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Yin H, Zhu J. Methods for quantification of glycopeptides by liquid separation and mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:887-917. [PMID: 35099083 PMCID: PMC9339036 DOI: 10.1002/mas.21771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/14/2021] [Accepted: 01/13/2022] [Indexed: 05/05/2023]
Abstract
Recent advances in analytical techniques provide the opportunity to quantify even low-abundance glycopeptides derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Herein, we discuss the sample preparation procedures and the mass spectrometry (MS) strategies that have facilitated glycopeptide quantification, as well as the standards used for glycopeptide quantification. For sample preparation, various glycopeptide enrichment methods are summarized including the columns used for glycopeptide separation in liquid chromatography separation. For MS analysis strategies, MS1 level-based quantification and MS2 level-based quantification are described, either with or without labeling, where we have covered isotope labeling, TMT/iTRAQ labeling, data dependent acquisition, data independent acquisition, multiple reaction monitoring, and parallel reaction monitoring. The strengths and weaknesses of these methods are compared, particularly those associated with the figures of merit that are important for clinical biomarker studies and the pathological and functional studies of glycoproteins in various diseases. Possible future developments for glycopeptide quantification are discussed.
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Affiliation(s)
- Haidi Yin
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
| | - Jianhui Zhu
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
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2
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Gao Z, Chen S, Du J, Wu Z, Ge W, Gao S, Zhou Z, Yang X, Xing Y, Shi M, Hu Y, Tang W, Xia J, Zhang X, Jiang J, Yang S. Quantitative analysis of fucosylated glycoproteins by immobilized lectin-affinity fluorescent labeling. RSC Adv 2023; 13:6676-6687. [PMID: 36860533 PMCID: PMC9969232 DOI: 10.1039/d3ra00072a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023] Open
Abstract
Human biofluids are often used to discover disease-specific glycosylation, since abnormal changes in protein glycosylation can discern physiopathological states. Highly glycosylated proteins in biofluids make it possible to identify disease signatures. Glycoproteomic studies on saliva glycoproteins showed that fucosylation was significantly increased during tumorigenesis and that glycoproteins became hyperfucosylated in lung metastases, and tumor stage is associated with fucosylation. Quantification of salivary fucosylation can be achieved by mass spectrometric analysis of fucosylated glycoproteins or fucosylated glycans; however, the use of mass spectrometry is non-trivial for clinical practice. Here, we developed a high-throughput quantitative method, lectin-affinity fluorescent labeling quantification (LAFLQ), to quantify fucosylated glycoproteins without relying on mass spectrometry. Lectins with a specific affinity for fucoses are immobilized on the resin and effectively capture fluorescently labeled fucosylated glycoproteins, which are further quantitatively characterized by fluorescence detection in a 96-well plate. Our results demonstrated that serum IgG can be accurately quantified by lectin and fluorescence detection. Quantification in saliva showed significantly higher fucosylation in lung cancer patients compared to healthy controls or other non-cancer diseases, suggesting that this method has the potential to quantify stage-related fucosylation in lung cancer saliva.
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Affiliation(s)
- Ziyuan Gao
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University Suzhou 215006 China
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University Suzhou 215123 China
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Soochow University Suzhou 215006 China
| | - Sufeng Chen
- Clinical Laboratory Center, Zhejiang Provincial People's Hospital Hangzhou Zhejiang 310014 China
| | - Jing Du
- Clinical Laboratory Center, Zhejiang Provincial People's Hospital Hangzhou Zhejiang 310014 China
| | - Zhen Wu
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University Shanghai 200438 China
| | - Wei Ge
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University Suzhou 215123 China
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University Suzhou 215004 China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University Lianyungang 222005 China
| | - Zeyang Zhou
- Department of General Surgery, The Second Affiliated Hospital of Soochow University Suzhou 215004 China
| | - Xiaodong Yang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University Suzhou 215004 China
| | - Yufei Xing
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University Suzhou 215004 China
| | - Minhua Shi
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University Suzhou 215004 China
| | - Yunyun Hu
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University Suzhou 215004 China
| | - Wen Tang
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University Suzhou 215004 China
| | - Jun Xia
- Clinical Laboratory Center, Zhejiang Provincial People's Hospital Hangzhou Zhejiang 310014 China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University Shanghai 200438 China
| | - Junhong Jiang
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University Suzhou 215006 China
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Soochow University Suzhou 215006 China
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University Suzhou 215123 China
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3
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Characterization of core fucosylation via sequential enzymatic treatments of intact glycopeptides and mass spectrometry analysis. Nat Commun 2022; 13:3910. [PMID: 35798744 PMCID: PMC9262967 DOI: 10.1038/s41467-022-31472-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/16/2022] [Indexed: 01/14/2023] Open
Abstract
Core fucosylation of N-linked glycoproteins has been linked to the functions of glycoproteins in physiological and pathological processes. However, quantitative characterization of core fucosylation remains challenging due to the complexity and heterogeneity of N-linked glycosylation. Here we report a mass spectrometry-based method that employs sequential treatment of intact glycopeptides with enzymes (STAGE) to analyze site-specific core fucosylation of glycoproteins. The STAGE method utilizes Endo F3 followed by PNGase F treatment to generate mass signatures for glycosites that are formerly modified by core fucosylated N-linked glycans. We benchmark the STAGE method and use it to characterize site specific core fucosylation of glycoproteins from human hepatocellular carcinoma and pancreatic ductal adenocarcinoma, resulting in the identification of 1130 and 782 core fucosylated glycosites, respectively. These results indicate that our STAGE method enables quantitative characterization of core fucosylation events from complex protein mixtures, which may benefit our understanding of core fucosylation functions in various diseases.
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4
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Lin Y, Zhang J, Arroyo A, Singal AG, Parikh ND, Lubman DM. A Fucosylated Glycopeptide as a Candidate Biomarker for Early Diagnosis of NASH Hepatocellular Carcinoma Using a Stepped HCD Method and PRM Evaluation. Front Oncol 2022; 12:818001. [PMID: 35372033 PMCID: PMC8970044 DOI: 10.3389/fonc.2022.818001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/21/2022] [Indexed: 12/19/2022] Open
Abstract
Aberrant specific N-glycosylation, especially the increase in fucosylation on specific peptide sites of serum proteins have been investigated as potential markers for diagnosis of nonalcoholic steatohepatitis (NASH)-related HCC. We have combined a workflow involving broad scale marker discovery in serum followed by targeted marker evaluation of these fucosylated glycopeptides. This workflow involved an LC-Stepped HCD-DDA-MS/MS method coupled with offline peptide fractionation for large-scale identification of N-glycopeptides directly from pooled serum samples (each n=10) as well as differential determination of N-glycosylation changes between disease states. We then evaluated the fucosylation level of the glycoprotein ceruloplasmin among 62 patient samples (35 cirrhosis, 27 early-stage NASH HCC) by LC-Stepped HCD-PRM-MS/MS to quantitatively analyze 18 targeted glycopeptides. Of these targets, we found the ratio of fucosylation of a tri-antennary glycopeptide from site N762, involving N762_ HexNAc(5)Hex(6)Fuc(2)NeuAc(3) (P=0.0486), increased significantly from cirrhosis to early HCC. This fucosylation ratio of a tri-antennary glycopeptide in CERU could be a potential biomarker for further validation in a larger sample set and could be a promising candidate for early detection of NASH HCC.
