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Rodrigues TB, Cunha RL, Barci PEP, Santos-Neto ÁJ, Lanças FM. Analysis of human biological samples using porous graphitic carbon columns and liquid chromatography-mass spectrometry: a review. Anal Bioanal Chem 2024; 416:5233-5253. [PMID: 39158631 DOI: 10.1007/s00216-024-05458-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/20/2024]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) has emerged as a powerful analytical technique for analyzing complex biological samples. Among various chromatographic stationary phases, porous graphitic carbon (PGC) columns have attracted significant attention due to their unique properties-such as the ability to separate both polar and non-polar compounds and their stability through all pH ranges and to high temperatures-besides the compatibility with LC-MS. This review discusses the applicability of PGC for SPE and separation in LC-MS-based analyses of human biological samples, highlighting the diverse applications of PGC-LC-MS in analyzing endogenous metabolites, pharmaceuticals, and biomarkers, such as glycans, proteins, oligosaccharides, sugar phosphates, and nucleotides. Additionally, the fundamental principles underlying PGC column chemistry and its advantages, challenges, and advances in method development are explored. This comprehensive review aims to provide researchers and practitioners with a valuable resource for understanding the capabilities and limitations of PGC columns in LC-MS-based analysis of human biological samples, thereby facilitating advancements in analytical methodologies and biomedical research.
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Affiliation(s)
- Taís Betoni Rodrigues
- Laboratory of Chromatography (CROMA), São Carlos Institute of Chemistry, University of São Paulo (USP), São Carlos, São Paulo, 13560-970, Brazil.
| | - Ricardo Leal Cunha
- Forensic Toxicology Laboratory, Scientific Police, São Cristóvão, Sergipe, 49100-000, Brazil
| | - Paulo Emílio Pereira Barci
- Laboratory of Chromatography (CROMA), São Carlos Institute of Chemistry, University of São Paulo (USP), São Carlos, São Paulo, 13560-970, Brazil
| | - Álvaro José Santos-Neto
- Laboratory of Chromatography (CROMA), São Carlos Institute of Chemistry, University of São Paulo (USP), São Carlos, São Paulo, 13560-970, Brazil
| | - Fernando Mauro Lanças
- Laboratory of Chromatography (CROMA), São Carlos Institute of Chemistry, University of São Paulo (USP), São Carlos, São Paulo, 13560-970, Brazil
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2
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Wang C, Zhang C, Gao X, Lin JM. Isomer-specific biomarker discovery in multiple myeloma with dual-derivatized N-glycans. Anal Bioanal Chem 2022; 414:5617-5626. [PMID: 35320367 DOI: 10.1007/s00216-022-04010-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/19/2022] [Accepted: 03/04/2022] [Indexed: 11/01/2022]
Abstract
As one of the most important post-translational modifications, protein glycosylation plays vital role in various physiological processes. With multitudinous glycosyltransferases, N-glycans present structural diversity in linkages and branching styles. Structure-specific glycan profiling may provide more potential biological information than compositional profiling. In this work, N-glycans released from human serum samples were derivatized with reduction and methylamination prior to profiling using nanoLC-ESI-MS with PGC as stationary phase. In addition, α 2-3 neuraminidase was also applied for distinguishing the linkage types of sialic acid corresponding to different isomers. Relative abundances of 280 isomeric N-glycans were compared and 20 isomers showed significant difference between multiple myeloma cases and healthy controls. ROC was performed to assess the significantly altered isomeric glycans and 6 AUCs have exceeded 0.80, providing high diagnostic accuracy for MM. PCA is also employed to establish the differences among sample sets. Furthermore, these specific isomers have also been used for early detection of multiple myeloma, presenting important clinical application value. Isomer-specific biomarker discovery in multiple myeloma with dual-derivatized N-glycans.
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Affiliation(s)
- Chang Wang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Chaoying Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Xinchang Gao
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China.
