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An Efficient and Economical N-Glycome Sample Preparation Using Acetone Precipitation. Metabolites 2022; 12:metabo12121285. [PMID: 36557323 PMCID: PMC9786591 DOI: 10.3390/metabo12121285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Due to the critical role of the glycome in organisms and its close connections with various diseases, much time and effort have been dedicated to glycomics-related studies in the past decade. To achieve accurate and reliable identification and quantification of glycans extracted from biological samples, several analysis methods have been well-developed. One commonly used methodology for the sample preparation of N-glycomics usually involves enzymatic cleavage by PNGase F, followed by sample purification using C18 cartridges to remove proteins. PNGase F and C18 cartridges are very efficient both for cleaving N-glycans and for protein removal. However, this method is most suitable for a limited quantity of samples. In this study, we developed a sample preparation method focusing on N-glycome extraction and purification from large-scale biological samples using acetone precipitation. The N-glycan yield was first tested on standard glycoprotein samples, bovine fetuin and complex biological samples, and human serum. Compared to C18 cartridges, most of the sialylated N-glycans from human serum were detected with higher abundance after acetone precipitation. However, C18 showed a slightly higher efficiency for protein removal. Using the unfiltered human serum as the baseline, around 97.7% of the proteins were removed by acetone precipitation, while more than 99.9% of the proteins were removed by C18 cartridges. Lastly, the acetone precipitation was applied to N-glycome extraction from egg yolks to demonstrate large-scale glycomics sample preparation.
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Peng W, Kobeissy F, Mondello S, Barsa C, Mechref Y. MS-based glycomics: An analytical tool to assess nervous system diseases. Front Neurosci 2022; 16:1000179. [PMID: 36408389 PMCID: PMC9671362 DOI: 10.3389/fnins.2022.1000179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/05/2022] [Indexed: 08/27/2023] Open
Abstract
Neurological diseases affect millions of peopleochemistryorldwide and are continuously increasing due to the globe's aging population. Such diseases affect the nervous system and are characterized by a progressive decline in brain function and progressive cognitive impairment, decreasing the quality of life for those with the disease as well as for their families and loved ones. The increased burden of nervous system diseases demands a deeper insight into the biomolecular mechanisms at work during disease development in order to improve clinical diagnosis and drug design. Recently, evidence has related glycosylation to nervous system diseases. Glycosylation is a vital post-translational modification that mediates many biological functions, and aberrant glycosylation has been associated with a variety of diseases. Thus, the investigation of glycosylation in neurological diseases could provide novel biomarkers and information for disease pathology. During the last decades, many techniques have been developed for facilitation of reliable and efficient glycomic analysis. Among these, mass spectrometry (MS) is considered the most powerful tool for glycan analysis due to its high resolution, high sensitivity, and the ability to acquire adequate structural information for glycan identification. Along with MS, a variety of approaches and strategies are employed to enhance the MS-based identification and quantitation of glycans in neurological samples. Here, we review the advanced glycomic tools used in nervous system disease studies, including separation techniques prior to MS, fragmentation techniques in MS, and corresponding strategies. The glycan markers in common clinical nervous system diseases discovered by utilizing such MS-based glycomic tools are also summarized and discussed.
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Affiliation(s)
- Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL, United States
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Chloe Barsa
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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3
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Mondello S, Sandner V, Goli M, Czeiter E, Amrein K, Kochanek PM, Gautam S, Cho BG, Morgan R, Nehme A, Fiumara G, Eid AH, Barsa C, Haidar MA, Buki A, Kobeissy FH, Mechref Y. Exploring serum glycome patterns after moderate to severe traumatic brain injury: A prospective pilot study. EClinicalMedicine 2022; 50:101494. [PMID: 35755600 PMCID: PMC9218141 DOI: 10.1016/j.eclinm.2022.101494] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 05/09/2022] [Accepted: 05/18/2022] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Glycans play essential functional roles in the nervous system and their pathobiological relevance has become increasingly recognized in numerous brain disorders, but not fully explored in traumatic brain injury (TBI). We investigated longitudinal glycome patterns in patients with moderate to severe TBI (Glasgow Coma Scale [GCS] score ≤12) to characterize glyco-biomarker signatures and their relation to clinical features and long-term outcome. METHODS This prospective single-center observational study included 51 adult patients with TBI (GCS ≤12) admitted to the neurosurgical unit of the University Hospital of Pecs, Pecs, Hungary, between June 2018 and April 2019. We used a high-throughput liquid chromatography-tandem mass spectrometry platform to assess serum levels of N-glycans up to 3 days after injury. Outcome was assessed using the Glasgow Outcome Scale-Extended (GOS-E) at 12 months post-injury. Multivariate statistical techniques, including principal component analysis and orthogonal partial least squares discriminant analysis, were used to analyze glycomics data and define highly influential structures driving class distinction. Receiver operating characteristic analyses were used to determine prognostic accuracy. FINDINGS We identified 94 N-glycans encompassing all typical structural types, including oligomannose, hybrid, and complex-type entities. Levels of high mannose, hybrid and sialylated structures were temporally altered (p<0·05). Four influential glycans were identified. Two brain-specific structures, HexNAc5Hex3DeoxyHex0NeuAc0 and HexNAc5Hex4DeoxyHex0NeuAc1, were substantially increased early after injury in patients with unfavorable outcome (GOS-E≤4) (area under the curve [AUC]=0·75 [95%CI 0·59-0·90] and AUC=0·71 [0·52-0·89], respectively). Serum levels of HexNAc7Hex7DeoxyHex1NeuAc2 and HexNAc8Hex6DeoxyHex0NeuAc0 were persistently increased in patients with favorable outcome, but undetectable in those with unfavorable outcome. Levels of HexNAc5Hex4DeoxyHex0NeuAc1 were acutely elevated in patients with mass lesions and in those requiring decompressive craniectomy. INTERPRETATION In spite of the exploratory nature of the study and the relatively small number of patients, our results provide to the best of our knowledge initial evidence supporting the utility of glycomics approaches for biomarker discovery and patient phenotyping in TBI. Further larger multicenter studies will be required to validate our findings and to determine their pathobiological value and potential applications in practice. FUNDING This work was funded by the Italian Ministry of Health (grant number GR-2013-02354960), and also partially supported by a NIH grant (1R01GM112490-08).
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Affiliation(s)
- Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy
- Corresponding author.
| | - Viktor Sandner
- Sartorius Data Analytics, Sartorius Stedim Austria GmbH, 1030 Vienna, Austria
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Box 41061, Lubbock, TX 79409-1061, USA
| | - Endre Czeiter
- Department of Neurosurgery, University of Pécs, H-7623 Pécs, Hungary
- Neurotrauma Research Group, Szentágothai Research Centre, University of Pécs, H-7624 Pécs, Hungary
- MTA-PTE Clinical Neuroscience MR Research Group, H-7623 Pécs, Hungary
| | - Krisztina Amrein
- Department of Neurosurgery, University of Pécs, H-7623 Pécs, Hungary
- Neurotrauma Research Group, Szentágothai Research Centre, University of Pécs, H-7624 Pécs, Hungary
- MTA-PTE Clinical Neuroscience MR Research Group, H-7623 Pécs, Hungary
| | - Patrick M. Kochanek
- Departments of Critical Care Medicine, Pediatrics, Anesthesiology, and Clinical and Translational Science, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh 15224, USA
| | - Sakshi Gautam
- Department of Chemistry and Biochemistry, Texas Tech University, Box 41061, Lubbock, TX 79409-1061, USA
| | - Byeong Gwan Cho
- Department of Chemistry and Biochemistry, Texas Tech University, Box 41061, Lubbock, TX 79409-1061, USA
| | - Ryan Morgan
- Department of Chemistry and Biochemistry, Texas Tech University, Box 41061, Lubbock, TX 79409-1061, USA
| | - Ali Nehme
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy
| | - Giacomo Fiumara
- Department of Mathematical and Computer Science, Physical Sciences and Earth Sciences, University of Messina, 98100 Messina, Italy
| | - Ali H. Eid
- Department of Biochemistry and Molecular Genetics, American University of Beirut, 1107-2020 Beirut, Lebanon
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Chloe Barsa
- Department of Biochemistry and Molecular Genetics, American University of Beirut, 1107-2020 Beirut, Lebanon
| | - Muhammad Ali Haidar
- Department of Biochemistry and Molecular Genetics, American University of Beirut, 1107-2020 Beirut, Lebanon
| | - Andras Buki
- Department of Neurosurgery, University of Pécs, H-7623 Pécs, Hungary
- Neurotrauma Research Group, Szentágothai Research Centre, University of Pécs, H-7624 Pécs, Hungary
- MTA-PTE Clinical Neuroscience MR Research Group, H-7623 Pécs, Hungary
| | - Firas H. Kobeissy
- Department of Biochemistry and Molecular Genetics, American University of Beirut, 1107-2020 Beirut, Lebanon
- Department of Psychiatry and Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Box 41061, Lubbock, TX 79409-1061, USA
- Corresponding author.
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Wang J, Peng W, Yu A, Fokar M, Mechref Y. Glycome Profiling of Cancer Cell Lines Cultivated in Physiological and Commercial Media. Biomolecules 2022; 12:biom12060743. [PMID: 35740868 PMCID: PMC9221004 DOI: 10.3390/biom12060743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 12/29/2022] Open
Abstract
A complex physiological culture medium (Plasmax) was introduced recently, composed of nutrients and metabolites at concentrations normally found in human plasma to mimic the in vivo environment for cell line cultivation. As glycosylation has been proved to be involved in cancer development, it is necessary to investigate the glycan expression changes in media with different nutrients. In this study, a breast cancer cell line, MDA-MB-231BR, and a brain cancer cell line, CRL-1620, were cultivated in Plasmax and commercial media to reveal cell line glycosylation discrepancies prompted by nutritional environments. Glycomics analyses of cell lines were performed using LC-MS/MS. The expressions of multiple fucosylated N-glycans, such as HexNAc4Hex3DeoxyHex1 and HexNAc5Hex3DeoxyHex1, derived from both cell lines exhibited a significant increase in Plasmax. Among the O-glycans, significant differences were also observed. Both cell lines cultivated in EMEM had the lowest amounts of O-glycans expressed. The original work described the development of Plasmax, which improves colony formation, and resulted in transcriptomic and metabolomic alterations of cancer cell lines, while our results indicate that Plasmax can significantly impact protein glycosylation. This study also provides information to guide the selection of media for in vitro cancer cell glycomics studies.