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Affiliation(s)
- Yu Lin
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Jie Zhang
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Ana Arroyo
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Amit G. Singal
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Neehar D. Parikh
- Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - David M. Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, United States
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Lin Y, Zhu J, Pan L, Zhang J, Tan Z, Olivares J, Singal AG, Parikh ND, Lubman DM. A Panel of Glycopeptides as Candidate Biomarkers for Early Diagnosis of NASH Hepatocellular Carcinoma Using a Stepped HCD Method and PRM Evaluation. J Proteome Res 2021; 20:3278-3289. [PMID: 33929864 DOI: 10.1021/acs.jproteome.1c00175] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Changes in N-glycosylation on specific peptide sites of serum proteins have been investigated as potential markers for diagnosis of nonalcoholic steatohepatitis (NASH)-related HCC. To accomplish this work, a novel workflow involving broad-scale marker discovery in serum followed by targeted marker evaluation of these glycopeptides were combined. The workflow involved an LC-Stepped HCD-DDA-MS/MS method coupled with offline peptide fractionation for large-scale identification of N-glycopeptides directly from pooled serum samples (each n = 10) as well as differential determination of N-glycosylation changes between disease states. We then evaluated several potentially diagnostic N-glycopeptides among 78 individual patient samples (40 cirrhosis, 28 early stage NASH HCC, and 10 late-stage NASH HCC) by LC-Stepped HCD-PRM-MS/MS to quantitatively analyze 65 targeted glycopeptides from 7 glycoproteins. Of these targets, we found site-specific N-glycopeptides n169GSLFAFR_HexNAc(4)Hex(5)NeuAc(2) and n242ISDGFDGIPDNVDAALALPAHSYSGR_HexNAc(5)Hex(6)Fuc(1)NeuAc(3) from VTNC were significantly increased comparing samples from patients with NASH cirrhosis and NASH HCC (p < 0.05). When combining results of these 2 glycopeptides with AFP, the ROC curve analysis demonstrated the AUC value increased to 0.834 (95% CI, 0.748-0.921) and 0.847 (95% CI, 0.766-0.932), respectively, as compared to that of AFP alone (AUC = 0.791, 95% CI, 0.690-0.892). These 2 glycopeptides may serve as potential biomarkers for early HCC diagnosis in patients with NASH related cirrhosis.
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Affiliation(s)
- Yu Lin
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Lingyun Pan
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Jie Zhang
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Zhijing Tan
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Jocelyn Olivares
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Amit G Singal
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Neehar D Parikh
- Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
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Limjiasahapong S, Kaewnarin K, Jariyasopit N, Hongthong S, Nuntasaen N, Robinson JL, Nookaew I, Sirivatanauksorn Y, Kuhakarn C, Reutrakul V, Khoomrung S. UPLC-ESI-MRM/MS for Absolute Quantification and MS/MS Structural Elucidation of Six Specialized Pyranonaphthoquinone Metabolites From Ventilago harmandiana. FRONTIERS IN PLANT SCIENCE 2021; 11:602993. [PMID: 33505413 PMCID: PMC7830255 DOI: 10.3389/fpls.2020.602993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
Pyranonaphthoquinones (PNQs) are important structural scaffolds found in numerous natural products. Research interest in these specialized metabolites lies in their natural occurrence and therapeutic activities. Nonetheless, research progress has thus far been hindered by the lack of analytical standards and analytical methods for both qualitative and quantitative analysis. We report here that various parts of Ventilago harmandiana are rich sources of PNQs. We developed an ultraperformance liquid chromatography-electrospray ionization multiple reaction monitoring/mass spectrometry method to quantitatively determine six PNQs from leaves, root, bark, wood, and heartwood. The addition of standards in combination with a stable isotope of salicylic acid-D6 was used to overcome the matrix effect with average recovery of 82% ± 1% (n = 15). The highest concentration of the total PNQs was found in the root (11,902 μg/g dry weight), whereas the lowest concentration was found in the leaves (28 μg/g dry weight). Except for the root, PNQ-332 was found to be the major compound in all parts of V. harmandiana, accounting for ∼48% of the total PNQs quantified in this study. However, PNQ-318A was the most abundant PNQ in the root sample, accounting for 27% of the total PNQs. Finally, we provide novel MS/MS spectra of the PNQs at different collision induction energies: 10, 20, and 40 eV (POS and NEG). For structural elucidation purposes, we propose complete MS/MS fragmentation pathways of PNQs using MS/MS spectra at collision energies of 20 and 40 eV. The MS/MS spectra along with our discussion on structural elucidation of these PNQs should be very useful to the natural products community to further exploring PNQs in V. harmandiana and various other sources.
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Affiliation(s)
- Suphitcha Limjiasahapong
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Khwanta Kaewnarin
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Narumol Jariyasopit
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sakchai Hongthong
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
- Division of Chemistry, Faculty of Science and Technology, Rajabhat Rajanagarindra University, Chachoengsao, Thailand
| | - Narong Nuntasaen
- The Forest Herbarium National Park, Wildlife and Plant Conservation Department, Ministry of Natural Resources and Environment, Bangkok, Thailand
| | - Jonathan L. Robinson
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Yongyut Sirivatanauksorn
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chutima Kuhakarn
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Vichai Reutrakul
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sakda Khoomrung
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
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7
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Protein Glycosylation Investigated by Mass Spectrometry: An Overview. Cells 2020; 9:cells9091986. [PMID: 32872358 PMCID: PMC7564411 DOI: 10.3390/cells9091986] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022] Open
Abstract
The protein glycosylation is a post-translational modification of crucial importance for its involvement in molecular recognition, protein trafficking, regulation, and inflammation. Indeed, abnormalities in protein glycosylation are correlated with several disease states such as cancer, inflammatory diseases, and congenial disorders. The understanding of cellular mechanisms through the elucidation of glycan composition encourages researchers to find analytical solutions for their detection. Actually, the multiplicity and diversity of glycan structures bond to the proteins, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies make their detection much trickier than other kinds of biopolymers. An overview of the most prominent techniques based on mass spectrometry (MS) for protein glycosylation (glycoproteomics) studies is here presented. The tricks and pre-treatments of samples are discussed as a crucial step prodromal to the MS analysis to improve the glycan ionization efficiency. Therefore, the different instrumental MS mode is also explored for the qualitative and quantitative analysis of glycopeptides and the glycans structural composition, thus contributing to the elucidation of biological mechanisms.
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Cao WQ, Jiang BY, Huang JM, Zhang L, Liu MQ, Yao J, Wu MX, Zhang LJ, Kong SY, Wang Y, Yang PY. Straightforward and Highly Efficient Strategy for Hepatocellular Carcinoma Glycoprotein Biomarker Discovery Using a Nonglycopeptide-Based Mass Spectrometry Pipeline. Anal Chem 2019; 91:12435-12443. [DOI: 10.1021/acs.analchem.9b03074] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Flowers SA, Lane CS, Karlsson NG. Deciphering Isomers with a Multiple Reaction Monitoring Method for the Complete Detectable O-Glycan Repertoire of the Candidate Therapeutic, Lubricin. Anal Chem 2019; 91:9819-9827. [PMID: 31246420 DOI: 10.1021/acs.analchem.9b01485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glycosylation is a fundamental post-translational modification, occurring on half of all proteins. Despite its significance, our understanding is limited, in part due to the inherent difficulty in studying these branched, multi-isomer structures. Accessible, detailed, and quantifiable methods for studying glycans, particularly O-glycans, are needed. Here we take a multiple reaction monitoring (MRM) approach to differentiate and relatively quantify all detectable glycans, including isomers, on the heavily O-glycosylated protein lubricin. Lubricin (proteoglycan 4) is essential for lubrication of the joint and eye. Given the therapeutic potential of lubricin, it is essential to understand its O-glycan repertoire in biological and recombinantly produced samples. O-Glycans were released by reductive β-elimination and defined, showing a range of 26 neutral, sulfated, sialylated, and both sulfated and sialylated core 1 (Galβ1-3GalNAcα1-) and core 2 (Galβ1-3(GlcNAcβ1-6)GalNAcα1-) structures. Isomer-specific MRM transitions allowed effective differentiation of neutral glycan isomers as well as sulfated isomeric structures, where the sulfate was retained on the fragment ions. This strategy was not as effective with labile sialylated structures; instead, it was observed that the optimal collision energy for the m/z 290.1 sialic acid B-fragment differed consistently between sialic acid isomers, allowing differentiation between isomers when fragmentation spectra were insufficient. This approach was also effective for purchased Neu5Acα2-3Galβ1-4Glc and Neu5Acα2-6Galβ1-4Glc and for Neu5Acα2-3Galβ1-4GlcNAc and Neu5Acα2-6Galβ1-4GlcNAc linkage isomers with the Neu5Acα2-6 consistently requiring more energy for optimal generation of the m/z 290.1 fragment. Overall, this method provides an effective and easily accessible approach for the quantification and annotation of complex released O-glycan samples.