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3
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Chiu KY, Wang Q, Gunawardena HP, Held M, Faik A, Chen H. Desalting Paper Spay Mass Spectrometry (DPS-MS) for Rapid Detection of Glycans and Glycoconjugates. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 469:116688. [PMID: 35386843 PMCID: PMC8981528 DOI: 10.1016/j.ijms.2021.116688] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The detection of glycans and glycoconjugates has gained increasing attention in biological fields. Traditional mass spectrometry (MS)-based methods for glycoconjugate analysis are challenged with poor intensity when dealing with complex biological samples. We developed a desalting paper spray mass spectrometry (DPS-MS) strategy to overcome the issue of signal suppression of carbohydrates in salted buffer. Glycans and glycoconjugates (i.e., glycopeptides, nucleotide sugars, etc.) in non-volatile buffer (e.g., Tris buffer) can be loaded on the paper substrate from which buffers can be removed by washing with ACN/H2O (90/10 v/v) solution. Glycans or glycoconjugates can then be eluted and spray ionized by adding ACN/H2O/formic acid (FA) (10/90/1 v/v/v) solvent and applying a high voltage (HV) to the paper substrate. This work also showed that DPS-MS is applicable for direct detection of intact glycopeptides and nucleotide sugars as well as determination of glycosylation profiling of antibody, such as NIST monoclonal antibody IgG (NISTmAb). NISTmAb was deglycosylated with PNGase F to release N-linked oligosaccharides. Twenty-six N-linked oligosaccharides were detected by DPS-MS within a 5-minute timeframe without the need for further enrichment or derivatization. This work demonstrates that DPS-MS allows fast and sensitive detection of glycans/oligosaccharides and glycosylated species in complex matrices and has great potential in bioanalysis.
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Affiliation(s)
- Kai-Yuan Chiu
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA, 07102
| | - Qi Wang
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA, 07102
| | - Harsha P Gunawardena
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania, USA, 19477
| | - Michael Held
- Deparment of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, Ohio USA, 45701
| | - Ahmed Faik
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, Ohio USA, 45701
- Department of Environmental and Plant Biology, Ohio University, Athens Ohio, USA, 45701
| | - Hao Chen
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA, 07102
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4
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Smith J, Millán-Martín S, Mittermayr S, Hilborne V, Davey G, Polom K, Roviello F, Bones J. 2-Dimensional ultra-high performance liquid chromatography and DMT-MM derivatization paired with tandem mass spectrometry for comprehensive serum N-glycome characterization. Anal Chim Acta 2021; 1179:338840. [PMID: 34535264 DOI: 10.1016/j.aca.2021.338840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 12/25/2022]
Abstract
Glycosylation is a prominent co- and post-translational modification which contributes to a variety of important biological functions. Protein glycosylation characteristics, particularly N-glycosylation, are influenced by changes in one's pathological state, such as through the presence of disease, and as such, there is great interest in N-glycans as potential disease biomarkers. Human serum is an attractive source for N-glycan based biomarker studies as circulatory proteins are representative of one's physiology, with many serum proteins containing N-glycosylation. The difficulty in comprehensively characterizing the serum N-glycome arises from the absence of a biosynthetic template resulting in great structural heterogeneity and complexity. To help overcome these challenges we developed a 2-dimensional liquid chromatography platform which utilizes offline weak anion exchange (WAX) chromatography in the first dimension and hydrophilic interaction liquid chromatography (HILIC) in the second dimension to separate N-glycans by charge, corresponding to degree of sialylation, and size, respectively. Performing these separations offline enables subsequent derivatization with 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMT-MM) for sialic acid linkage determination and the identification of sialic acid linkage isomers. Subsequent tandem mass spectrometry analysis revealed the identification of 212 complete and partial N-glycan structures including low abundant N-glycans containing acetyl and sulphate modifications. The identifications obtained through this platform were then applied to N-glycans released from a set of stage 3 gastric cancer serum samples obtained from patients before (pre-op) and after (post-op) tumour resection to investigate how the serum N-glycome can facilitate differentiation between the two pathological states.
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Affiliation(s)
- Josh Smith
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co. Dublin, A94 X099, Ireland; School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Silvia Millán-Martín
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co. Dublin, A94 X099, Ireland
| | - Stefan Mittermayr
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co. Dublin, A94 X099, Ireland
| | - Vivian Hilborne
- Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA
| | - Gavin Davey
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Karol Polom
- Department of General Surgery and Surgical Oncology, University of Siena, Siena, Italy; Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Franco Roviello
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
| | - Jonathan Bones
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co. Dublin, A94 X099, Ireland; School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland.