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Affiliation(s)
- Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (J.W.); (W.P.); (A.Y.)
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (J.W.); (W.P.); (A.Y.)
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (J.W.); (W.P.); (A.Y.)
| | - Mohamed Fokar
- Center of Biotechnology and Genomics, Texas Tech University, Lubbock, TX 79409, USA;
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (J.W.); (W.P.); (A.Y.)
- Center of Biotechnology and Genomics, Texas Tech University, Lubbock, TX 79409, USA;
- Correspondence: ; Tel.: +1-806-742-3059
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Wang J, Dong X, Yu A, Huang Y, Peng W, Mechref Y. Isomeric separation of permethylated glycans by extra-long reversed-phase liquid chromatography (RPLC)-MS/MS. Analyst 2022; 147:2048-2059. [PMID: 35311852 PMCID: PMC9117491 DOI: 10.1039/d2an00010e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Glycosylation is known as a critical biological process that can largely affect the properties and the functions of proteins. Glycan isomers have been shown to be involved in a variety of disease progressions. However, the separation and identification of glycan isomers has been a challenge for years due to the microheterogeneity of glycan isomeric structures. Therefore, effective and stable techniques have been investigated over the last few decades to improve isomeric separations of glycans. RPLC has been widely used in biomolecule analysis because of its extraordinary reproducibility and reliability in retention time and separation resolution. However, so far, no studies have achieved high resolution of glycan isomers using this technique. In this study, we focused on further boosting the isomeric separation of permethylated glycans using a 500 mm reversed-phase LC column. To achieve better resolutions on permethylated glycans, different LC conditions were optimized using glycan standards, including core- and branch-fucosylated N-glycan isomers and sialic acid linked isomers, which were both successfully separated. Then, the optimal separation strategy was applied to achieve separations of N- and O-glycan isomers derived from model glycoproteins, including bovine fetuin, ribonuclease B and κ-casein. Baseline separations were observed on multiple sialylated linkage isomers. However, the separation performance of high-mannose isomers needs further improvement. The reproducibility and stability of this long C18 column was also tested by doing run-to-run, day-to-day and month-to-month comparisons of retention times on multiple glycans and the %RSD was found less than 0.92%. Finally, we applied this approach to separate glycan isomers derived from complex biological samples, including blood serum and cell lines, where baseline separations were attained on several isomeric structures. Compared to the separation efficiency of PGC and MGC columns, the RPLC C18 column provides lower resolution but more robust reproducibility, which makes it a good complementary alternative for isomeric separations of glycans.
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Affiliation(s)
- Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, USA.
| | - Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University, USA.
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, USA.
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, USA.
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, USA.
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, USA.
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6
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Coura MDM, Barbosa EA, Brand GD, Bloch C, de Sousa JB. Identification of Differential N-Glycan Compositions in the Serum and Tissue of Colon Cancer Patients by Mass Spectrometry. BIOLOGY 2021; 10:biology10040343. [PMID: 33923867 PMCID: PMC8074232 DOI: 10.3390/biology10040343] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 01/08/2023]
Abstract
Simple Summary Incidence of colorectal cancer (CRC) has been rising in Brazil. To date, no reliable biomarker has been described in CRC for diagnosis and prognosis. Modifications in the N-glycosylation profile are usually associated with many cancers, as CRC. In turn, mass spectrometry (MS)-based methods are the most accurate technology in quantification of N-glycans. Therefore, we described a unique pattern of compositions altered in serum and tissues of stages II and III colon cancer patients, identified by MALDI-TOF/MS and LC-MS technology. N-glycans were mostly found decreased in serum whilst oligomannosidic, hypogalactosylated, and tetra-antennary forms were overexpressed in tumor tissues. Total N-glycome in serum of cancer patients was different from the profile found in serum of healthy individuals. Strikingly, no correlation between tissue N-glycosylation profile and serum profile was observed in cancer patients, posing the question where these compositions are originated from. Abstract Colorectal cancer (CRC) ranks second as the leading cause of cancer-related deaths worldwide. N-glycosylation is one of the most common posttranslational protein modifications. Therefore, we studied the total serum N-glycome (TSNG) of 13 colon cancer patients compared to healthy controls using MALDI-TOF/MS and LC-MS. N-glycosylation of cancer tumor samples from the same cohort were further quantified using a similar methodology. In total, 23 N-glycan compositions were down-regulated in the serum of colon cancer patients, mostly galactosylated forms whilst the mannose-rich HexNAc2Hex7, the fucosylated bi-antennary glycan HexNAc4Hex5Fuc1NeuAc2, and the tetra-antennary HexNAc6Hex7NeuAc3 were up-regulated in serum. Hierarchical clustering analysis of TSNG correctly singled out 85% of the patients from controls. Albeit heterogenous, N-glycosylation of tumor samples showed overrepresented oligomannosidic, bi-antennary hypogalactosylated, and branched compositions related to normal colonic tissue, in both MALDI-TOF/MS and LC-MS analysis. Moreover, compositions found upregulated in tumor tissue were mostly uncorrelated to compositions in serum of cancer patients. Mass spectrometry-based N-glycan profiling in serum shows potential in the discrimination of patients from healthy controls. However, the compositions profile in serum showed no parallel with N-glycans in tumor microenvironment, which suggests a different origin of compositions found in serum of cancer patients.
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Affiliation(s)
- Marcelo de M.A. Coura
- Division of Colorectal Surgery, University Hospital of Brasilia, School of Medicine, University of Brasilia, SGAN 605, Brasilia-DF 70840-901, Brazil;
- Correspondence:
| | - Eder A. Barbosa
- Laboratory of Mass Spectrometry, EMBRAPA Genetic Resources and Biotechnology, Parque Estação Biológica, PqEB, Av. W5 Norte, Brasilia-DF 70770-917, Brazil; (E.A.B.); (C.B.J.)
- Laboratory for the Synthesis and Analysis of Biomolecules, Institute of Chemistry, Campus Universitario Darcy Ribeiro, University of Brasilia, Brasilia-DF 70910-900, Brazil;
| | - Guilherme D. Brand
- Laboratory for the Synthesis and Analysis of Biomolecules, Institute of Chemistry, Campus Universitario Darcy Ribeiro, University of Brasilia, Brasilia-DF 70910-900, Brazil;
| | - Carlos Bloch
- Laboratory of Mass Spectrometry, EMBRAPA Genetic Resources and Biotechnology, Parque Estação Biológica, PqEB, Av. W5 Norte, Brasilia-DF 70770-917, Brazil; (E.A.B.); (C.B.J.)
| | - Joao B. de Sousa
- Division of Colorectal Surgery, University Hospital of Brasilia, School of Medicine, University of Brasilia, SGAN 605, Brasilia-DF 70840-901, Brazil;
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Habazin S, Štambuk J, Šimunović J, Keser T, Razdorov G, Novokmet M. Mass Spectrometry-Based Methods for Immunoglobulin G N-Glycosylation Analysis. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:73-135. [PMID: 34687008 DOI: 10.1007/978-3-030-76912-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mass spectrometry and its hyphenated techniques enabled by the improvements in liquid chromatography, capillary electrophoresis, novel ionization, and fragmentation modes are truly a cornerstone of robust and reliable protein glycosylation analysis. Boost in immunoglobulin G (IgG) glycan and glycopeptide profiling demands for both applied biomedical and research applications has brought many new advances in the field in terms of technical innovations, sample preparation, improved throughput, and confidence in glycan structural characterization. This chapter summarizes mass spectrometry basics, focusing on IgG and monoclonal antibody N-glycosylation analysis on several complexity levels. Different approaches, including antibody enrichment, glycan release, labeling, and glycopeptide preparation and purification, are covered and illustrated with recent breakthroughs and examples from the literature omitting excessive theoretical frameworks. Finally, selected highly popular methodologies in IgG glycoanalytics such as liquid chromatography-mass spectrometry and matrix-assisted laser desorption ionization are discussed more thoroughly yet in simple terms making this text a practical starting point either for the beginner in the field or an experienced clinician trying to make sense out of the IgG glycomic or glycoproteomic dataset.
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Affiliation(s)
- Siniša Habazin
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Jerko Štambuk
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | | | - Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | | | - Mislav Novokmet
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia.
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8
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Gutierrez Reyes CD, Jiang P, Donohoo K, Atashi M, Mechref YS. Glycomics and glycoproteomics: Approaches to address isomeric separation of glycans and glycopeptides. J Sep Sci 2020; 44:403-425. [PMID: 33090644 DOI: 10.1002/jssc.202000878] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/29/2020] [Accepted: 10/06/2020] [Indexed: 11/11/2022]
Abstract
Changes in the glycome of human proteins and cells are associated with the progression of multiple diseases such as Alzheimer's, diabetes mellitus, many types of cancer, and those caused by viruses. Consequently, several studies have shown essential modifications to the isomeric glycan moieties for diseases in different stages. However, the elucidation of extensive isomeric glycan profiles remains challenging because of the lack of analytical techniques with sufficient resolution power to separate all glycan and glycopeptide iso-forms. Therefore, the development of sensitive and accurate approaches for the characterization of all the isomeric forms of glycans and glycopeptides is essential to tracking the progression of pathology in glycoprotein-related diseases. This review describes the isomeric separation achievements reported in glycomics and glycoproteomics in the last decade. It focuses on the mass spectrometry-based analytical strategies, stationary phases, and derivatization techniques that have been developed to enhance the separation mechanisms in liquid chromatography systems and the detection capabilities of mass spectrometry systems.
