expression is started from D-shaped larvae. This gene is also expressed in almost all the adult tissues examined except smooth muscle, with the highest expression level in hemocytes. Besides, PyGRP94 was demonstrated to be induced by heat shock and both Gram-positive (Micrococcus luteus) and Gram-negative (Vibrio anguillarum) bacterial infection, with much more dramatic changes being observed after V. anguillarum challenge. Our results suggest the involvement of PyGRP94 in response to thermal stress, and that it might play an important role in the innate immune defense of scallop.
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Affiliation(s)
- Shuyue Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Xu Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Tingting Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Huizhen Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Xiangchao Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Jiarun Lou
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Qiang Xing
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Xiaoli Hu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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15
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Kozlik P, Goldman R, Sanda M. Study of structure-dependent chromatographic behavior of glycopeptides using reversed phase nanoLC. Electrophoresis 2017; 38:2193-2199. [PMID: 28444931 DOI: 10.1002/elps.201600547] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/15/2017] [Accepted: 04/19/2017] [Indexed: 11/09/2022]
Abstract
Analysis of glycosylation is challenging due to micro- and macro-heterogeneity of the protein attachment. A combination of LC with MS/MS is one of the most powerful tools for glycopeptide analysis. In this work, we show the effect of various monosaccharide units on the retention time of glycopeptides. Retention behavior of several glycoforms of six peptides obtained from tryptic digest of haptoglobin, hemopexin, and sex hormone-binding globulin was studied on a reversed phase chromatographic column. We observed reduction of the retention time with increasing number of monosaccharide units of glycans attached to the same peptide backbone. Fucosylation of larger glycans provides less significant retention time shift than for smaller ones. Retention times of glycopeptides were expressed as relative retention times. These relative retention times were used for calculation of upper and lower limits of glycopeptide retention time windows under the reversed phase conditions. We then demonstrated on the case of a glycopeptide of haptoglobin that the predicted retention time window boosts confidence of identification and minimizes false-positive identification. Relative retention time, as a qualitative parameter, is expected to improve LC-MS/MS characterization of glycopeptides.
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Affiliation(s)
- Petr Kozlik
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.,Department of Analytical Chemistry, Faculty of Science, Charles University, Czech Republic
| | - Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
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16
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Abstract
Protein glycosylation is one of the most important posttranslational modifications. Numerous biological functions are related to protein glycosylation. However, analytical challenges remain in the glycoprotein analysis. To overcome the challenges associated with glycoprotein analysis, many analytical techniques were developed in recent years. Enrichment methods were used to improve the sensitivity of detection, while HPLC and mass spectrometry methods were developed to facilitate the separation of glycopeptides/proteins and enhance detection, respectively. Fragmentation techniques applied in modern mass spectrometers allow the structural interpretation of glycopeptides/proteins, while automated software tools started replacing manual processing to improve the reliability and throughput of the analysis. In this chapter, the current methodologies of glycoprotein analysis were discussed. Multiple analytical techniques are compared, and advantages and disadvantages of each technique are highlighted.
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