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5
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Paton B, Suarez M, Herrero P, Canela N. Glycosylation Biomarkers Associated with Age-Related Diseases and Current Methods for Glycan Analysis. Int J Mol Sci 2021; 22:5788. [PMID: 34071388 PMCID: PMC8198018 DOI: 10.3390/ijms22115788] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 12/23/2022] Open
Abstract
Ageing is a complex process which implies the accumulation of molecular, cellular and organ damage, leading to an increased vulnerability to disease. In Western societies, the increase in the elderly population, which is accompanied by ageing-associated pathologies such as cardiovascular and mental diseases, is becoming an increasing economic and social burden for governments. In order to prevent, treat and determine which subjects are more likely to develop these age-related diseases, predictive biomarkers are required. In this sense, some studies suggest that glycans have a potential role as disease biomarkers, as they modify the functions of proteins and take part in intra- and intercellular biological processes. As the glycome reflects the real-time status of these interactions, its characterisation can provide potential diagnostic and prognostic biomarkers for multifactorial diseases. This review gathers the alterations in protein glycosylation profiles that are associated with ageing and age-related diseases, such as cancer, type 2 diabetes mellitus, metabolic syndrome and several chronic inflammatory diseases. Furthermore, the review includes the available techniques for the determination and characterisation of glycans, such as liquid chromatography, electrophoresis, nuclear magnetic resonance and mass spectrometry.
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Affiliation(s)
- Beatrix Paton
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
| | - Manuel Suarez
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Pol Herrero
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
| | - Núria Canela
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
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Wang Q, Bhattarai M, Zhao P, Alnsour T, Held M, Faik A, Chen H. Fast and Sensitive Detection of Oligosaccharides Using Desalting Paper Spray Mass Spectrometry (DPS-MS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2226-2235. [PMID: 32910855 PMCID: PMC8189650 DOI: 10.1021/jasms.0c00310] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Conventional mass spectrometry (MS)-based analytical methods for small carbohydrate fragments (oligosaccharides, degree of polymerization 2-12) are time-consuming due to the need for an offline sample pretreatment such as desalting. Herein, we report a new paper spray ionization method, named desalting paper spray (DPS), which employs a piece of triangular filter paper for both sample desalting and ionization. Unlike regular paper spray ionization (PSI) and nanoelectrospray ionization (nanoESI), DPS-MS allows fast and sensitive detection of oligosaccharides in biological samples having complex matrices (e.g., Tris, PBS, HEPES buffers, or urine). When an oligosaccharide sample is loaded onto the filter paper substrate (10 × 5 mm, height × base) made mostly of cellulose, oligosaccharides are adsorbed on the paper via hydrophilic interactions with cellulose. Salts and buffers can be washed away using an ACN/H2O (90/10 v/v) solution, while oligosaccharides can be eluted from the paper using a solution of ACN/H2O/formic acid (FA) (10/90/1 v/v/v) and directly spray-ionized from the tip of the paper. Various saccharides at trace levels (e.g., 50 fmol) in nonvolatile buffer can be quickly analyzed by DPS-MS (<5 min per sample). DPS-MS is also applicable for direct detection of oligosaccharides from glycosyltransferase (GT) reactions, a challenging task that typically requires a radioactive assay. Quantitative analysis of acceptor and product oligosaccharides shows increased product with increased GT enzymes used for the reaction, a result in line with the radioactivity assay. This work suggests that DPS-MS has potential for rapid oligosaccharide analysis from biological samples.
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Affiliation(s)
- Qi Wang
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey
| | - Matrika Bhattarai
- Department of Environmental and Plant Biology & Molecular and Cellular Biology Program, Ohio University, Athens, Ohio
| | - Pengyi Zhao
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey
| | - Tariq Alnsour
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey
| | - Michael Held
- Deparment of Chemistry and Biochemistry, Ohio University, Athens, Ohio
- Corresponding Authors: Hao Chen - Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey. , Ahmed Faik – Department of Environmental and Plant Biology, Ohio University, Athens, Ohio. , Michael Held – Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio.
| | - Ahmed Faik
- Department of Environmental and Plant Biology & Molecular and Cellular Biology Program, Ohio University, Athens, Ohio
- Corresponding Authors: Hao Chen - Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey. , Ahmed Faik – Department of Environmental and Plant Biology, Ohio University, Athens, Ohio. , Michael Held – Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio.
| | - Hao Chen
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey
- Corresponding Authors: Hao Chen - Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey. , Ahmed Faik – Department of Environmental and Plant Biology, Ohio University, Athens, Ohio. , Michael Held – Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio.