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Affiliation(s)
| | - Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Kaitlyn Donohoo
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Yehia S Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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9
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Dong X, Mondello S, Kobeissy F, Ferri R, Mechref Y. Serum Glycomics Profiling of Patients with Primary Restless Legs Syndrome Using LC–MS/MS. J Proteome Res 2020; 19:2933-2941. [DOI: 10.1021/acs.jproteome.9b00549] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina 98122, Italy
- Sleep Research Centre, Department of Neurology IC, Oasi Research Institute—IRCCS, Troina 94018, Italy
| | - Firas Kobeissy
- Department of Biochemistry & Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Raffaele Ferri
- Sleep Research Centre, Department of Neurology IC, Oasi Research Institute—IRCCS, Troina 94018, Italy
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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10
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Quaranta A, Spasova M, Passarini E, Karlsson I, Ndreu L, Thorsén G, Ilag LL. N-Glycosylation profiling of intact target proteins by high-resolution mass spectrometry (MS) and glycan analysis using ion mobility-MS/MS. Analyst 2020; 145:1737-1748. [DOI: 10.1039/c9an02081k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glycosylation characterization could lead to the discovery of biomarkers and is crucial in quality control of biopharmaceuticals. Here we present a method to quantify glycoforms on intact proteins, with parallel glycan identification by IMS-MS/MS.
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Affiliation(s)
- Alessandro Quaranta
- Department of Environmental Science and Analytical Chemistry
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Maya Spasova
- Department of Environmental Science and Analytical Chemistry
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Elena Passarini
- Department of Environmental Science and Analytical Chemistry
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Isabella Karlsson
- Department of Environmental Science and Analytical Chemistry
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Lorena Ndreu
- Department of Environmental Science and Analytical Chemistry
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Gunnar Thorsén
- IVL Swedish Environmental Research Institute
- 11428 Stockholm
- Sweden
| | - Leopold L. Ilag
- Department of Environmental Science and Analytical Chemistry
- Stockholm University
- 10691 Stockholm
- Sweden
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Glycan reductive amino acid coded affinity tagging (GRACAT) for highly specific analysis of N-glycome by mass spectrometry. Anal Chim Acta 2019; 1089:90-99. [DOI: 10.1016/j.aca.2019.08.054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/20/2019] [Accepted: 08/23/2019] [Indexed: 12/31/2022]
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12
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Klein J, Carvalho L, Zaia J. Application of network smoothing to glycan LC-MS profiling. Bioinformatics 2019; 34:3511-3518. [PMID: 29790907 DOI: 10.1093/bioinformatics/bty397] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/10/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Glycosylation is one of the most heterogeneous and complex protein post-translational modifications. Liquid chromatography coupled mass spectrometry (LC-MS) is a common high throughput method for analyzing complex biological samples. Accurate study of glycans require high resolution mass spectrometry. Mass spectrometry data contains intricate sub-structures that encode mass and abundance, requiring several transformations before it can be used to identify biological molecules, requiring automated tools to analyze samples in a high throughput setting. Existing tools for interpreting the resulting data do not take into account related glycans when evaluating individual observations, limiting their sensitivity. Results We developed an algorithm for assigning glycan compositions from LC-MS data by exploring biosynthetic network relationships among glycans. Our algorithm optimizes a set of likelihood scoring functions based on glycan chemical properties but uses network Laplacian regularization and optionally prior information about expected glycan families to smooth the likelihood and thus achieve a consistent and more representative solution. Our method was able to identify as many, or more glycan compositions compared to previous approaches, and demonstrated greater sensitivity with regularization. Our network definition was tailored to N-glycans but the method may be applied to glycomics data from other glycan families like O-glycans or heparan sulfate where the relationships between compositions can be expressed as a graph. Availability and implementation Built Executable http://www.bumc.bu.edu/msr/glycresoft/ and Source Code: https://github.com/BostonUniversityCBMS/glycresoft. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joshua Klein
- Program for Bioinformatics, Boston University, Boston, MA, USA
| | - Luis Carvalho
- Program for Bioinformatics, Boston University, Boston, MA, USA.,Department of Math and Statistics, Boston University, Boston, MA, USA
| | - Joseph Zaia
- Program for Bioinformatics, Boston University, Boston, MA, USA.,Department of Biochemistry, Boston University, Boston, MA, USA
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13
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Dong X, Peng W, Yu CY, Zhou S, Donohoo KB, Tang H, Mechref Y. 8-plex LC-MS/MS Analysis of Permethylated N-Glycans Achieved by Using Stable Isotopic Iodomethane. Anal Chem 2019; 91:11794-11802. [PMID: 31356052 PMCID: PMC7412976 DOI: 10.1021/acs.analchem.9b02411] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Glycosylation is an important post-translational modification of proteins. Many diseases, such as cancer, have proved to be related to aberrant glycosylation. High throughput quantitative methods have gained attention recently in the study of glycomics. With the development of high-resolution mass spectrometry, the sensitivity of detection in glycomics has largely improved; however, most of the commonly used MS-based techniques are focused on relative quantitative analysis, which can hardly provide direct comparative glycomic quantitation results. In this study, we developed a novel multiplex glycomic analysis method on an LC-ESI-MS platform. Reduced glycans were stable isotopic labeled during the permethylation procedure, with the use of iodomethane reagents CH2DI, CHD2I, CD3I, 13CH3I, 13CH2DI, 13CHD2I, 13CD3I, and CH3I. Up to 8-plex glycomic profiling was possible in a single analysis by LC-MS, and a 100 k mass resolution was sufficient to allow a baseline resolution of the mass differences among the 8-plex labeled glycans. The major advantages of this method are that it overcomes quantitative fluctuations caused by nanoESI, it facilitates a level of comparative quantitative glycomic analysis that accurately reflects the quantitative information in samples, and it dramatically shortens analysis time. Quantitation validation was tested on glycans released from bovine fetuin and model glycoprotein mixtures (RNase B, bovine fetuin, and IgG) with good linearity (R2 = 0.9884) and a dynamic range from 0.1 to 10. The 8-plex strategy was successfully applied to a comparative glycomic study of cancer cell lines. The results demonstrate that different distributions of sialylated glycans are related to the metastatic properties of cell lines and provide important clues for a better understanding of breast cancer brain metastasis.
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Affiliation(s)
- Xue Dong
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas, 79409, United States
| | - Wenjing Peng
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas, 79409, United States
| | - Chuan-Yih Yu
- School of Informatics & Computing, Indiana University, Bloomington, Indiana, 47408, United States
| | - Shiyue Zhou
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas, 79409, United States
| | - Kaitlyn B. Donohoo
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas, 79409, United States
| | - Haixu Tang
- School of Informatics & Computing, Indiana University, Bloomington, Indiana, 47408, United States
| | - Yehia Mechref
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas, 79409, United States
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14
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Bacteriophage T4 capsid as a nanocarrier for Peptide-N-Glycosidase F immobilization through self-assembly. Sci Rep 2019; 9:4865. [PMID: 30890747 PMCID: PMC6424964 DOI: 10.1038/s41598-019-41378-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/13/2019] [Indexed: 11/12/2022] Open
Abstract
Enzyme immobilization is widely applied in biocatalysis to improve stability and facilitate recovery and reuse of enzymes. However, high cost of supporting materials and laborious immobilization procedures has limited its industrial application and commercialization. In this study, we report a novel self-assembly immobilization system using bacteriophage T4 capsid as a nanocarrier. The system utilizes the binding sites of the small outer capsid protein, Soc, on the T4 capsid. Enzymes as Soc fusions constructed with regular molecular cloning technology expressed at the appropriate time during phage assembly and self-assembled onto the capsids. The proof of principle experiment was carried out by immobilizing β-galactosidase, and the system was successfully applied to the immobilization of an important glycomics enzyme, Peptide-N-Glycosidase F. Production of Peptide-N-Glycosidase F and simultaneous immobilization was finished within seven hours. Characterizations of the immobilized Peptide-N-Glycosidase F indicated high retention of activity and well reserved deglycosylation capacity. The immobilized Peptide-N-Glycosidase F was easily recycled by centrifugation and exhibited good stability that sustained five repeated uses. This novel system uses the self-amplified T4 capsid as the nanoparticle-type of supporting material, and operates with a self-assembly procedure, making it a simple and low-cost enzyme immobilization technology with promising application potentials.
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15
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Hu M, Lan Y, Lu A, Ma X, Zhang L. Glycan-based biomarkers for diagnosis of cancers and other diseases: Past, present, and future. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 162:1-24. [PMID: 30905444 DOI: 10.1016/bs.pmbts.2018.12.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Glycans are essential biomolecules in regulating human physiology and pathology ranging from signal transduction to microbial infections. Developing complex human diseases, such as cancer, diabetes, and cardiovascular diseases, are a combination of genetic and environmental factors. Genetics dominates embryonic development and the passing of genes to the next generation whereas the information in glycans reflects the impact of internal and external environmental factors, such as diseases, lifestyle, and social factors, on a person's health and disease. The reason behind this is that glycans are not directly encoded in a genetic template. Instead, they are assembled dynamically by hundreds of enzymes organized in more than 10 complex biosynthetic pathways. Any environmental changes affecting enzymatic activities or the availability of high-energy monosaccharide donors in a specific location will disturb the final structure of glycans. The glycan structure-dependent biological activities subsequently enable or disable gene expressions, which partially explain that it is difficult to pinpoint specific genetic defects to aging-associated diseases. Glycan-based biomarkers are currently used for diagnosis of diabetes, cancers, and other complex diseases. We will recapitulate the discovery of glucose, glycated proteins, glycan-, and glycoprotein-based biomarkers followed by summarizing clinically used glycan/glycoprotein-based biomarkers. The potential serum/plasma-derived N- and O-linked glycans as biomarkers will also be discussed.
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Affiliation(s)
- Minghui Hu
- Systems Biology and Medicine Center for Complex Diseases, Affiliated Hospital of Qingdao University, Qingdao, China; Clinical Laboratory, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ying Lan
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Alexander Lu
- Program in Neuroscience, Saint Louis University, St. Louis, MO, United States
| | - Xuexiao Ma
- Department of Spine Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lijuan Zhang
- Systems Biology and Medicine Center for Complex Diseases, Affiliated Hospital of Qingdao University, Qingdao, China.