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Affiliation(s)
- Sarah A Flowers
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy , University of Gothenburg , Medicinaregatan 9A , 40530 Gothenburg , Sweden.,Department of Neuroscience , Georgetown University , 3970 Reservoir Road NW, New Research Building EP20 , Washington, D.C. , United States
| | - Catherine S Lane
- SCIEX , Phoenix House, Lakeside Drive, Centre Park , Warrington WA1 1RX , United Kingdom
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy , University of Gothenburg , Medicinaregatan 9A , 40530 Gothenburg , Sweden
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10
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Zhu J, Warner E, Parikh ND, Lubman DM. Glycoproteomic markers of hepatocellular carcinoma-mass spectrometry based approaches. MASS SPECTROMETRY REVIEWS 2019; 38:265-290. [PMID: 30472795 PMCID: PMC6535140 DOI: 10.1002/mas.21583] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/19/2018] [Indexed: 05/03/2023]
Abstract
Hepatocellular carcinoma (HCC) is the third most-common cause of cancer-related death worldwide. Most cases of HCC develop in patients that already have liver cirrhosis and have been recommended for surveillance for an early onset of HCC. Cirrhosis is the final common pathway for several etiologies of liver disease, including hepatitis B and C, alcohol, and increasingly non-alcoholic fatty liver disease. Only 20-30% of patients with HCC are eligible for curative therapy due primarily to inadequate early-detection strategies. Reliable, accurate biomarkers for HCC early detection provide the highest likelihood of curative therapy and survival; however, current early-detection methods that use abdominal ultrasound and serum alpha fetoprotein are inadequate due to poor adherence and limited sensitivity and specificity. There is an urgent need for convenient and highly accurate validated biomarkers for HCC early detection. The theme of this review is the development of new methods to discover glycoprotein-based markers for detection of HCC with mass spectrometry approaches. We outline the non-mass spectrometry based methods that have been used to discover HCC markers including immunoassays, capillary electrophoresis, 2-D gel electrophoresis, and lectin-FLISA assays. We describe the development and results of mass spectrometry-based assays for glycan screening based on either MALDI-MS or ESI analysis. These analyses might be based on the glycan content of serum or on glycan screening for target molecules from serum. We describe some of the specific markers that have been developed as a result, including for proteins such as Haptoglobin, Hemopexin, Kininogen, and others. We discuss the potential role for other technologies, including PGC chromatography and ion mobility, to separate isoforms of glycan markers. Analyses of glycopeptides based on new technologies and innovative softwares are described and also their potential role in discovery of markers of HCC. These technologies include new fragmentation methods such as EThcD and stepped HCD, which can identify large numbers of glycopeptide structures from serum. The key role of lectin extraction in various assays for intact glycopeptides or their truncated versions is also described, where various core-fucosylated and hyperfucosylated glycopeptides have been identified as potential markers of HCC. Finally, we describe the role of LC-MRMs or lectin-FLISA MRMs as a means to validate these glycoprotein markers from patient samples. These technological advancements in mass spectrometry have the potential to lead to novel biomarkers to improve the early detection of HCC.
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Affiliation(s)
- Jianhui Zhu
- Department of Surgery, The University of Michigan, Ann Arbor 48109, Michigan
| | - Elisa Warner
- Department of Surgery, The University of Michigan, Ann Arbor 48109, Michigan
| | - Neehar D. Parikh
- Department of Internal Medicine, The University of Michigan, Ann Arbor 48109, Michigan
| | - David M. Lubman
- Department of Surgery, The University of Michigan, Ann Arbor 48109, Michigan
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11
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Analysis of Hepatocellular Carcinoma Tissue for Biomarker Discovery. MOLECULAR AND TRANSLATIONAL MEDICINE 2019. [DOI: 10.1007/978-3-030-21540-8_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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12
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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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13
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Lang R, Leinenbach A, Karl J, Swiatek-de Lange M, Kobold U, Vogeser M. An endoglycosidase-assisted LC-MS/MS-based strategy for the analysis of site-specific core-fucosylation of low-concentrated glycoproteins in human serum using prostate-specific antigen (PSA) as example. Clin Chim Acta 2018; 480:1-8. [DOI: 10.1016/j.cca.2018.01.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
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14
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Frost DC, Li L. Recent advances in mass spectrometry-based glycoproteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 95:71-123. [PMID: 24985770 DOI: 10.1016/b978-0-12-800453-1.00003-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein glycosylation plays fundamental roles in many biological processes as one of the most common, and the most complex, posttranslational modification. Alterations in glycosylation profile are now known to be associated with many diseases. As a result, the discovery and detailed characterization of glycoprotein disease biomarkers is a primary interest of biomedical research. Advances in mass spectrometry (MS)-based glycoproteomics and glycomics are increasingly enabling qualitative and quantitative approaches for site-specific structural analysis of protein glycosylation. While the complexity presented by glycan heterogeneity and the wide dynamic range of clinically relevant samples like plasma, serum, cerebrospinal fluid, and tissue make comprehensive analyses of the glycoproteome a challenging task, the ongoing efforts into the development of glycoprotein enrichment, enzymatic digestion, and separation strategies combined with novel quantitative MS methodologies have greatly improved analytical sensitivity, specificity, and throughput. This review summarizes current MS-based glycoproteomics approaches and highlights recent advances in its application to cancer biomarker and neurodegenerative disease research.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA; Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA.