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7
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Aydoğan C, Rigano F, Krčmová LK, Chung DS, Macka M, Mondello L. Miniaturized LC in Molecular Omics. Anal Chem 2020; 92:11485-11497. [DOI: 10.1021/acs.analchem.0c01436] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Cemil Aydoğan
- Biochemistry Division, Department of Chemistry, Bingöl University, Bingöl 12000,Turkey
- Department of Food Engineering, Bingöl University, Bingöl 12000,Turkey
| | - Francesca Rigano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98168, Italy
| | - Lenka Kujovská Krčmová
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, Hradec Králové 500 05, Czech Republic
- Department of Clinical Biochemistry and Diagnostics, University Hospital, Sokolská 581, Hradec Králové 500 05, Czech Republic
| | - Doo Soo Chung
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Mirek Macka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00Brno, Czech Republic
- School of Natural Sciences and Australian Centre for Research on Separation Science (ACROSS), University of Tasmania, Private Bag 75, Hobart 7001, Australia
| | - Luigi Mondello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98168, Italy
- Chromaleont s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98168, Italy
- Department of Sciences and Technologies for Human and Environment, University Campus Bio-Medico of Rome, Rome I-00128, Italy
- BeSep s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98168, Italy
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8
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Relative content detection of oligomannose modification of IgM heavy chain induced by TNP-antigen in an early vertebrate through nanoLC-MS/MS. Talanta 2020; 219:121346. [PMID: 32887075 DOI: 10.1016/j.talanta.2020.121346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 01/23/2023]
Abstract
N-glycan modification is reported to be important in regulating the structure and function of immunoglobulins in mammals. While, the study on teleost immunoglobulin glycosylation is still limitted. In this study, we constructed a TNP-antigen driven model, and detected the site-specific N-glycans of PBS-immunized and TNP-specific Oreochromis niloticus serum IgM through 18O-labeling and nanoLC-MS/MS. These methods are widely used for peptide enrichment and protein modification identification, but rarely used in detecting the level of N-glycosylation in teleost Igs that driven by specific antigen. The results revealed that there are four N-glycosylation sites in O.niloticus IgM heavy chain, namely, the Asn-315 site in the CH2 domain, the Asn-338 site in the CH3 domain, and the Asn-509 and Asn-551 sites in the CH4 domain, All of the four residues were efficiently N-glycosylated. After immunized with TNP-antigen, the signal strength of oligomannose in the TNP-specific IgM in primary mass spectrometry was significantly higher than that in the PBS-immunized IgM. Notably, the TNP-specific IgM had an Asn-509 site fully occupied with oligomannose, while only a small amount of oligomannose was found in the PBS-immunized IgM of this site. N-glycans in other sites were mainly complex-type with a low content of fucosylation and sialylated. The oligomannose in TNP-specific IgM was further verified to be essential for the binding of IgM and MBL. These results demonstrated that the TNP-antigen induced the site-specific oligomannose modification of O.niloticus IgM heavy chain, and played an important role in the interaction of IgM and MBL, which provided insights into the evolutionary understanding of the IgM oligomannose modification and function.
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Cao WQ, Liu MQ, Kong SY, Wu MX, Huang ZZ, Yang PY. Novel methods in glycomics: a 2019 update. Expert Rev Proteomics 2020; 17:11-25. [PMID: 31914820 DOI: 10.1080/14789450.2020.1708199] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Introduction: Glycomics, which aims to define the glycome of a biological system to better assess the biological attributes of the glycans, has attracted increasing interest. However, the complexity and diversity of glycans present challenging barriers to glycome definition. Technological advances are major drivers in glycomics.Areas covered: This review summarizes the main methods and emphasizes the most recent advances in mass spectrometry-based methods regarding glycomics following the general workflow in glycomic analysis.Expert opinion: Recent mass spectrometry-based technological advances have significantly lowered the barriers in glycomics. The field of glycomics is moving toward both generic and precise analysis.