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16
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Dong X, Mondello S, Kobeissy F, Talih F, Ferri R, Mechref Y. LC-MS/MS glycomics of idiopathic rapid eye movement sleep behavior disorder. Electrophoresis 2018; 39:3096-3103. [PMID: 30168606 PMCID: PMC6625764 DOI: 10.1002/elps.201800316] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 12/15/2022]
Abstract
Idiopathic REM sleep behavior disorder (iRBD) is now considered a prodromal stage of an α-synucleinopathy-related to neurodegenerative disease such as Parkinson's diseases. Emerging evidence has shown that post-translational modification or glycosylation are implicated in dynamic disease mechanisms and the onset of many pathological conditions. We hypothesized that the characterization of the glycosylation pattern of patients with RBD would be of great value to understand the pathophysiology and underlying mechanisms and represent potentially useful biomarkers for disease-associated molecular changes. To test this hypothesis, we assessed the serum glycome of patients with RBD and compared to that of healthy controls. NanoRPLC-MS was used to generate quantitative N-glycan profiles while high-temperature PGC-LC-MS platform was employed to generate quantitative isomeric N-glycan profiles. By analyzing permethylated glycans derived from human blood sera on C18-LC-MS/MS, we identified 59 N-glycan structures in healthy (control) cohort, 56 N-glycans in RBD cohort. Sixteen N-glycans structures were found to be significantly altered in the RBD cohort (p < 0.05). N-glycans with the composition of HexNAc4 Hex5 Fuc1 , HexNAc5 Hex5 , and HexNAc4 Hex5 Fuc1 NeuAc1 presented the most substantial difference between controls and RBD patients (p < 0.01). HexNAc4 Hex5 Fuc1 NeuAc1 showed a relatively high abundance (3.1 ± 0.7% in the control cohort versus 4 ± 3% in the idiopathic RBD cohort). These N-glycans can be potential diagnostic biomarker candidates and provide a window into underlying neurodegenerative processes in patients with idiopathic RBD. In addition, 7 N-glycan isomers were significantly different between controls and RBD patients (p < 0.05). HexNAc4 Hex5 Fuc1 NeuAc1 (4511-2) and HexNAc4 Hex5 Fuc1 NeuAc2 (4512-2) showed the most substantial difference between the control and idiopathic RBD cohorts (p < 0.001). Levels of both these two isomeric structures were higher in the idiopathic RBD cohort. Further larger studies are required to assess the reproducibility of these findings and to elucidate the role played by the changes in glycan structures in the pathogenetic mechanisms of RBD. This information will be instrumental in developing molecular therapeutic targets to promote neuroprotection and prevention of neurodegeneration.
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Affiliation(s)
- Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University
| | - Stefania Mondello
- Sleep Research Centre, Department of Neurology IC, Oasi Research Institute- IRCCS, Troina, Italy
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Firas Kobeissy
- Department of Biochemistry & Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Farid Talih
- Department of Psychiatry, American University of Beirut, Beirut, Lebanon
| | - Raffaele Ferri
- Sleep Research Centre, Department of Neurology IC, Oasi Research Institute- IRCCS, Troina, Italy
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University
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17
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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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18
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Banazadeh A, Williamson S, Zabet M, Hussien A, Mechref Y. Magnetic carbon nanocomposites as a MALDI co-matrix enhancing MS-based glycomics. Anal Bioanal Chem 2018; 410:7395-7404. [PMID: 30196422 PMCID: PMC6375713 DOI: 10.1007/s00216-018-1345-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/13/2018] [Accepted: 08/28/2018] [Indexed: 01/26/2023]
Abstract
More than 50% of all known proteins are glycosylated, which is critical for many biological processes such as protein folding and signal transduction. Glycosylation has proven to be associated with different mammalian diseases such as breast and liver cancers. Therefore, characterization of glycans is highly important to facilitate a better understanding of the development and progression of many human diseases. Although matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) offers several advantages such as ease of operation and short analysis times, however, due to the complexity of glycan structures and their low ionization efficiency, there are still challenges that need to be addressed to achieve sensitive glycan analysis. Here, magnetic carbon nanocomposites (CNPs@Fe3O4 NCs) were used as a new MALDI matrix or co-matrix for the analysis of glycans derived from different model glycoproteins and human blood serum samples. The addition of CNPs@Fe3O4 NCs to the matrix significantly enhanced glycan signal intensity by several orders of magnitude, and effectively controlled/reduced/eliminated in-source decay (ISD) fragmentation. The latter was attained by modulating CNPs@Fe3O4 NCs concentrations and allowed the simultaneous study of intact and fragmented glycans, and pseudo-MS3 analysis. Moreover, CNPs@Fe3O4 NCs was also effectively employed to desalt samples directly on MALDI plate, thus enabling direct MALDI-MS analysis of unpurified permethylated glycans derived from both model glycoproteins and biological samples. On-plate desalting enhanced sensitivity by reducing sample loss. Graphical abstract ᅟ.
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Affiliation(s)
- Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Seth Williamson
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Masoud Zabet
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, 79409, USA
| | - Ahmed Hussien
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA.,Department of Biotechnology, Institute of Graduate Studies and Research, University of Alexandria, Alexandria, 21526, Egypt
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA. .,Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, 79409, USA.
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19
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Banazadeh A, Peng W, Veillon L, Mechref Y. Carbon Nanoparticles and Graphene Nanosheets as MALDI Matrices in Glycomics: a New Approach to Improve Glycan Profiling in Biological Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1892-1900. [PMID: 29916086 PMCID: PMC6298861 DOI: 10.1007/s13361-018-1985-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/28/2018] [Accepted: 04/28/2018] [Indexed: 05/15/2023]
Abstract
Glycomics continues to be a highly dynamic and interesting research area due to the need to comprehensively understand the biological attributes of glycosylation in many important biological functions such as the immune response, cell development, cell differentiation/adhesion, and host-pathogen interactions. Although matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) has proven to be suitable for glycomic profiling studies, there is a need for improved sensitivity in the detection of native glycans, which ionize inefficiently. In this study, we investigated the efficiencies of graphene nanosheets (GNs) and carbon nanoparticles (CNPs) as MALDI matrices and co-matrices in glycan profiling. Our results indicated an enhancement of signal intensity by several orders of magnitude upon using GNs and CNPs in MALDI analysis of N-glycans derived from a variety of biological samples. Interestingly, increasing the amounts of CNPs and GNs improved not only the signal intensities but also prompted in-source decay (ISD) fragmentations, which produced extensive glycosidic and cross-ring cleavages. Our results indicated that the extent of ISD fragmentation could be modulated by CNP and GN concentrations, to obtain MS2 and pseudo-MS3 spectra. The results for glycan profiling in high salt solutions confirmed high salt-tolerance capacities for both CNPs and GNs. Finally, the results showed that by using CNPs and GNs as co-matrices, DHB crystal formation was more homogeneous which improved shot-to-shot reproducibility and sensitivity. Graphical Abstract ᅟ.
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Affiliation(s)
- Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Lucas Veillon
- 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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20
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de Oliveira RM, Ornelas Ricart CA, Araujo Martins AM. Use of Mass Spectrometry to Screen Glycan Early Markers in Hepatocellular Carcinoma. Front Oncol 2018; 7:328. [PMID: 29379771 PMCID: PMC5775512 DOI: 10.3389/fonc.2017.00328] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Association between altered glycosylation patterns and poor prognosis in cancer points glycans as potential specific tumor markers. Most proteins are glycosylated and functionally arranged on cell surface and extracellular matrix, mediating interactions and cellular signaling. Thereby, aberrant glycans may be considered a pathological phenotype at least as important as changes in protein expression for cancer and other complex diseases. As most serum glycoproteins have hepatic origin, liver disease phenotypes, such as hepatocellular carcinoma (HCC), may present altered glycan profile and display important modifications. One of the prominent obstacles in HCC is the diagnostic in advanced stages when patients have several liver dysfunctions, limiting treatment options and life expectancy. The characterization of glycomic profiles in pathological conditions by means of mass spectrometry (MS) may lead to the discovery of early diagnostic markers using non-invasive approaches. MS is a powerful analytical technique capable of elucidating many glycobiological issues and overcome limitations of the serological markers currently applied in clinical practice. Therefore, MS-based glycomics of tumor biomarkers is a promising tool to increase early detection and monitoring of disease.
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Affiliation(s)
- Raphaela Menezes de Oliveira
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil
| | - Carlos Andre Ornelas Ricart
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil
| | - Aline Maria Araujo Martins
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil.,University Hospital Walter Cantídeo, Surgery Department, Federal University of Ceara, Fortaleza, Brazil
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21
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Advanced LC-MS Methods for N-Glycan Characterization. ADVANCES IN THE USE OF LIQUID CHROMATOGRAPHY MASS SPECTROMETRY (LC-MS) - INSTRUMENTATION DEVELOPMENTS AND APPLICATIONS 2018. [DOI: 10.1016/bs.coac.2017.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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22
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Veillon L, Huang Y, Peng W, Dong X, Cho BG, Mechref Y. Characterization of isomeric glycan structures by LC-MS/MS. Electrophoresis 2017; 38:2100-2114. [PMID: 28370073 PMCID: PMC5581235 DOI: 10.1002/elps.201700042] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/21/2017] [Accepted: 03/12/2017] [Indexed: 12/12/2022]
Abstract
The characterization of glycosylation is critical for obtaining a comprehensive view of the regulation and functions of glycoproteins of interest. Due to the complex nature of oligosaccharides, stemming from variable compositions and linkages, and ion suppression effects, the chromatographic separation of glycans, including isomeric structures, is necessary for exhaustive characterization by MS. This review introduces the fundamental principles underlying the techniques in LC utilized by modern day glycomics researchers. Recent advances in porous graphitized carbon, reverse phase, ion exchange, and hydrophilic interaction LC utilized in conjunction with MS, for the characterization of protein glycosylation, are described with an emphasis on methods capable of resolving isomeric glycan structures.
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Affiliation(s)
- Lucas Veillon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
| | | | | | | | - Byeong G. Cho
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
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23
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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24
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Mulagapati S, Koppolu V, Raju TS. Decoding of O-Linked Glycosylation by Mass Spectrometry. Biochemistry 2017; 56:1218-1226. [PMID: 28196325 DOI: 10.1021/acs.biochem.6b01244] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein glycosylation (N- and O-linked) plays an important role in many biological processes, including protein structure and function. However, the structural elucidation of glycans, specifically O-linked glycans, remains a major challenge and is often overlooked during protein analysis. Recently, mass spectrometry (MS) has matured as a powerful technology for high-quality analytical characterization of O-linked glycans. This review summarizes the recent developments and insights of MS-based glycomics technologies, with a focus on mucin-type O-glycan analysis. Three main MS-based approaches are outlined: O-glycan profiling (structural analysis of released O-glycan), a "bottom-up" approach (analysis of an O-glycan covalently attached to a glycopeptide), and a "top-down" approach (analysis of a glycan attached to an intact glycoprotein). In addition, the most widely used MS ionization techniques, i.e., matrix-assisted laser desorption ionization and electrospray ionization, as well as ion activation techniques like collision-induced dissociation, electron capture dissociation, and electron transfer dissociation during O-glycan analysis are discussed. The MS technical approaches mentioned above are already major improvements for studying O-linked glycosylation and appear to be valuable for in-depth analysis of the type of O-glycan attached, branching patterns, and the occupancy of O-glycosylation sites.