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15
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Ma J, Sanda M, Wei R, Zhang L, Goldman R. Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM. J Proteomics 2018; 189:67-74. [PMID: 29427759 DOI: 10.1016/j.jprot.2018.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 12/22/2022]
Abstract
Aberrant core fucosylation of proteins has been linked to liver diseases. In this study, we carried out multiple reaction monitoring (MRM) quantification of core fucosylated N-glycopeptides of serum proteins partially deglycosylated by a combination of endoglycosidases (endoF1, endoF2, and endoF3). To minimize variability associated with the preparatory steps, the analysis was performed without enrichment of glycopeptides or fractionation of serum besides the nanoRP chromatography. Specifically, we quantified core fucosylation of 22 N-glycopeptides derived from 17 proteins together with protein abundance of these glycoproteins in a cohort of 45 participants (15 disease-free control, 15 fibrosis and 15 cirrhosis patients) using a multiplex nanoUPLC-MS-MRM workflow. We find increased core fucosylation of 5 glycopeptides at the stage of liver fibrosis (i.e., N630 of serotransferrin, N107 of alpha-1-antitrypsin, N253 of plasma protease C1 inhibitor, N397 of ceruloplasmin, and N86 of vitronectin), increase of additional 6 glycopeptides at the stage of cirrhosis (i.e., N138 and N762 of ceruloplasmin, N354 of clusterin, N187 of hemopexin, N71 of immunoglobulin J chain, and N127 of lumican), while the degree of core fucosylation of 10 glycopeptides did not change. Interestingly, although we observe an increase in the core fucosylation at N86 of vitronectin in liver fibrosis, core fucosylation decreases on the N169 glycopeptide of the same protein. Our results demonstrate that the changes in core fucosylation are protein and site specific during the progression of fibrotic liver disease and independent of the changes in the quantity of N-glycoproteins. It is expected that the fully optimized multiplex LC-MS-MRM assay of core fucosylated glycopeptides will be useful for the serologic assessment of the fibrosis of liver. BIOLOGICAL SIGNIFICANCE: We have quantified the difference in core fucosylation among three comparison groups (healthy control, fibrosis and cirrhosis patients) using a sensitive and selective LC-MS-MRM method. Despite an overall increase in core fucosylation of many of the glycoproteins that we examined, core fucosylation changed in a protein- and site-specific manner. Moreover, increased and decreased fucosylation was observed on different N-glycopeptides of the same protein. Altered core fucosylation of N-glycopeptides might be used as an alternative serologic assay for the evaluation of fibrotic liver disease.
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Affiliation(s)
- Junfeng Ma
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Miloslav Sanda
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Renhuizi Wei
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Lihua Zhang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Radoslav Goldman
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA; Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA.
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16
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Zhou J, Yang W, Hu Y, Höti N, Liu Y, Shah P, Sun S, Clark D, Thomas S, Zhang H. Site-Specific Fucosylation Analysis Identifying Glycoproteins Associated with Aggressive Prostate Cancer Cell Lines Using Tandem Affinity Enrichments of Intact Glycopeptides Followed by Mass Spectrometry. Anal Chem 2017; 89:7623-7630. [PMID: 28627880 PMCID: PMC5599242 DOI: 10.1021/acs.analchem.7b01493] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Fucosylation (Fuc) of glycoproteins plays an important role in regulating protein function and has been associated with the development of several cancer types including prostate cancer (Pca). Therefore, the research of Fuc glycoproteins has attracted increasing attention recently in the analytical field. Herein, a strategy based on lectin affinity enrichments of intact glycopeptides followed by mass spectrometry has been established to evaluate the specificities of various Fuc-binding lectins for glycosite-specific Fuc analysis of nonaggressive (NAG) and aggressive (AG) Pca cell lines. The enrichment specificities of Fuc glycopeptides using lectins (LCA, PSA, AAL, LTL, UEA I, and AOL) and MAX extraction cartridges alone, or in tandem, were evaluated. Our results showed that the use of lectin enrichment significantly increased the ratio of fucosylated glycopeptides to total glycopeptides compared to MAX enrichment. Furthermore, tandem use of lectin followed by MAX increased the number of identifications of Fuc glycopeptides compared to using lectin enrichment alone. LCA, PSA, and AOL showed stronger binding capacity than AAL, LTL, and UEA I. Also, LCA and PSA bound specifically to core Fuc, whereas AOL, AAL, and UEA I showed binding to both core Fuc and branch Fuc. The optimized enrichment method with tandem enrichment of LCA followed by MAX (LCA-MAX) was then applied to examine the Fuc glycoproteomes in two NAG and two AG Pca cell lines. In total, 973 intact Fuc glycopeptides were identified and quantified from 252 Fuc proteins by using the tandem-mass-tags (TMT) labeling and nanoliquid chromatography-mass spectrometry (nanoLC-MS/MS) analysis. Further data analysis revealed that 51 Fuc glycopeptides were overexpressed more than 2-fold in AG cell lines compared to NAG cells. The analysis of protein core fucosylation has great potential for aiding our understanding of invasive activity of AG Pca and may lead to the development of diagnostic approaches for AG Pca.
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Affiliation(s)
- Jianliang Zhou
- Department of Pathology, Johns Hopkins University, Baltimore 21287, Maryland United States
- Department of Traditional Chinese Medicines, Zhejiang Institute for Food and Drug Control, Hangzhou 310052, China
| | - Weiming Yang
- Department of Pathology, Johns Hopkins University, Baltimore 21287, Maryland United States
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore 21287, Maryland United States
| | - Naseruddin Höti
- Department of Pathology, Johns Hopkins University, Baltimore 21287, Maryland United States
| | - Yang Liu
- Department of Pathology, Johns Hopkins University, Baltimore 21287, Maryland United States
| | - Punit Shah
- Department of Pathology, Johns Hopkins University, Baltimore 21287, Maryland United States
| | - Shisheng Sun
- Department of Pathology, Johns Hopkins University, Baltimore 21287, Maryland United States
| | - David Clark
- Department of Pathology, Johns Hopkins University, Baltimore 21287, Maryland United States
| | - Stefani Thomas
- Department of Pathology, Johns Hopkins University, Baltimore 21287, Maryland United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore 21287, Maryland United States
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17
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Zhou S, Wooding KM, Mechref Y. Analysis of Permethylated Glycan by Liquid Chromatography (LC) and Mass Spectrometry (MS). Methods Mol Biol 2017; 1503:83-96. [PMID: 27743360 DOI: 10.1007/978-1-4939-6493-2_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The development of a reliable and high-throughput glycomic profiling strategy is in high demand due to the biological roles of glycans and their association with different diseases. Native analysis can be quite difficult because of the low ionization efficiency and microheterogeneity of glycans. In this chapter, the sample preparation protocols and LC-MS analysis of permethylated glycan strategies are introduced. Solid-phase permethylation is a fast, convenient, and high-yield method to stabilize sialic acid and improve glycan ionization efficiency and analysis in positive mode; this results in a more sensitive and reliable glycomic profiling strategy. Several modifications in the LC method are also mentioned in this chapter. Online purification simplifies sample preparation and reduces sample loss. Elevating the column temperature significantly improves the peak shape of permethylated glycans and results in isomeric separation. The identification and quantification of permethylated glycans can be achieved through high resolution MS and MS/MS experiments using a MRM method; both approaches are reliable, sensitive, and conducive to high-throughput glycomic studies.
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Affiliation(s)
- Shiyue Zhou
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Kerry M Wooding
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA.
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18
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Abstract
The core-fucosylated (CF) glycoproteins are widely distributed in mammalian tissues and regulated under pathological conditions, especially in cancer progression. The Food and Drug Administration (FDA) has approved the core-fucosylated α-fetoprotein as a biomarker for the early diagnosis of hepatocellular carcinoma (HCC). An approach for identifying CF glycoproteins has significantly practical value. Here we introduce a novel method for identification of CF glycoproteome in human plasma. The method integrates tandem glycopeptide enrichment, stepped fragmentation, and "glycan diagnostic ion"-based spectrum refinement. With this method, the productivity of identifying CF glycopeptides will be significantly improved. We anticipate that this method could be widely utilized to explore the CF glycoproteins and their regulation under physiological or pathological condition.