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Affiliation(s)
- Wei-Qian Cao
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Ming-Qi Liu
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Si-Yuan Kong
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Meng-Xi Wu
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Zheng-Ze Huang
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Peng-Yuan Yang
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
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10
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Fabijanczuk K, Gaspar K, Desai N, Lee J, Thomas DA, Beauchamp JL, Gao J. Resin and Magnetic Nanoparticle-Based Free Radical Probes for Glycan Capture, Isolation, and Structural Characterization. Anal Chem 2019; 91:15387-15396. [PMID: 31718152 DOI: 10.1021/acs.analchem.9b01303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
By combining the merits of solid supports and free radical activated glycan sequencing (FRAGS) reagents, we develop a multifunctional solid-supported free radical probe (SS-FRAGS) that enables glycan enrichment and characterization. SS-FRAGS comprises a solid support, free radical precursor, disulfide bond, pyridyl, and hydrazine moieties. Thio-activated resin and magnetic nanoparticles (MNPs) are chosen as the solid support to selectively capture free glycans via the hydrazine moiety, allowing for their enrichment and isolation. The disulfide bond acts as a temporary covalent linkage between the solid support and the captured glycan, allowing the release of glycans via the cleavage of the disulfide bond by dithiothreitol. The basic pyridyl functional group provides a site for the formation of a fixed charge, enabling detection by mass spectrometry and avoiding glycan rearrangement during collisional activation. The free radical precursor generates a nascent free radical upon collisional activation and thus simultaneously induces systematic and predictable fragmentation for glycan structure elucidation. A radical-driven glycan deconstruction diagram (R-DECON) is developed to visually summarize the MS2 results and thus allow for the assembly of the glycan skeleton, making the differentiation of isobaric glycan isomers unambiguous. For application to a real-world sample, we demonstrate the efficacy of the SS-FRAGS by analyzing glycan structures enzymatically cleaved from RNase-B.
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Affiliation(s)
- Kimberly Fabijanczuk
- Department of Chemistry and Biochemistry and Center for Quantitative Obesity Research , Montclair State University , Montclair , New Jersey 07043 , United States
| | - Kaylee Gaspar
- Department of Chemistry and Biochemistry and Center for Quantitative Obesity Research , Montclair State University , Montclair , New Jersey 07043 , United States
| | - Nikunj Desai
- Department of Chemistry and Biochemistry and Center for Quantitative Obesity Research , Montclair State University , Montclair , New Jersey 07043 , United States
| | - Jungeun Lee
- Department of Chemistry and Biochemistry and Center for Quantitative Obesity Research , Montclair State University , Montclair , New Jersey 07043 , United States
| | - Daniel A Thomas
- Arthur Amos Noyes Laboratory of Chemical Physics , California Institute of Technology , Pasadena , California 91125 , United States
| | - J L Beauchamp
- Arthur Amos Noyes Laboratory of Chemical Physics , California Institute of Technology , Pasadena , California 91125 , United States
| | - Jinshan Gao
- Department of Chemistry and Biochemistry and Center for Quantitative Obesity Research , Montclair State University , Montclair , New Jersey 07043 , United States
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11
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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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12
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 PMCID: PMC7757723 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Gege Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California, Davis, Davis, California 95616, United States
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13
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Zhang Q, Li Z, Wang Y, Zheng Q, Li J. Mass spectrometry for protein sialoglycosylation. MASS SPECTROMETRY REVIEWS 2018; 37:652-680. [PMID: 29228471 DOI: 10.1002/mas.21555] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/17/2017] [Indexed: 06/07/2023]
Abstract
Sialic acids are a family of structurally unique and negatively charged nine-carbon sugars, normally found at the terminal positions of glycan chains on glycoproteins and glycolipids. The glycosylation of proteins is a universal post-translational modification in eukaryotic species and regulates essential biological functions, in which the most common sialic acid is N-acetyl-neuraminic acid (2-keto-5-acetamido-3,5-dideoxy-D-glycero-D-galactononulopyranos-1-onic acid) (Neu5NAc). Because of the properties of sialic acids under general mass spectrometry (MS) conditions, such as instability, ionization discrimination, and mixed adducts, the use of MS in the analysis of protein sialoglycosylation is still challenging. The present review is focused on the application of MS related methodologies to the study of both N- and O-linked sialoglycans. We reviewed MS-based strategies for characterizing sialylation by analyzing intact glycoproteins, proteolytic digested glycopeptides, and released glycans. The review concludes with future perspectives in the field.