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Affiliation(s)
- SriHariRaju Mulagapati
- Bioassay Development and Quality, Analytical Sciences, Biopharmaceutical Development, MedImmune , Gaithersburg, Maryland 20878, United States
| | - Veerendra Koppolu
- Bioassay Development and Quality, Analytical Sciences, Biopharmaceutical Development, MedImmune , Gaithersburg, Maryland 20878, United States
| | - T Shantha Raju
- Bioassay Development and Quality, Analytical Sciences, Biopharmaceutical Development, MedImmune , Gaithersburg, Maryland 20878, United States
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25
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Abstract
Glycosylation is one of the most common and essential protein modifications. Glycans conjugated to biomolecules modulate the function of such molecules through both direct recognition of glycan structures and indirect mechanisms that involve the control of protein turnover rates, stability, and conformation. The biological attributes of glycans in numerous biological processes and implications in a number of diseases highlight the necessity for comprehensive characterization of protein glycosylation. This chapter reviews cutting-edge methods and tools developed to facilitate quantitative glycomics. This chapter highlights the different methods employed for the release and purification of glycans from biological samples. The most effective labeling methods developed for sensitive quantitative glycomics are also described and discussed. The chromatographic approaches that have been used effectively in glycomics are also highlighted.
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Affiliation(s)
- L Veillon
- Texas Tech University, Lubbock, TX, United States
| | - S Zhou
- Texas Tech University, Lubbock, TX, United States
| | - Y Mechref
- Texas Tech University, Lubbock, TX, United States.
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26
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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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27
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Reversed-phase separation methods for glycan analysis. Anal Bioanal Chem 2016; 409:359-378. [PMID: 27888305 PMCID: PMC5203856 DOI: 10.1007/s00216-016-0073-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 10/26/2016] [Accepted: 10/31/2016] [Indexed: 12/21/2022]
Abstract
Reversed-phase chromatography is a method that is often used for glycan separation. For this, glycans are often derivatized with a hydrophobic tag to achieve retention on hydrophobic stationary phases. The separation and elution order of glycans in reversed-phase chromatography is highly dependent on the hydrophobicity of the tag and the contribution of the glycan itself to the retention. The contribution of the different monosaccharides to the retention strongly depends on the position and linkage, and isomer separation may be achieved. The influence of sialic acids and fucoses on the retention of glycans is still incompletely understood and deserves further study. Analysis of complex samples may come with incomplete separation of glycan species, thereby complicating reversed-phase chromatography with fluorescence or UV detection, whereas coupling with mass spectrometry detection allows the resolution of complex mixtures. Depending on the column properties, eluents, and run time, separation of isomeric and isobaric structures can be accomplished with reversed-phase chromatography. Alternatively, porous graphitized carbon chromatography and hydrophilic interaction liquid chromatography are also able to separate isomeric and isobaric structures, generally without the necessity of glycan labeling. Hydrophilic interaction liquid chromatography, porous graphitized carbon chromatography, and reversed-phase chromatography all serve different research purposes and thus can be used for different research questions. A great advantage of reversed-phase chromatography is its broad distribution as it is used in virtually every bioanalytical research laboratory, making it an attracting platform for glycan analysis. Glycan isomer separation by reversed phase liquid chromatography ![]()
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Lan Y, Hao C, Zeng X, He Y, Zeng P, Guo Z, Zhang L. Serum glycoprotein-derived N- and O-linked glycans as cancer biomarkers. Am J Cancer Res 2016; 6:2390-2415. [PMID: 27904760 PMCID: PMC5126262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023] Open
Abstract
Early detection of cancer is the key to improving survival. Since most clinically used serum cancer biomarkers are either glycoproteins or glycan structures that can be recognized by specific monoclonal antibodies, developing glycan structure-based biomarkers from human serum/plasma glycoproteins through mass spectrometry (MS) analysis are active research field during the past decades. Numerous studies have shown that changes in serum/plasma glycan structures occur during cancer initiation, progression, and treatment. This review describes N- and O-linked glycan structures identified from serum/plasma glycoprotein (s) by MS analysis with focus on alterations associated with different types of human cancers. The global changes in serum N- and O-linked glycan structures, especially the glycans that are not made by cancer cells such as B lymphocyte-derived IgG and liver-synthesized haptoglobin and α1 acid glycoprotein, suggest that glycans might be the long sought diagnostic biomarkers associated with system malfunction in the blood circulation of cancer patients. Therefore, N- and O-linked glycan structures have great potential to serve as cancer diagnosis, prognosis, and treatment monitoring biomarkers to facilitate personalized medicine.
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Affiliation(s)
- Ying Lan
- Institute of Cerebrovascular Diseases, Affiliated Hospital of Qingdao UniversityQingdao 266003, China
- School of Medicine and Pharmacy, Ocean University of ChinaQingdao 266003, China
| | - Cui Hao
- Institute of Cerebrovascular Diseases, Affiliated Hospital of Qingdao UniversityQingdao 266003, China
- School of Medicine and Pharmacy, Ocean University of ChinaQingdao 266003, China
| | - Xuan Zeng
- Institute of Cerebrovascular Diseases, Affiliated Hospital of Qingdao UniversityQingdao 266003, China
- School of Medicine and Pharmacy, Ocean University of ChinaQingdao 266003, China
| | - Yanli He
- Institute of Cerebrovascular Diseases, Affiliated Hospital of Qingdao UniversityQingdao 266003, China
- School of Medicine and Pharmacy, Ocean University of ChinaQingdao 266003, China
| | - Pengjiao Zeng
- Institute of Cerebrovascular Diseases, Affiliated Hospital of Qingdao UniversityQingdao 266003, China
- School of Medicine and Pharmacy, Ocean University of ChinaQingdao 266003, China
| | - Zhihua Guo
- Institute of Cerebrovascular Diseases, Affiliated Hospital of Qingdao UniversityQingdao 266003, China
| | - Lijuan Zhang
- Institute of Cerebrovascular Diseases, Affiliated Hospital of Qingdao UniversityQingdao 266003, China
- School of Medicine and Pharmacy, Ocean University of ChinaQingdao 266003, China
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29
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Mehta N, Porterfield M, Struwe WB, Heiss C, Azadi P, Rudd PM, Tiemeyer M, Aoki K. Mass Spectrometric Quantification of N-Linked Glycans by Reference to Exogenous Standards. J Proteome Res 2016; 15:2969-80. [PMID: 27432553 DOI: 10.1021/acs.jproteome.6b00132] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Environmental and metabolic processes shape the profile of glycoprotein glycans expressed by cells, whether in culture, developing tissues, or mature organisms. Quantitative characterization of glycomic changes associated with these conditions has been achieved historically by reductive coupling of oligosaccharides to various fluorophores following release from glycoprotein and subsequent HPLC or capillary electrophoretic separation. Such labeling-based approaches provide a robust means of quantifying glycan amount based on fluorescence yield. Mass spectrometry, on the other hand, has generally been limited to relative quantification in which the contribution of the signal intensity for an individual glycan is expressed as a percent of the signal intensity summed over the total profile. Relative quantification has been valuable for highlighting changes in glycan expression between samples; sensitivity is high, and structural information can be derived by fragmentation. We have investigated whether MS-based glycomics is amenable to absolute quantification by referencing signal intensities to well-characterized oligosaccharide standards. We report the qualification of a set of N-linked oligosaccharide standards by NMR, HPLC, and MS. We also demonstrate the dynamic range, sensitivity, and recovery from complex biological matrices for these standards in their permethylated form. Our results indicate that absolute quantification for MS-based glycomic analysis is reproducible and robust utilizing currently available glycan standards.
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Affiliation(s)
| | | | - Weston B Struwe
- National Institute for Bioprocessing Research and Training (NIBRT) , Dublin, Ireland
| | | | | | - Pauline M Rudd
- National Institute for Bioprocessing Research and Training (NIBRT) , Dublin, Ireland.,University College , Dublin, Ireland
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30
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Planinc A, Dejaegher B, Heyden YV, Viaene J, Van Praet S, Rappez F, Van Antwerpen P, Delporte C. LC-MS analysis combined with principal component analysis and soft independent modelling by class analogy for a better detection of changes in N-glycosylation profiles of therapeutic glycoproteins. Anal Bioanal Chem 2016; 409:477-485. [PMID: 27287011 DOI: 10.1007/s00216-016-9683-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/25/2016] [Accepted: 06/01/2016] [Indexed: 12/12/2022]
Abstract
Therapeutic proteins are among the top selling drugs in the pharmaceutical industry. More than 60 % of the approved therapeutic proteins are glycosylated. Nowadays, it is well accepted that changes in glycosylation may affect the safety and the efficacy of the therapeutic proteins. For this reason, it is important to characterize both the protein and the glycan structures. In this study, analytical and data processing methods were developed ensuring an easier characterization of glycoprofiles. N-glycans were (i) enzymatically released using peptide-N-glycosidase F (PNGase F), (ii) reduced, and (iii) analyzed by hydrophilic interaction liquid chromatography coupled to a high-resolution mass spectrometer (HILIC-HRMS). Glycosylation changes were analyzed in human plasma immunoglobulin G samples which had previously been artificially modified by adding other glycoproteins (such as ribonuclease B and fetuin) or by digesting with enzyme (neuraminidase). Principal component analysis (PCA) and classification through soft independent modelling by class analogy (SIMCA) were used to detect minor glycosylation changes. Using HILIC-MS-PCA/SIMCA approach, it was possible to detect small changes in N-glycosylation, which had not been detected directly from the extracted-ion chromatograms, which is current technique to detect N-glycosylation changes in batch-to-batch analysis. The HILIC-MS-PCA/SIMCA approach is highly sensitive approach due to the sensitivity of MS and appropriate data processing approaches. It could help in assessing the changes in glycosylation, controlling batch-to-batch consistency, and establishing acceptance limits according to the glycosylation changes, ensuring safety and efficacy. Graphical abstract N-glycosylation characterization using LC-MS-PCA approach.