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19
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Yu H, Wang F, Lin L, Cao W, Liu Y, Qin L, Lu H, He F, Shen H, Yang P. Mapping and analyzing the human liver proteome: progress and potential. Expert Rev Proteomics 2016; 13:833-43. [PMID: 27448621 DOI: 10.1080/14789450.2016.1213132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The liver is an important organ in humans. Hepatocellular carcinoma (HCC) is one of the deadliest cancers in the world. Progress in the Human Liver Proteome Project (HLPP) has improved understanding of the liver and the liver cancer proteome. AREAS COVERED Here, we summarize the recent progress in liver proteome modification profiles, proteomic studies in liver cancer, proteomic study in the search for novel liver cancer biomarkers and drug targets, and progress of the Chromosome Centric Human Proteome Project (CHPP) in the past five years in the Institutes of Biomedical Sciences (IBS) of Fudan University. Expert commentary: Recent advances and findings discussed here provide great promise of improving the outcome of patients with liver cancer.
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Affiliation(s)
- Hongxiu Yu
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China.,b Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai , China
| | - Fang Wang
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China
| | - Ling Lin
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China
| | - Weiqian Cao
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China
| | - Yinkun Liu
- c China Liver Cancer Institute, Zhongshan Hospital , Fudan University , Shanghai , China
| | - Lunxiu Qin
- c China Liver Cancer Institute, Zhongshan Hospital , Fudan University , Shanghai , China
| | - Haojie Lu
- b Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai , China
| | - Fuchu He
- d State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Radiation Medicine , Beijing , China
| | - Huali Shen
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China.,b Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai , China
| | - Pengyuan Yang
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China.,b Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai , China
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20
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Ma C, Qu J, Li X, Zhao X, Li L, Xiao C, Edmunds G, Gashash E, Song J, Wang PG. Improvement of core-fucosylated glycoproteome coverage via alternating HCD and ETD fragmentation. J Proteomics 2016; 146:90-8. [PMID: 27282921 DOI: 10.1016/j.jprot.2016.06.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/16/2016] [Accepted: 06/02/2016] [Indexed: 01/03/2023]
Abstract
UNLABELLED Core-fucosylation (CF) plays important roles in regulating biological processes in eukaryotes. Alterations of CF-glycosites or CF-glycans in bodily fluids correlate with cancer development. Therefore, global research of protein core-fucosylation with an emphasis on proteomics can explain pathogenic and metastasis mechanisms and aid in the discovery of new potential biomarkers for early clinical diagnosis. In this study, a precise and high throughput method was established to identify CF-glycosites from human plasma. We found that alternating HCD and ETD fragmentation (AHEF) can provide a complementary method to discover CF-glycosites. A total of 407 CF-glycosites among 267 CF-glycoproteins were identified in a mixed sample made from six normal human plasma samples. Among the 407 CF-glycosites, 10 are without the N-X-S/T/C consensus motif, representing 2.5% of the total number identified. All identified CF-glycopeptide results from HCD and ETD fragmentation were filtered with neutral loss peaks and characteristic ions of GlcNAc from HCD spectra, which assured the credibility of the results. This study provides an effective method for CF-glycosites identification and a valuable biomarker reference for clinical research. BIOLOGICAL SIGNIFICANCE CF-glycosytion plays an important role in regulating biological processes in eukaryotes. Alterations of the glycosites and attached CF-glycans are frequently observed in various types of cancers. Thus, it is crucial to develop a strategy for mapping human CF-glycosylation. Here, we developed a complementary method via alternating HCD and ETD fragmentation (AHEF) to analyze CF-glycoproteins. This strategy reveals an excellent complementarity of HCD and ETD in the analysis of CF-glycoproteins, and provides a valuable biomarker reference for clinical research.
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Affiliation(s)
- Cheng Ma
- Department of Chemistry, Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, United States.
| | - Jingyao Qu
- Department of Chemistry, Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - Xu Li
- Department of Chemistry, Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - Xinyuan Zhao
- National Institute of Biological Sciences, Beijing 102206, People's Republic of China
| | - Lei Li
- Department of Chemistry, Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - Cong Xiao
- Department of Chemistry, Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - Garrett Edmunds
- Department of Chemistry, Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - Ebtesam Gashash
- Department of Chemistry, Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - Jing Song
- Department of Chemistry, Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - Peng George Wang
- Department of Chemistry, Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, United States.
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21
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Stavenhagen K, Plomp R, Wuhrer M. Site-Specific Protein N- and O-Glycosylation Analysis by a C18-Porous Graphitized Carbon–Liquid Chromatography-Electrospray Ionization Mass Spectrometry Approach Using Pronase Treated Glycopeptides. Anal Chem 2015; 87:11691-9. [DOI: 10.1021/acs.analchem.5b02366] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Kathrin Stavenhagen
- Division
of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
| | - Rosina Plomp
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Manfred Wuhrer
- Division
of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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22
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Zhou S, Hu Y, DeSantos-Garcia JL, Mechref Y. Quantitation of permethylated N-glycans through multiple-reaction monitoring (MRM) LC-MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:596-603. [PMID: 25698222 PMCID: PMC4514032 DOI: 10.1007/s13361-014-1054-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/09/2014] [Accepted: 11/09/2014] [Indexed: 05/20/2023]
Abstract
The important biological roles of glycans and their implications in disease development and progression have created a demand for the development of sensitive quantitative glycomics methods. Quantitation of glycans existing at low abundance is still analytically challenging. In this study, an N-linked glycans quantitation method using multiple-reaction monitoring (MRM) on a triple quadrupole instrument was developed. Optimum normalized collision energy (CE) for both sialylated and fucosylated N-glycan was determined to be 30%, whereas it was found to be 35% for either fucosylated or sialylated N-glycans. The optimum CE for mannose and complex type N-glycan was determined to be 35%. Additionally, the use of three transitions was shown to facilitate reliable quantitation. A total of 88 N-glycan compositions in human blood serum were quantified using this MRM approach. Reliable detection and quantitation of these glycans was achieved when the equivalence of 0.005 μL of blood serum was analyzed. Accordingly, N-glycans down to the 100th of a μL level can be reliably quantified in pooled human blood serum, spanning a dynamic concentration range of three orders of magnitude. MRM was also effectively utilized to quantitatively compare the expression of N-glycans derived from brain-targeting breast carcinoma cells (MDA-MB-231BR) and metastatic breast cancer cells (MDA-MB-231). Thus, the described MRM method of permethylated N-glycan enables a rapid and reliable identification and quantitation of glycans derived from glycoproteins purified or present in complex biological samples.
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Affiliation(s)
| | | | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
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23
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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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24
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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 PMCID: PMC5780646 DOI: 10.1002/prca.201400152] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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
| | - Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC, USA
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25
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Ruhaak LR, Lebrilla CB. Applications of Multiple Reaction Monitoring to Clinical Glycomics. Chromatographia 2014; 78:335-342. [PMID: 25892741 DOI: 10.1007/s10337-014-2783-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Multiple reaction monitoring or MRM is widely acknowledged for its accuracy of quantitation. The applications have mostly been in the analysis of small molecules and proteins, but its utility is expanding. Protein glycosylation was recently identified as a new paradigm in biomarker discovery for health and disease. A number of recent studies have now identified differential glycosylation patterns associated with health and disease states, including aging, pregnancy, rheumatoid arthritis and different types of cancer. While the use of MRM in clinical glycomics is still in its infancy, it can likely play a role in the quantitation of protein glycosylation in the clinical setting. Here, we aim to review the current advances in the nascent application of MRM in the field of glycomics.