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Affiliation(s)
- Qiwei Zhang
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Institute for Interdisciplinary Research, Institute of Environment and Health, School of Chemical and Environmental Engineering, Jianghan University, Wuhan, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Zack Li
- School of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Yawei Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Qi Zheng
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Institute for Interdisciplinary Research, Institute of Environment and Health, School of Chemical and Environmental Engineering, Jianghan University, Wuhan, China
| | - Jianjun Li
- National Research Council Canada, Ottawa, Ontario, Canada
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14
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Liu Y, Wang C, Wang R, Wu Y, Zhang L, Liu BF, Cheng L, Liu X. Isomer-specific profiling of N-glycans derived from human serum for potential biomarker discovery in pancreatic cancer. J Proteomics 2018; 181:160-169. [DOI: 10.1016/j.jprot.2018.04.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 04/02/2018] [Accepted: 04/11/2018] [Indexed: 02/03/2023]
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15
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A review of nanoscale LC-ESI for metabolomics and its potential to enhance the metabolome coverage. Talanta 2018; 182:380-390. [PMID: 29501168 DOI: 10.1016/j.talanta.2018.01.084] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 12/22/2022]
Abstract
Liquid chromatography-electrospray ionisation-mass spectrometry (LC-ESI-MS) platforms are widely used to perform high throughput untargeted profiling of biological samples for metabolomics-based approaches. However, these LC-ESI platforms usually favour the detection of metabolites present at relatively high concentrations because of analytical limitations such as ion suppression, thus reducing overall sensitivity. To counter this issue of sensitivity, the latest in terms of analytical platforms can be adopted to enable a greater portion of the metabolome to be analysed in a single analytical run. Here, nanoflow liquid chromatography-nanoelectrospray ionisation (nLC-nESI), which has previously been utilised successfully in proteomics, is explored for use in metabolomic and exposomic research. As a discovery based field, the markedly increased sensitivity of these nLC-nESI platforms offer the potential to uncover the roles played by low abundant signalling metabolites (e.g. steroids, eicosanoids) in health and disease studies, and would also enable an improvement in the detection of xenobiotics present at trace levels in biological matrices to better characterise the chemical exposome. This review aims to give an insight into the advantages associated with nLC-nESI for metabolomics-based approaches. Initially we detail the source of improved sensitivity prior to reviewing the available approaches to achieving nanoflow rates and nanospray ionisation for metabolomics. The robustness of nLC-nESI platforms was then assessed using the literature available from a metabolomic viewpoint. We also discuss the challenging point of sample preparation which needs to be addressed to fully enjoy the benefits of these nLC-nESI platforms. Finally, we assess metabolomic analysis utilising nano scale platforms and look ahead to the future of metabolomics using these new highly sensitive platforms.
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Chen H, Deng Z, Huang C, Wu H, Zhao X, Li Y. Mass spectrometric profiling reveals association of N-glycan patterns with epithelial ovarian cancer progression. Tumour Biol 2017; 39:1010428317716249. [DOI: 10.1177/1010428317716249] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aberrant changes of N-glycan modifications on proteins have been linked to various diseases including different cancers, suggesting possible avenue for exploring their etiologies based on N-glycomic analysis. Changes in N-glycan patterns during epithelial ovarian cancer development have so far been investigated mainly using serum, plasma, ascites, and cell lines. However, changes in patterns of N-glycans in tumor tissues during epithelial ovarian cancer progression have remained largely undefined. To investigate whether changes in N-glycan patterns correlate with oncogenesis and progression of epithelial ovarian cancer, we profiled N-glycans from formalin-fixed paraffin-embedded tissue slides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and quantitatively compared among different pathological grades of epithelial ovarian cancer and healthy controls. Our results show that among the 80 compositions of N-glycan detected, expression levels of high-mannose type were higher in epithelial ovarian cancer samples than that observed in healthy controls, accompanied by reduced levels of hybrid-type glycans. By applying receiver operating characteristic analysis, we show that a combined panel composed of four high-mannose and three fucosylated neutral complex N-glycans allows for good discrimination of epithelial ovarian cancer from healthy controls. Furthermore, using a statistical analysis of variance assay, we found that different N-glycan patterns, including 2 high-mannose-type, 2 fucosylated and sialylated complex structures, and 10 fucosylated neutral complex N-glycans, exhibited specific changes in N-glycan abundance across epithelial ovarian cancer grades. Together, our results provide strong evidence that N-glycomic changes are a strong indicator for epithelial ovarian cancer pathological grades and should provide avenues to identify novel biomarkers for epithelial ovarian cancer diagnosis and monitoring.