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Affiliation(s)
- Ana Planinc
- Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Campus Plaine, CP 205/05B, 1050, Brussels, Belgium.
| | - Bieke Dejaegher
- Laboratory of Instrumental Analysis and Bioelectrochemistry, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050, Brussels, Belgium.,Department of Analytical Chemistry and Pharmaceutical Technology (FABI), Center for Pharmaceutical Research (CePhaR), Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Yvan Vander Heyden
- Department of Analytical Chemistry and Pharmaceutical Technology (FABI), Center for Pharmaceutical Research (CePhaR), Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Johan Viaene
- Department of Analytical Chemistry and Pharmaceutical Technology (FABI), Center for Pharmaceutical Research (CePhaR), Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Serge Van Praet
- Pharmacy, Centre Hospitalier Universitaire Saint-Pierre, Brussels, Belgium
| | - Florence Rappez
- Pharmacy, Centre Hospitalier Universitaire Saint-Pierre, Brussels, Belgium
| | - Pierre Van Antwerpen
- Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Campus Plaine, CP 205/05B, 1050, Brussels, Belgium
| | - Cédric Delporte
- Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Campus Plaine, CP 205/05B, 1050, Brussels, Belgium
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31
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Zhou S, Hu Y, Mechref Y. High-temperature LC-MS/MS of permethylated glycans derived from glycoproteins. Electrophoresis 2016; 37:1506-13. [PMID: 26914157 PMCID: PMC4962687 DOI: 10.1002/elps.201500568] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 11/06/2022]
Abstract
Various glycomic analysis methods have been developed due to the essential roles of glycans in biological processes as well as the potential application of glycomics in biomarker discovery in many diseases. Permethylation is currently considered to be one of the most common derivatization methods in MS-based glycomic analysis. Permethylation not only improves ionization efficiency and stability of sialylated glycans in positive mode but also allows for enhanced separation performance on reversed-phase liquid chromatography (RPLC). Recently, RPLC-MS analysis of permethylated glycans exhibited excellent performance in sensitivity and reproducibility and became a widely-applied comprehensive strategy in glycomics. However, separating permethylated glycans by RPLC always suffers from peak broadening for high-molecular-weight branched glycans, which probably due to the low exchange rate between the stationary phase and mobile phase limited by intermolecular interactions of the methyl groups associated with the branching of the glycan structures. In this study, we employed high separation temperature conditions for RPLC of permethylated glycans, thus achieving enhanced peak capacity, improving peak shape, and enhancing separation efficiency. Additionally, partial isomeric separation were observed in RPLC of permethylated glycans at high-temperature. Mathematical processing of the correlation between retention time and molecular weight also revealed the advantage of high-temperature LC method for both manual and automatic glycan identification.
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Affiliation(s)
- Shiyue Zhou
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Yunli Hu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
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32
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Planinc A, Bones J, Dejaegher B, Van Antwerpen P, Delporte C. Glycan characterization of biopharmaceuticals: Updates and perspectives. Anal Chim Acta 2016; 921:13-27. [PMID: 27126786 DOI: 10.1016/j.aca.2016.03.049] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/21/2016] [Accepted: 03/29/2016] [Indexed: 02/01/2023]
Abstract
Therapeutic proteins are rapidly becoming the most promising class of pharmaceuticals on the market due to their successful treatment of a vast array of serious diseases, such as cancers and immune disorders. Therapeutic proteins are produced using recombinant DNA technology. More than 60% of therapeutic proteins are posttranslationally modified following biosynthesis by the addition of N- or O-linked glycans. Glycosylation is the most common posttranslational modifications of proteins. However, it is also the most demanding and complex posttranslational modification from the analytical point of view. Moreover, research has shown that glycosylation significantly impacts stability, half-life, mechanism of action and safety of a therapeutic protein. Considering the exponential growth of biotherapeutics, this present review of the literature (2009-2015) focuses on the characterization of protein glycosylation, which has witnessed an improvement in methodology. Furthermore, it discusses current issues in the fields of production and characterization of therapeutic proteins. This review also highlights the problem of non-standard requirements for the approval of biosimilars with regard to their glycosylation and discusses recent developments and perspectives for improved glycan characterization.
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Affiliation(s)
- Ana Planinc
- Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Universite Libre de Bruxelles (ULB), Brussels, Belgium
| | - Jonathan Bones
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Bieke Dejaegher
- Laboratory of Instrumental Analysis and Bioelectrochemistry, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, B-1050 Brussels, Belgium; Department of Analytical Chemistry and Pharmaceutical Technology (FABI), Center for Pharmaceutical Research (CePhaR), Faculty of Medicines and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Pierre Van Antwerpen
- Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Universite Libre de Bruxelles (ULB), Brussels, Belgium
| | - Cédric Delporte
- Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Universite Libre de Bruxelles (ULB), Brussels, Belgium.
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33
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Pu Y, Ridgeway ME, Glaskin RS, Park MA, Costello CE, Lin C. Separation and Identification of Isomeric Glycans by Selected Accumulation-Trapped Ion Mobility Spectrometry-Electron Activated Dissociation Tandem Mass Spectrometry. Anal Chem 2016; 88:3440-3. [PMID: 26959868 PMCID: PMC4821751 DOI: 10.1021/acs.analchem.6b00041] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
One of the major challenges in structural characterization of oligosaccharides is the presence of many structural isomers in most naturally occurring glycan mixtures. Although ion mobility spectrometry (IMS) has shown great promise in glycan isomer separation, conventional IMS separation occurs on the millisecond time scale, largely restricting its implementation to fast time-of-flight (TOF) analyzers which often lack the capability to perform electron activated dissociation (ExD) tandem MS analysis and the resolving power needed to resolve isobaric fragments. The recent development of trapped ion mobility spectrometry (TIMS) provides a promising new tool that offers high mobility resolution and compatibility with high-performance Fourier transform ion cyclotron resonance (FTICR) mass spectrometers when operated under the selected accumulation-TIMS (SA-TIMS) mode. Here, we present our initial results on the application of SA-TIMS-ExD-FTICR MS to the separation and identification of glycan linkage isomers.
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Affiliation(s)
- Yi Pu
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, US
| | | | - Rebecca S. Glaskin
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, US
| | | | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, US
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, US
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34
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Aich U, Lakbub J, Liu A. State-of-the-art technologies for rapid and high-throughput sample preparation and analysis ofN-glycans from antibodies. Electrophoresis 2016; 37:1468-88. [DOI: 10.1002/elps.201500551] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/15/2016] [Accepted: 01/17/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Udayanath Aich
- Biopharmaceutical Analytical Sciences; Biopharmaceutical Development, GlaxoSmithKline; King of Prussia PA USA
| | - Jude Lakbub
- Biopharmaceutical Analytical Sciences; Biopharmaceutical Development, GlaxoSmithKline; King of Prussia PA USA
| | - Aston Liu
- Biopharmaceutical Analytical Sciences; Biopharmaceutical Development, GlaxoSmithKline; King of Prussia PA USA
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35
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Dotz V, Haselberg R, Shubhakar A, Kozak RP, Falck D, Rombouts Y, Reusch D, Somsen GW, Fernandes DL, Wuhrer M. Mass spectrometry for glycosylation analysis of biopharmaceuticals. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.04.024] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Defaus S, Gupta P, Andreu D, Gutiérrez-Gallego R. Mammalian protein glycosylation--structure versus function. Analyst 2015; 139:2944-67. [PMID: 24779027 DOI: 10.1039/c3an02245e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Carbohydrates fulfil many common as well as extremely important functions in nature. They show a variety of molecular displays--e.g., free mono-, oligo-, and polysaccharides, glycolipids, proteoglycans, glycoproteins, etc.--with particular roles and localizations in living organisms. Structure-specific peculiarities are so many and diverse that it becomes virtually impossible to cover them all from an analytical perspective. Hence this manuscript, focused on mammalian glycosylation, rather than a complete list of analytical descriptors or recognized functions for carbohydrate structures, comprehensively reviews three central issues in current glycoscience, namely (i) structural analysis of glycoprotein glycans, covering both classical and novel approaches for teasing out the structural puzzle as well as potential pitfalls of these processes; (ii) an overview of functions attributed to carbohydrates, covering from monosaccharide to complex, well-defined epitopes and full glycans, including post-glycosylational modifications, and (iii) recent technical advances allowing structural identification of glycoprotein glycans with simultaneous assignation of biological functions.
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Affiliation(s)
- S Defaus
- Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona Biomedical Research Park, 08003 Barcelona, Spain.
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37
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Wildburger NC, Zhou S, Zacharias LG, Kroes RA, Moskal JR, Schmidt M, Mirzaei P, Gumin J, Lang FF, Mechref Y, Nilsson CL. Integrated Transcriptomic and Glycomic Profiling of Glioma Stem Cell Xenografts. J Proteome Res 2015; 14:3932-9. [PMID: 26185906 DOI: 10.1021/acs.jproteome.5b00549] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bone marrow-derived human mesenchymal stem cells (BM-hMSCs) have the innate ability to migrate or home toward and engraft in tumors such as glioblastoma (GBM). Because of this unique property of BM-hMSCs, we have explored their use for cell-mediated therapeutic delivery for the advancement of GBM treatment. Extravasation, the process by which blood-borne cells—such as BM-hMSCs—enter the tissue, is a highly complex process but is heavily dependent upon glycosylation for glycan-glycan and glycan-protein adhesion between the cell and endothelium. However, in a translationally significant preclinical glioma stem cell xenograft (GSCX) model of GBM, BM-hMSCs demonstrate unequal tropism toward these tumors. We hypothesized that there may be differences in the glycan compositions between the GSCXs that elicit homing ("attractors") and those that do not ("non-attractors") that facilitate or impede the engraftment of BM-hMSCs in the tumor. In this study, glycotranscriptomic analysis revealed significant heterogeneity within the attractor phenotype and the enrichment of high mannose type N-glycan biosynthesis in the non-attractor phenotype. Orthogonal validation with topical PNGase F deglycosylation on the tumor regions of xenograft tissue, followed by nLC-ESI-MS, confirmed the presence of increased high mannose type N-glycans in the non-attractors. Additional evidence provided by our glycomic study revealed the prevalence of terminal sialic acid-containing N-glycans in non-attractors and terminal galactose and N-acetyl-glucosamine N-glycans in attractors. Our results provide the first evidence for differential glycomic profiles in attractor and non-attractor GSCXs and extend the scope of molecular determinates in BM-hMSC homing to glioma.