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Affiliation(s)
- L Renee Ruhaak
- Department of Chemistry, University of California Davis. One Shields Avenue, Davis, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis. One Shields Avenue, Davis, CA, USA
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26
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Ma C, Zhang Q, Qu J, Zhao X, Li X, Liu Y, Wang PG. A precise approach in large scale core-fucosylated glycoprotein identification with low- and high-normalized collision energy. J Proteomics 2014; 114:61-70. [PMID: 25220145 DOI: 10.1016/j.jprot.2014.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/26/2014] [Accepted: 09/02/2014] [Indexed: 01/03/2023]
Abstract
UNLABELLED The core fucosylation (CF) of N-glycoproteins plays important roles in regulating protein functions during biological development, and it has also been shown to be up-regulated in several high metastasis cancer cell lines. Therefore, global profiling and quantitative characterization of CF-glycoproteins may reveal potent biomarkers for clinical applications. However, due to the complex fragmentation pattern of CF-glycopeptides, accurately identifying CF-glycosylation sites via mass spectrometry with high throughput remains a formidable challenge. In this study, we established a precise CF-glycosylation site identification strategy with UHPLC LTQ-Orbitrap Elite under low- and high-normalized collision energy (LHNCE) conditions. To demonstrate the feasibility of LHNCE, the CF-glycopeptides of target proteins in clinical plasma samples were applied and compared as a preliminary demonstration and resulted in the assignment of 357 unique CF-glycosylation sites from 209 CF-glycoproteins. In this study, the largest human plasma CF-glycosylation site database was constructed, and at least three-fold more CF-sites were identified compared to previously published studies. The results further demonstrated that LHNCE provides an important approach for CF-glycoprotein function studies and biomarker screening in cancer research. BIOLOGICAL SIGNIFICANCE Core-fucosylation (CF) is a kind of N-linked glycosylation in which an α1,6-linked fucose is added to the innermost N-acetylglucosamine (GlcNAc) residue. It has been proved that core-fucosylation is involved in regulating biological processes in mammals. Abnormal core-fucosylation has been demonstrated in human pathological processes, such as metastasis. For example, the CF-glycosylation of an α-fetoprotein isoform (AFP-L3) was approved as a biomarker of hepatocellular carcinoma (HCC). In addition, GP73 is also a well-known biomarker and its CF-glycosylation level will increase in liver cancer patients. Therefore, it is crucial to develop a strategy for mapping human CF-glycosylation.
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Affiliation(s)
- Cheng Ma
- Center for Diagnostics & Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Qi Zhang
- Department of Parasitology, Faculty of Biology, Philipps University Marburg, Marburg, Hessen 35043, Germany
| | - Jingyao Qu
- Center for Diagnostics & Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States; National Glycoengineering Research Center, The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Xinyuan Zhao
- National Institute of Biological Sciences, Beijing 102206, People's Republic of China
| | - Xu Li
- Center for Diagnostics & Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Yunpeng Liu
- Center for Diagnostics & Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States; National Glycoengineering Research Center, The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Peng George Wang
- Center for Diagnostics & Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States; National Glycoengineering Research Center, The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, People's Republic of China.
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Rapid development of proteomics in China: from the perspective of the Human Liver Proteome Project and technology development. SCIENCE CHINA-LIFE SCIENCES 2014; 57:1162-71. [PMID: 25119674 DOI: 10.1007/s11427-014-4714-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/01/2014] [Indexed: 12/17/2022]
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Cao Q, Zhao X, Zhao Q, Lv X, Ma C, Li X, Zhao Y, Peng B, Ying W, Qian X. Strategy integrating stepped fragmentation and glycan diagnostic ion-based spectrum refinement for the identification of core fucosylated glycoproteome using mass spectrometry. Anal Chem 2014; 86:6804-11. [PMID: 24914453 DOI: 10.1021/ac501154a] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Core fucosylation (CF) is a special glycosylation pattern of proteins that has a strong relationship with cancer. The Food and Drug Administration (FDA) has approved the core fucosylated α-fetoprotein as a biomarker for the early diagnosis of hepatocellular carcinoma (HCC). The technology for identifying core fucosylated proteins has significant practical value. The major method for core fucosylated glycoprotein/glycopeptide analysis is neutral loss-based MS(3) scanning under collision-induced dissociation (CID) by ion trap mass spectrometry. However, due to the limited speed and low resolution of the MS(3) scan mode, it is difficult to achieve high-throughput, with only dozens of core fucosylated proteins identified in a single run. In this work, we developed a novel strategy for the identification of CF glycopeptides at a large scale, integrating the stepped fragmentation function, one novel feature of quadrupole-orbitrap mass spectrometry, with "glycan diagnostic ion"-based spectrum optimization. By using stepped fragmentation, we were able to obtain both highly accurate glycan and peptide information of a simplified CF glycopeptide in one spectrum. Moreover, the spectrum could be recorded with the same high speed as the conventional MS(2) scan. By using the "glycan diagnostic ion"-based spectrum refinement method, the efficiency of the CF glycopeptide discovery was significantly improved. We demonstrated the feasibility and reproducibility of our method by analyzing CF glycoproteomes of mouse liver tissue and HeLa cell samples spiked with standard CF glycoprotein. In total, 1364 and 856 CF glycopeptides belonging to 702 and 449 CF glycoproteins were identified, respectively, within a 78-min gradient analysis, which was approximately a 7-fold increase in the identification efficiency of CF glycopeptides compared to the currently used method. In this work, we took core fucosylated glycopeptides as a practical example to demonstrate the great potential of our novel method for use in glycoproteome analysis, and we also anticipate using the flexible novel method in other research fields.
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Affiliation(s)
- Qichen Cao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
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29
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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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30
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Hong Q, Lebrilla CB, Miyamoto S, Ruhaak LR. Absolute quantitation of immunoglobulin G and its glycoforms using multiple reaction monitoring. Anal Chem 2013; 85:8585-93. [PMID: 23944609 DOI: 10.1021/ac4009995] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Studies aimed toward glycan biomarker discovery have focused on glycan characterization by the global profiling of released glycans. Site-specific glycosylation analysis is less developed but may provide new types of biomarkers with higher sensitivity and specificity. Quantitation of peptide-conjugated glycans directly facilitates the differential analysis of distinct glycoforms associated with specific proteins at distinct sites. We have developed a method using MRM to monitor protein glycosylation normalized to absolute protein concentrations to examine quantitative changes in glycosylation at a site-specific level. This new approach provides information regarding both the absolute amount of protein and the site-specific glycosylation profile and will thus be useful to determine if altered glycosylation profiles in serum/plasma are due to a change in protein glycosylation or a change in protein concentration. The remarkable sensitivity and selectivity of MRM enable the detection of low abundance IgG glycopeptides, even when IgG was digested directly in serum with no cleanup prior to the liquid chromatography. Our results show a low limit of detection of 60 amol and a wide dynamic range of 3 orders magnitude for IgG protein quantitation. The results show that IgG glycopeptides can be analyzed directly from serum (without enrichment) and yield more accurate abundances when normalized to the protein content. This report represents the most comprehensive study so far of the use of multiple reaction monitoring for the quantitation of glycoproteins and their glycosylation patterns in biofluids.