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Affiliation(s)
- Huanhuan Chen
- Key Laboratory of Marine Drugs, Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Zaian Deng
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chuncui Huang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hongmei Wu
- GuangDong Bio-Healtech Advanced Co., Ltd, Foshan, China
| | - Xia Zhao
- Key Laboratory of Marine Drugs, Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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17
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Chen Z, Zhong X, Tie C, Chen B, Zhang X, Li L. Development of a hydrophilic interaction liquid chromatography coupled with matrix-assisted laser desorption/ionization-mass spectrometric imaging platform for N-glycan relative quantitation using stable-isotope labeled hydrazide reagents. Anal Bioanal Chem 2017; 409:4437-4447. [PMID: 28540462 DOI: 10.1007/s00216-017-0387-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/20/2017] [Accepted: 04/28/2017] [Indexed: 12/21/2022]
Abstract
In this work, the capability of newly developed hydrophilic interaction liquid chromatography (HILIC) coupled with matrix-assisted laser desorption/ionization-mass spectrometric imaging (MALDI-MSI) platform for quantitative analysis of N-glycans has been demonstrated. As a proof-of-principle experiment, heavy and light stable-isotope labeled hydrazide reagents labeled maltodextrin ladder were used to demonstrate the feasibility of the HILIC-MALDI-MSI platform for reliable quantitative analysis of N-glycans. MALDI-MSI analysis by an Orbitrap mass spectrometer enabled high-resolution and high-sensitivity detection of N-glycans eluted from HILIC column, allowing the re-construction of LC chromatograms as well as accurate mass measurements for structural inference. MALDI-MSI analysis of the collected LC traces showed that the chromatographic resolution was preserved. The N-glycans released from human serum was used to demonstrate the utility of this novel platform in quantitative analysis of N-glycans from a complex sample. Benefiting from the minimized ion suppression provided by HILIC separation, comparison between MALDI-MS and the newly developed platform HILIC-MALDI-MSI revealed that HILIC-MALDI-MSI provided higher N-glycan coverage as well as better quantitation accuracy in the quantitative analysis of N-glycans released from human serum. Graphical abstract Reconstructed chromatograms based on HILIC-MALDI-MSI results of heavy and light labeled maltodextrin enabling quantitative glycan analysis.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
| | - Xuefei Zhong
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Cai Tie
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Bingming Chen
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Xinxiang Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA.
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI, 53705, USA.
- School of Life Sciences, Tianjin University, No.92 Weijin Road, Nankai District, Tianjin, 300072, China.
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18
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Tabasum S, Noreen A, Kanwal A, Zuber M, Anjum MN, Zia KM. Glycoproteins functionalized natural and synthetic polymers for prospective biomedical applications: A review. Int J Biol Macromol 2017; 98:748-776. [PMID: 28111295 DOI: 10.1016/j.ijbiomac.2017.01.078] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/05/2017] [Accepted: 01/16/2017] [Indexed: 02/06/2023]
Abstract
Glycoproteins have multidimensional properties such as biodegradability, biocompatibility, non-toxicity, antimicrobial and adsorption properties; therefore, they have wide range of applications. They are blended with different polymers such as chitosan, carboxymethyl cellulose (CMC), polyvinyl pyrrolidone (PVP), polycaprolactone (PCL), heparin, polystyrene fluorescent nanoparticles (PS-NPs) and carboxyl pullulan (PC) to improve their properties like thermal stability, mechanical properties, resistance to pH, chemical stability and toughness. Considering the versatile charateristics of glycoprotein based polymers, this review sheds light on synthesis and characterization of blends and composites of glycoproteins, with natural and synthetic polymers and their potential applications in biomedical field such as drug delivery system, insulin delivery, antimicrobial wound dressing uses, targeting of cancer cells, development of anticancer vaccines, development of new biopolymers, glycoproteome research, food product and detection of dengue glycoproteins. All the technical scientific issues have been addressed; highlighting the recent advancement.