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Affiliation(s)
| | - Shiyue Zhou
- Department of Chemistry and Biochemistry, Texas Tech University , 2500 Broadway, Lubbock, Texas 79409, United States
| | - Lauren G Zacharias
- Department of Chemistry and Biochemistry, Texas Tech University , 2500 Broadway, Lubbock, Texas 79409, United States
| | - Roger A Kroes
- The Falk Center for Molecular Therapeutics, McCormick School of Engineering and Applied Sciences, Northwestern University , 1801 Maple Street, Evanston, Illinois 60201, United States
| | - Joseph R Moskal
- The Falk Center for Molecular Therapeutics, McCormick School of Engineering and Applied Sciences, Northwestern University , 1801 Maple Street, Evanston, Illinois 60201, United States
| | - Mary Schmidt
- The Falk Center for Molecular Therapeutics, McCormick School of Engineering and Applied Sciences, Northwestern University , 1801 Maple Street, Evanston, Illinois 60201, United States
| | - Parvin Mirzaei
- Department of Chemistry and Biochemistry, Texas Tech University , 2500 Broadway, Lubbock, Texas 79409, United States
| | - Joy Gumin
- Department of Neurosurgery and The Brain Tumor Center, The University of Texas M.D. Anderson Cancer Center , 1515 Holcombe Boulevard, Houston, Texas 77030, United States
| | - Frederick F Lang
- Department of Neurosurgery and The Brain Tumor Center, The University of Texas M.D. Anderson Cancer Center , 1515 Holcombe Boulevard, Houston, Texas 77030, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University , 2500 Broadway, Lubbock, Texas 79409, United States
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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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Junot C, Fenaille F, Colsch B, Bécher F. High resolution mass spectrometry based techniques at the crossroads of metabolic pathways. MASS SPECTROMETRY REVIEWS 2014; 33:471-500. [PMID: 24288070 DOI: 10.1002/mas.21401] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 06/02/2023]
Abstract
The metabolome is the set of small molecular mass compounds found in biological media, and metabolomics, which refers to as the analysis of metabolome in a given biological condition, deals with the large scale detection and quantification of metabolites in biological media. It is a data driven and multidisciplinary approach combining analytical chemistry for data acquisition, and biostatistics, informatics and biochemistry for mining and interpretation of these data. Since the middle of the 2000s, high resolution mass spectrometry is widely used in metabolomics, mainly because the detection and identification of metabolites are improved compared to low resolution instruments. As the field of HRMS is quickly and permanently evolving, the aim of this work is to review its use in different aspects of metabolomics, including data acquisition, metabolite annotation, identification and quantification. At last, we would like to show that, thanks to their versatility, HRMS instruments are the most appropriate to achieve optimal metabolome coverage, at the border of other omics fields such as lipidomics and glycomics.
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Affiliation(s)
- Christophe Junot
- Commissariat à l'Energie Atomique, Centre de Saclay, DSV/iBiTec-S/SPI, Laboratoire d'Etude du Métabolisme des Médicaments, 91191, Gif-sur-Yvette Cedex, France
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40
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Xie J, Zhang Y, Wang W, Hou J. Identification and simultaneous determination of glycyrrhizin, formononetin, glycyrrhetinic acid, liquiritin, isoliquiritigenin, and licochalcone A in licorice by LC-MS/MS. ACTA CHROMATOGR 2014. [DOI: 10.1556/achrom.26.2014.3.9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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41
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Kronewitter SR, Marginean I, Cox JT, Zhao R, Hagler CD, Shukla AK, Carlson TS, Adkins JN, Camp DG, Moore RJ, Rodland KD, Smith RD. Polysialylated N-glycans identified in human serum through combined developments in sample preparation, separations, and electrospray ionization-mass spectrometry. Anal Chem 2014; 86:8700-10. [PMID: 25118826 PMCID: PMC4151788 DOI: 10.1021/ac501839b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The N-glycan diversity of human serum glycoproteins, i.e., the human blood serum N-glycome, is both complex and constrained by the range of glycan structures potentially synthesizable by human glycosylation enzymes. The known glycome, however, has been further limited by methods of sample preparation, available analytical platforms, e.g., based upon electrospray ionization-mass spectrometry (ESI-MS), and software tools for data analysis. In this report several improvements have been implemented in sample preparation and analysis to extend ESI-MS glycan characterization and to include polysialylated N-glycans. Sample preparation improvements included acidified, microwave-accelerated, PNGase F N-glycan release to promote lactonization, and sodium borohydride reduction, that were both optimized to improve quantitative yields and conserve the number of glycoforms detected. Two-stage desalting (during solid phase extraction and on the analytical column) increased sensitivity by reducing analyte signal division between multiple reducing-end-forms or cation adducts. Online separations were improved by using extended length graphitized carbon columns and adding TFA as an acid modifier to a formic acid/reversed phase gradient, providing additional resolving power and significantly improved desorption of both large and heavily sialylated glycans. To improve MS sensitivity and provide gentler ionization conditions at the source-MS interface, subambient pressure ionization with nanoelectrospray (SPIN) was utilized. When these improved methods are combined together with the Glycomics Quintavariate Informed Quantification (GlyQ-IQ) recently described (Kronewitter et al. Anal. Chem. 2014, 86, 6268-6276), we are able to significantly extend glycan detection sensitivity and provide expanded glycan coverage. We demonstrated the application of these advances in the context of the human serum glycome, and for which our initial observations included the detection of a new class of heavily sialylated N-glycans, including polysialylated N-glycans.
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Affiliation(s)
- Scott R Kronewitter
- Biological Sciences Division, Pacific Northwest National Laboratory , P.O. Box 999, Richland, Washington 99352, United States
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Tsai TH, Wang M, Di Poto C, Hu Y, Zhou S, Zhao Y, Varghese RS, Luo Y, Tadesse MG, Ziada DH, Desai CS, Shetty K, Mechref Y, Ressom HW. LC-MS profiling of N-Glycans derived from human serum samples for biomarker discovery in hepatocellular carcinoma. J Proteome Res 2014; 13:4859-68. [PMID: 25077556 PMCID: PMC4227556 DOI: 10.1021/pr500460k] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Defining
clinically relevant biomarkers for early stage hepatocellular
carcinoma (HCC) in a high-risk population of cirrhotic patients has
potentially far-reaching implications for disease management and patient
health. Changes in glycan levels have been associated with the onset
of numerous diseases including cancer. In the present study, we used
liquid chromatography coupled with electrospray ionization mass spectrometry
(LC–ESI-MS) to analyze N-glycans in sera from 183 participants
recruited in Egypt and the U.S. and identified candidate biomarkers
that distinguish HCC cases from cirrhotic controls. N-Glycans were
released from serum proteins and permethylated prior to the LC–ESI-MS
analysis. Through two complementary LC–ESI-MS quantitation
approaches, global profiling and targeted quantitation, we identified
11 N-glycans with statistically significant differences between HCC
cases and cirrhotic controls. These glycans can further be categorized
into four structurally related clusters, matching closely with the
implications of important glycosyltransferases in cancer progression
and metastasis. The results of this study illustrate the power of
the integrative approach combining complementary LC–ESI-MS
based quantitation approaches to investigate changes in N-glycan levels
between HCC cases and patients with liver cirrhosis.
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Affiliation(s)
- Tsung-Heng Tsai
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center , Washington, DC 20057, United States
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43
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Zhang Q, Feng X, Li H, Liu BF, Lin Y, Liu X. Methylamidation for isomeric profiling of sialylated glycans by nanoLC-MS. Anal Chem 2014; 86:7913-9. [PMID: 25022802 DOI: 10.1021/ac501844b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The analysis of isomeric glycans is a challenging task. In this work, a new strategy was developed for isomer-specific glycan profiling using nanoLC-MS with PGC as the stationary phase. Native glycans were derivatized in the presence of methylamine and trispyrrolidinophosphonium hexafluorophosphate and reduced by the ammonia-borane complex. Methylamidation stabilized the retention time and peak width and improved the detection sensitivity of sialylated glycans to 2-80-fold in comparison to previous ESI-MS methods using the positive-ion mode. Up to 19 tetrasialylated glycan species were identified in the derivatized human serum sample, which were difficult to detect in the sample without derivatization. Furthermore, due to high detection sensitivity and chromatographic resolution, more isomeric glycans could be identified from the model glycoprotein Fetuin and the human serum sample. As a result, up to seven isomers were observed for the disialylated biantennary glycan released from Fetuin, and three of them were identified for the first time in this study. Using the developed analytical strategy, a total of 293 glycan species were obtained from the human serum sample, representing an increase of over 100 peaks in comparison to the underivatized sample. The strategy greatly facilitates the profiling of isomeric glycans and the analysis of trace-level samples.
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Affiliation(s)
- Qiwei Zhang
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, China
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44
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Zhang Q, Li H, Feng X, Liu BF, Liu X. Purification of derivatized oligosaccharides by solid phase extraction for glycomic analysis. PLoS One 2014; 9:e94232. [PMID: 24705408 PMCID: PMC3976416 DOI: 10.1371/journal.pone.0094232] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/12/2014] [Indexed: 12/02/2022] Open
Abstract
Profiling of glycans released from proteins is very complex and important. To enhance the detection sensitivity, chemical derivatization is required for the analysis of carbohydrates. Due to the interference of excess reagents, a simple and reliable purification method is usually necessary for the derivatized oligosaccharides. Various SPE based methods have been applied for the clean-up process. To demonstrate the differences among these methods, seven types of self-packed SPE cartridges were systematically compared in this study. The optimized conditions were determined for each type of cartridge and it was found that microcrystalline cellulose was the most appropriate SPE material for the purification of derivatized oligosaccharide. Normal phase HPLC analysis of the derivatized maltoheptaose was realized with a detection limit of 0.12 pmol (S N−1 = 3) and a recovery over 70%. With the optimized SPE method, relative quantification analysis of N-glycans from model glycoproteins were carried out accurately and over 40 N-glycans from human serum samples were determined regardless of the isomers. Due to the high stability and sensitivity, microcrystalline cellulose cartridge showed potential applications in glycomics analysis.