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Affiliation(s)
- Qiuting Hong
- Department of Chemistry, University of California , One Shields Avenue, Davis, California, 95616, United States
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31
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Kaji H, Ocho M, Togayachi A, Kuno A, Sogabe M, Ohkura T, Nozaki H, Angata T, Chiba Y, Ozaki H, Hirabayashi J, Tanaka Y, Mizokami M, Ikehara Y, Narimatsu H. Glycoproteomic Discovery of Serological Biomarker Candidates for HCV/HBV Infection-Associated Liver Fibrosis and Hepatocellular Carcinoma. J Proteome Res 2013; 12:2630-40. [PMID: 23586699 DOI: 10.1021/pr301217b] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hiroyuki Kaji
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Makoto Ocho
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Akira Togayachi
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Atsushi Kuno
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Maki Sogabe
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Takashi Ohkura
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Hirofumi Nozaki
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Takashi Angata
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Yasunori Chiba
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Hidenori Ozaki
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Jun Hirabayashi
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Yasuhito Tanaka
- Department of Virology and Liver
Unit, Nagoya City University Graduate School of Medical Sciences, Mizuho, Nagoya, Aichi, Japan
| | - Masashi Mizokami
- Department of Virology and Liver
Unit, Nagoya City University Graduate School of Medical Sciences, Mizuho, Nagoya, Aichi, Japan
| | - Yuzuru Ikehara
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Hisashi Narimatsu
- Research Center for Medical
Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
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32
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Alley WR, Mann BF, Novotny MV. High-sensitivity analytical approaches for the structural characterization of glycoproteins. Chem Rev 2013; 113:2668-732. [PMID: 23531120 PMCID: PMC3992972 DOI: 10.1021/cr3003714] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- William R. Alley
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
| | - Benjamin F. Mann
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
- Indiana University School of Medicine, Indiana University, Indianapolis, Indiana, United States
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33
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Flowers SA, Ali L, Lane CS, Olin M, Karlsson NG. Selected reaction monitoring to differentiate and relatively quantitate isomers of sulfated and unsulfated core 1 O-glycans from salivary MUC7 protein in rheumatoid arthritis. Mol Cell Proteomics 2013; 12:921-31. [PMID: 23457413 DOI: 10.1074/mcp.m113.028878] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Rheumatoid arthritis is a common and debilitating systemic inflammatory condition affecting up to 1% of the world's population. This study aimed to investigate the immunological significance of O-glycans in chronic arthritis at a local and systemic level. O-Glycans released from synovial glycoproteins during acute and chronic arthritic conditions were compared and immune-reactive glycans identified. The sulfated core 1 O-glycan (Galβ1-3GalNAcol) was immune reactive, showing a different isomeric profile in the two conditions. From acute reactive arthritis, three isomers could be sequenced, but in patients with chronic rheumatoid arthritis, only a single 3-Gal sulfate-linked isomer could be identified. The systemic significance of this glycan epitope was investigated using the salivary mucin MUC7 in patients with rheumatoid arthritis and normal controls. To analyze this low abundance glycan, a selected reaction monitoring (SRM) method was developed to differentiate and relatively quantitate the core 1 O-glycan and the sulfated core 1 O-glycan Gal- and GalNAc-linked isomers. The acquisition of highly sensitive full scan linear ion trap MS/MS spectra in addition to quantitative SRM data allowed the 3- and 6-linked Gal isomers to be differentiated. The method was used to relatively quantitate the core 1 glycans from MUC7 to identify any systemic changes in this carbohydrate epitope. A statistically significant increase in sulfation was identified in salivary MUC7 from rheumatoid arthritis patients. This suggests a potential role for this epitope in chronic inflammation. This study was able to develop an SRM approach to specifically identify and relatively quantitate sulfated core 1 isomers and the unsulfated structure. The expansion of this method may afford an avenue for the high throughput investigation of O-glycans.
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Affiliation(s)
- Sarah A Flowers
- Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, Medicinaregatan 9A, 405 30, Gothenburg, Sweden
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Kuzmanov U, Kosanam H, Diamandis EP. The sweet and sour of serological glycoprotein tumor biomarker quantification. BMC Med 2013; 11:31. [PMID: 23390961 PMCID: PMC3751898 DOI: 10.1186/1741-7015-11-31] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 02/07/2013] [Indexed: 12/25/2022] Open
Abstract
Aberrant and dysregulated protein glycosylation is a well-established event in the process of oncogenesis and cancer progression. Years of study on the glycobiology of cancer have been focused on the development of clinically viable diagnostic applications of this knowledge. However, for a number of reasons, there has been only sparse and varied success. The causes of this range from technical to biological issues that arise when studying protein glycosylation and attempting to apply it to practical applications. This review focuses on the pitfalls, advances, and future directions to be taken in the development of clinically applicable quantitative assays using glycan moieties from serum-based proteins as analytes. Topics covered include the development and progress of applications of lectins, mass spectrometry, and other technologies towards this purpose. Slowly but surely, novel applications of established and development of new technologies will eventually provide us with the tools to reach the ultimate goal of quantification of the full scope of heterogeneity associated with the glycosylation of biomarker candidate glycoproteins in a clinically applicable fashion.
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Affiliation(s)
- Uros Kuzmanov
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, 6th floor, 60 Murray Street, Box 32, Toronto, ON M5T 3L9, Canada
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35
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Sanda M, Pompach P, Brnakova Z, Wu J, Makambi K, Goldman R. Quantitative liquid chromatography-mass spectrometry-multiple reaction monitoring (LC-MS-MRM) analysis of site-specific glycoforms of haptoglobin in liver disease. Mol Cell Proteomics 2013; 12:1294-305. [PMID: 23389048 DOI: 10.1074/mcp.m112.023325] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Development of liver disease is associated with the appearance of multiply fucosylated glycoforms of haptoglobin. To analyze the disease-related haptoglobin glycoforms in liver cirrhosis and hepatocellular carcinoma, we have optimized an LC-MS-multiple reaction monitoring (MRM) workflow for glycopeptide quantification. The final quantitative analysis included 24 site-specific glycoforms generated by treatment of a tryptic digest of haptoglobin with α(2-3,6,8)-neuraminidase and β(1-4)-galactosidase. The combination of LC-MS-MRM with exoglycosidase digests allowed resolution of isobaric glycoforms of the haptoglobin-T3 glycopeptide for quantification of the multiply fucosylated Lewis Y-containing glycoforms we have identified in the context of liver disease. Fourteen multiply fucosylated glycoforms of the 20 examined increased significantly in the liver disease group compared with healthy controls with an average 5-fold increase in intensity (p < 0.05). At the same time, two tri-antennary glycoforms without fucoses did not increase in the liver disease group, and two tetra-antennary glycoforms without fucoses showed a marginal increase (at most 40%) in intensity. Our analysis of 30 individual patient samples (10 healthy controls, 10 cirrhosis patients, and 10 hepatocellular carcinoma patients) showed that these glycoforms were substantially increased in a small subgroup of liver disease patients but did not significantly differ between the groups of hepatocellular carcinoma and cirrhosis patients. The tri- and tetra-antennary singly fucosylated glycoforms are associated with a MELD score and low platelet counts (p < 0.05). The exoglycosidase-assisted LC-MS-MRM workflow, optimized for the quantification of fucosylated glycoforms of haptoglobin, can be used for quantification of these glycoforms on other glycopeptides with appropriate analytical behavior.
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Affiliation(s)
- Miloslav Sanda
- Department of Oncology, Georgetown University, Washington, DC 20057, USA
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36
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Shetty V, Philip R. Mass Spectrometry Investigation of Glycosylation Aberration via De-N-Glycopeptide Analysis. Aust J Chem 2013. [DOI: 10.1071/ch13159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Proteomics research on glycan alterations has received great attention owing to their implications in disease initiation and progression. Determination of the glycoprotein expression remains one of the most challenging tasks as the glycan residues in a given glycoprotein exist in complex branched structures and differ in linkage. In view of the vital role of glycan changes in cellular processes and disease progression, there has been an increased interest in developing methodologies for the detection of these changes. A subset of proteomics methods are discussed here that demonstrate the utility of the glycan-free de-N-glycopeptide analysis for the screening of complex glycoproteome as well as discovery of glycopeptide/glycoprotein biomarkers.
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37
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Song E, Pyreddy S, Mechref Y. Quantification of glycopeptides by multiple reaction monitoring liquid chromatography/tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1941-54. [PMID: 22847692 PMCID: PMC3673029 DOI: 10.1002/rcm.6290] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Protein glycosylation has a major influence on functions of proteins. Studies have shown that aberrations in glycosylation are indicative of disease conditions. This has prompted major research activities for comparative studies of glycoproteins in biological samples. Multiple reaction monitoring (MRM) is a highly sensitive technique which has been recently explored for quantitative proteomics. In this work, MRM was adopted for quantification of glycopeptides derived from both model glycoproteins and depleted human blood serum using glycan oxonium ions as transitions. The utilization of oxonium ions aids in identifying the different types of glycans bound to peptide backbones. MRM experiments were optimized by evaluating different parameters that have a major influence on quantification of glycopeptides, which include MRM time segments, number of transitions, and normalized collision energies. The results indicate that oxonium ions could be adopted for the characterization and quantification of glycopeptides in general, eliminating the need to select specific transitions for individual precursor ions. Also, the specificity increased with the number of transitions and a more sensitive analysis can be obtained by providing specific time segments. This approach can be applied to comparative and quantitative studies of glycopeptides in biological samples as illustrated for the case of depleted blood serum sample.
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Affiliation(s)
| | | | - Yehia Mechref
- Corresponding author Department of Chemistry and Biochemistry Texas Tech University Lubbock, TX 79409-1061 Tel: 806-742-3059 Fax: 806-742-1289
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38
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Recent progress in quantitative glycoproteomics. Glycoconj J 2012; 29:249-58. [PMID: 22699565 DOI: 10.1007/s10719-012-9398-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 05/17/2012] [Accepted: 05/21/2012] [Indexed: 12/19/2022]
Abstract
Protein glycosylation is acknowledged as one of the major posttranslational modifications that elicit significant effects on protein folding, conformation, distribution, stability, and activity. The changes in glycoprotein abundance, glycosylation degree, and glycan structure are associated with a variety of diseases. Therefore, the quantitative study of glycoproteomics has become a new and popular research topic, and is quickly emerging as an important technique for biomarker discovery. Mass spectrometry-based protein quantification technologies provide a powerful tool for the systematic and quantitative assessment of the quantitative differences in the protein profiles of different samples. Combined with various glycoprotein/glycopeptide enrichment strategies and other glycoprotein analysis methods, these techniques have been further developed for application in quantitative glycoproteomics. A comprehensive quantitative analysis of the glycoproteome in a complex biological sample remains challenging because of the enormous complexity of biological samples, intrinsic characteristics of glycoproteins, and lack of universal quantitative technology. In this review, recently developed technologies in quantitative glycoproteome, especially those focused on two of the most common types of glycosylation (N-linked and O-linked glycoproteome), were summarized. The strengths and weaknesses of the various approaches were also discussed.
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Abstract
Oligosaccharides in human milk strongly influence the composition of the gut microflora of neonates. Because it is now clear that the microflora play important roles in the development of the infant immune system, human milk oligosaccharides (HMO) are studied frequently. Milk samples contain complex mixtures of HMO, usually comprising several isomeric structures that can be either linear or branched. Traditionally, HMO profiling was performed using HPLC with fluorescence or UV detection. By using porous graphitic carbon liquid chromatography MS, it is now possible to separate and identify most of the isomers, facilitating linkage-specific analysis. Matrix-assisted laser desorption ionization time-of-flight analysis allows fast profiling, but does not allow isomer separation. Novel MS fragmentation techniques have facilitated structural characterization of HMO that are present at lower concentrations. These techniques now facilitate more accurate studies of HMO consumption as well as Lewis blood group determinations.
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40
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Shi T, Su D, Liu T, Tang K, Camp DG, Qian WJ, Smith RD. Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics. Proteomics 2012; 12:1074-92. [PMID: 22577010 PMCID: PMC3375056 DOI: 10.1002/pmic.201100436] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 01/12/2012] [Indexed: 12/13/2022]
Abstract
Selected reaction monitoring (SRM) - also known as multiple reaction monitoring (MRM) - has emerged as a promising high-throughput targeted protein quantification technology for candidate biomarker verification and systems biology applications. A major bottleneck for current SRM technology, however, is insufficient sensitivity for, e.g. detecting low-abundance biomarkers likely present at the low ng/mL to pg/mL range in human blood plasma or serum, or extremely low-abundance signaling proteins in cells or tissues. Herein, we review recent advances in methods and technologies, including front-end immunoaffinity depletion, fractionation, selective enrichment of target proteins/peptides including posttranslational modifications, as well as advances in MS instrumentation which have significantly enhanced the overall sensitivity of SRM assays and enabled the detection of low-abundance proteins at low- to sub-ng/mL level in human blood plasma or serum. General perspectives on the potential of achieving sufficient sensitivity for detection of pg/mL level proteins in plasma are also discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Dian Su
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Keqi Tang
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - David G. Camp
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Richard D. Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
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Evans C, Noirel J, Ow SY, Salim M, Pereira-Medrano AG, Couto N, Pandhal J, Smith D, Pham TK, Karunakaran E, Zou X, Biggs CA, Wright PC. An insight into iTRAQ: where do we stand now? Anal Bioanal Chem 2012; 404:1011-27. [PMID: 22451173 DOI: 10.1007/s00216-012-5918-6] [Citation(s) in RCA: 220] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 01/09/2023]
Abstract
The iTRAQ (isobaric tags for relative and absolute quantification) technique is widely employed in proteomic workflows requiring relative quantification. Here, we review the iTRAQ literature; in particular, we focus on iTRAQ usage in relation to other commonly used quantitative techniques e.g. stable isotope labelling in culture (SILAC), label-free methods and selected reaction monitoring (SRM). As a result, we identify several issues arising with respect to iTRAQ. Perhaps frustratingly, iTRAQ's attractiveness has been undermined by a number of technical and analytical limitations: it may not be truly quantitative, as the changes in abundance reported will generally be underestimated. We discuss weaknesses and strengths of iTRAQ as a methodology for relative quantification in the light of this and other technical issues. We focus on technical developments targeted at iTRAQ accuracy and precision, use of 4-plex over 8-plex reagents and application of iTRAQ to post-translational modification (PTM) workflows. We also discuss iTRAQ in relation to label-free approaches, to which iTRAQ is losing ground.
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Affiliation(s)
- Caroline Evans
- The ChELSI Institute, Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
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42
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Lin Z, Lo A, Simeone DM, Ruffin MT, Lubman DM. An N-glycosylation Analysis of Human Alpha-2-Macroglobulin Using an Integrated Approach. ACTA ACUST UNITED AC 2012; 5:127-134. [PMID: 23028207 DOI: 10.4172/jpb.1000224] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Assignment of glycosylation sites and site microheterogeneity is of both biological and clinical significance. Herein, the detailed N-glycosylation pattern of human serum alpha-2-macroglobulin was studied using an integrative approach, including permethylation of N-glycans, collision induced dissociation (CID) and electron transfer dissociation (ETD) of chymotryptic N-glycopeptides, and partial deglycosylation of chymotryptic N-glycopeptides with endo-β-N-acetylglucosaminidase F3 (Endo F3). Three N-glycosylation sites were found to be occupied by four biantennary complex type N-glycans using N-glycan analysis and the ETD/CID method. Endo F3 assisted mass spectrometric analysis yielded five N-glycosylation sites with and without core fucosylation. In total, six out of eight potential N-glycosylation sites were identified using this approach. This integrative approach was performed using only 10 μL of human serum for both N-glycosylation site assignment and site microheterogeneity determination.
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Affiliation(s)
- Zhenxin Lin
- Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109, USA
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