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Affiliation(s)
- Qiwei Zhang
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics–Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Henghui Li
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics–Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaojun Feng
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics–Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- * E-mail: (XJF); (XL)
| | - Bi-Feng Liu
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics–Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Liu
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics–Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- * E-mail: (XJF); (XL)
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Dauber A, Ercan A, Lee J, James P, Jacobs PP, Ashline DJ, Wang SR, Miller T, Hirschhorn JN, Nigrovic PA, Sackstein R. Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect. Hum Mol Genet 2014; 23:2880-7. [PMID: 24403049 DOI: 10.1093/hmg/ddu001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Leukocyte adhesion deficiency type II is a hereditary disorder of neutrophil migration caused by mutations in the guanosine diphosphate-fucose transporter gene (SLC35C1). In these patients, inability to generate key fucosylated molecules including sialyl Lewis X leads to leukocytosis and recurrent infections, in addition to short stature and developmental delay. We report two brothers with short stature and developmental delay who are compound heterozygotes for novel mutations in SLC35C1 resulting in partial in vivo defects in fucosylation. Specifically, plasma glycoproteins including immunoglobulin G demonstrated marked changes in glycoform distribution. While neutrophil rolling on endothelial selectins was partially impeded, residual adhesion proved sufficient to avoid leukocytosis or recurrent infection. These findings demonstrate a surprising degree of immune redundancy in the face of substantial alterations in adhesion molecule expression, and show that short stature and developmental delay may be the sole presenting signs in this disorder.
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46
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Ito E, Nakajima K, Waki H, Miseki K, Shimada T, Sato TA, Kakehi K, Suzuki M, Taniguchi N, Suzuki A. Structural Characterization of Pyridylaminated Oligosaccharides Derived from Neutral Glycosphingolipids by High-Sensitivity Capillary Electrophoresis–Mass Spectrometry. Anal Chem 2013; 85:7859-65. [DOI: 10.1021/ac401460f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emi Ito
- Systems Glycobiology Research
Group, RIKEN−Max Planck Joint Research Center, Global Research
Cluster, RIKEN, 2-1 Hirosawa, Wako-shi,
Saitama 351-0198, Japan
| | - Kazuki Nakajima
- Systems Glycobiology Research
Group, RIKEN−Max Planck Joint Research Center, Global Research
Cluster, RIKEN, 2-1 Hirosawa, Wako-shi,
Saitama 351-0198, Japan
| | - Hiroaki Waki
- Analytical Division, Shimadzu Corporation, 1 Nishinokyo-Ku, Kuwabaracho,
Nakagyo-ku, Kyoto 604-8511, Japan
| | - Kozo Miseki
- Analytical Division, Shimadzu Corporation, 1 Nishinokyo-Ku, Kuwabaracho,
Nakagyo-ku, Kyoto 604-8511, Japan
| | - Takashi Shimada
- Life Science Research Center, Shimadzu Corporation, 5-1-1 Tsukiji, Chuo-ku, Tokyo
105-0045, Japan
| | - Taka-Aki Sato
- Life Science Research Center, Shimadzu Corporation, 5-1-1 Tsukiji, Chuo-ku, Tokyo
105-0045, Japan
| | - Kazuaki Kakehi
- School
of Pharmacy, Kinki University, 3-4-1 Kowakae,
Higashi-Osaka 577-8502,
Japan
| | - Minoru Suzuki
- Life Science Research Center, Shimadzu Corporation, 5-1-1 Tsukiji, Chuo-ku, Tokyo
105-0045, Japan
| | - Naoyuki Taniguchi
- Systems Glycobiology Research
Group, RIKEN−Max Planck Joint Research Center, Global Research
Cluster, RIKEN, 2-1 Hirosawa, Wako-shi,
Saitama 351-0198, Japan
| | - Akemi Suzuki
- Institute of Glycoscience, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa,
259-1292, Japan
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47
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Wang C, Yuan J, Li X, Wang Z, Huang L. Sulfonyl hydrazine-functionalized polymer as a specific capturer of reducing glycans from complex samples for high-throughput analysis by electrospray ionization mass spectrometry. Analyst 2013; 138:5344-56. [PMID: 23875183 DOI: 10.1039/c3an00931a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Qualitative and quantitative studies of glycosylation patterns of various biologically important proteins represent a key field for the understanding of their complex structure-function relationships. However, the analysis of glycoprotein glycans is usually undermined by tedious sample processing steps prior to detection, including deproteination, desalting and removal of some other non-glycan impurities, which results in considerable sample loss and increased difficulty of quantitative analysis. Herein we report a facile and versatile method for the quantitative isolation of reducing glycans from complex samples using sulfonyl hydrazine-functionalized polystyrene (SHPS) beads, namely the SHPS-based glycan capturing procedure. This method allows the chemoselective and efficient condensation of the aldehyde group of reducing glycans with the active sulfonyl hydrazine group of SHPS beads under anhydrous conditions, resulting in the formation of sulfonyl hydrazone conjugates. The non-glycan components in samples, such as proteins, salts and some other impurities, can be completely removed by washing the sulfonyl hydrazone conjugates. Regeneration of the reducing glycans can be performed via mild hydrolysis of the washed sulfonyl hydrazone conjugates. This procedure is compatible with almost all the current techniques for the derivatization or detection of reducing glycans. We have obtained essential data for this method, including optimized reaction conditions, linearity and reproducibility for glycan quantitation, as well as a final glycan recovery ratio. Moreover, mass spectrometric analysis of the glycans from some complex biological samples, including milk, human blood plasma and fetal bovine serum, was achieved, demonstrating good applicability of this novel procedure.
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Affiliation(s)
- Chengjian Wang
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Science, Northwest University, Xi'an 710069, China
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48
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Hu Y, Desantos-Garcia JL, Mechref Y. Comparative glycomic profiling of isotopically permethylated N-glycans by liquid chromatography/electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:865-77. [PMID: 23495056 PMCID: PMC3673025 DOI: 10.1002/rcm.6512] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 12/15/2012] [Accepted: 01/15/2013] [Indexed: 05/13/2023]
Abstract
RATIONALE Mass spectrometry based comparative glycomics is essential for disease biomarker discovery. However, developing a reliable quantification method is still a challenging task. METHODS We here report an isotopic labeling strategy employing stable isotopic iodomethane for comparative glycomic profiling by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS). N-Glycans released from model glycoproteins and blood serum samples were permethylated with iodomethane ('light') and iodomethane-d1 or -d3 ('heavy') reagents. Permethylated samples were then mixed at equal volumes prior to LC/ESI-MS analysis. RESULTS Peak intensity ratios of N-glycans isotopically permethylated (Heavy/Light, H/L) were almost equal to the theoretical values. Observed differences were mainly related to the purity of 'heavy' iodomethane reagents (iodomethane-d1 or -d3). The data suggested the efficacy of this strategy to simultaneously quantify N-glycans derived from biological samples representing different cohorts. Accordingly, this strategy is effective in comparing multiple samples in a single LC/ESI-MS analysis. The potential of this strategy for defining glycomic differences in blood serum samples representing different esophageal diseases was explored. CONCLUSIONS LC/ESI-MS comparative glycomic profiling of isotopically permethylated N-glycans derived from biological samples and glycoproteins reliably defined glycan changes associated with biological conditions or glycoproteins expression. As a biological application, this strategy permitted the reliable quantification of glycomic changes associated with different esophageal diseases, including high grade dysplasia, Barrett's disease, and esophageal adenocarcinoma.
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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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49
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Yu CY, Mayampurath A, Hu Y, Zhou S, Mechref Y, Tang H. Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry. Bioinformatics 2013; 29:1706-7. [PMID: 23610369 DOI: 10.1093/bioinformatics/btt190] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED As a common post-translational modification, protein glycosylation plays an important role in many biological processes, and it is known to be associated with human diseases. Mass spectrometry (MS)-based glycomic profiling techniques have been developed to measure the abundances of glycans in complex biological samples and applied to the discovery of putative glycan biomarkers. To automate the annotation of glycomic profiles in the liquid chromatography-MS (LC-MS) data, we present here a user-friendly software tool, MultiGlycan, implemented in C# on Windows systems. We tested MultiGlycan by using several glycomic profiling datasets acquired using LC-MS under different preparations and show that MultiGlycan executes fast and generates robust and reliable results. AVAILABILITY MultiGlycan can be freely downloaded at http://darwin.informatics.indiana.edu/MultiGlycan/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chuan-Yih Yu
- School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA.
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50
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Abstract
Because routine preparation of glycan samples involves multiple reaction and cleaning steps at which sample loss occurs, glycan analysis is typically performed using large tissue samples. This type of analysis yields no detailed molecular spatial information and requires special care to maintain proper storage and shipping conditions. We describe here a new glycan sample preparation protocol using minimized sample preparation steps and optimized procedures. Tissue sections and spotted samples first undergo on-surface enzymatic digestion to release N-glycans. The released glycans are then reduced and permethylated prior to online purification and LC-electrospray ionization (ESI)-MS analysis. The efficiency of this protocol was initially evaluated using model glycoproteins and human blood serum (HBS) spotted on glass or Teflon slides. The new protocol permitted the detection of permethylated N-glycans derived from 10 ng RNase B. On the other hand, 66 N-glycans were identified when injecting the equivalent of permethylated glycans derived from a 0.1-μL aliquot of HBS. On-tissue enzymatic digestion of nude mouse brain tissue permitted the detection of 43 N-glycans. The relative peak areas of these 43 glycans were comparable to those from a C57BL/6 mouse reported by the Consortium for Functional Glycomics (CFG). However, the sample size analyzed in the protocol described here was substantially smaller than for the routine method (submicrogram vs mg). The on-tissue N-glycan profiling method permits high sensitivity and reproducibility and can be widely applied to assess the spatial distribution of glycans associated with tissue sections, and may be correlated with immunoflourescence imaging when adjacent tissue sections are analyzed.
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Affiliation(s)
- Yunli Hu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Shiyue Zhou
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Sarah I. Khalil
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Calvin L Renteria
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
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