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Affiliation(s)
- Shazia Tabasum
- Institute of Chemistry, Government College University, Faisalabad 38030, Pakistan
| | - Aqdas Noreen
- Institute of Chemistry, Government College University, Faisalabad 38030, Pakistan
| | - Arooj Kanwal
- Institute of Chemistry, Government College University, Faisalabad 38030, Pakistan
| | - Mohammad Zuber
- Institute of Chemistry, Government College University, Faisalabad 38030, Pakistan
| | | | - Khalid Mahmood Zia
- Institute of Chemistry, Government College University, Faisalabad 38030, Pakistan.
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19
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Yang S, Höti N, Yang W, Liu Y, Chen L, Li S, Zhang H. Simultaneous analyses of N-linked and O-linked glycans of ovarian cancer cells using solid-phase chemoenzymatic method. Clin Proteomics 2017; 14:3. [PMID: 28100988 PMCID: PMC5237303 DOI: 10.1186/s12014-017-9137-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/29/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Glycans play critical roles in a number of biological activities. Two common types of glycans, N-linked and O-linked, have been extensively analyzed in the last decades. N-glycans are typically released from glycoproteins by enzymes, while O-glycans are released from glycoproteins by chemical methods. It is important to identify and quantify both N- and O-linked glycans of glycoproteins to determine the changes of glycans. METHODS The effort has been dedicated to study glycans from ovarian cancer cells treated with O-linked glycosylation inhibitor qualitatively and quantitatively. We used a solid-phase chemoenzymatic approach to systematically identify and quantify N-glycans and O-glycans in the ovarian cancer cells. It consists of three steps: (1) immobilization of proteins from cells and derivatization of glycans to protect sialic acids; (2) release of N-glycans by PNGase F and quantification of N-glycans by isobaric tags; (3) release and quantification of O-glycans by β-elimination in the presence of 1-phenyl-3-methyl-5-pyrazolone (PMP). RESULTS We used ovarian cancer cell lines to study effect of O-linked glycosylation inhibitor on protein glycosylation. Results suggested that the inhibition of O-linked glycosylation reduced the levels of O-glycans. Interestingly, it appeared to increase N-glycan level in a lower dose of the O-linked glycosylation inhibitor. The sequential release and analyses of N-linked and O-linked glycans using chemoenzymatic approach are a platform for studying N-glycans and O-glycans in complex biological samples. CONCLUSION The solid-phase chemoenzymatic method was used to analyze both N-linked and O-linked glycans sequentially released from the ovarian cancer cells. The biological studies on O-linked glycosylation inhibition indicate the effects of O-glycosylation inhibition to glycan changes in both O-linked and N-linked glycan expression.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Naseruddin Höti
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Weiming Yang
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Yang Liu
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Shuwei Li
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD 20850 USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
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20
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Stine KJ. Application of Porous Materials to Carbohydrate Chemistry and Glycoscience. Adv Carbohydr Chem Biochem 2017; 74:61-136. [PMID: 29173727 DOI: 10.1016/bs.accb.2017.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
There is a growing interest in using a range of porous materials to meet research needs in carbohydrate chemistry and glycoscience in general. Among the applications of porous materials reviewed in this chapter, enrichment of glycans from biological samples prior to separation and analysis by mass spectrometry is a major emphasis. Porous materials offer high surface area, adjustable pore sizes, and tunable surface chemistry for interacting with glycans, by boronate affinity, hydrophilic interactions, molecular imprinting, and polar interactions. Among the materials covered in this review are mesoporous silica and related materials, porous graphitic carbon, mesoporous carbon, porous polymers, and nanoporous gold. In some applications, glycans are enzymatically or chemically released from glycoproteins or glycopeptides, and the porous materials have the advantage of size selectivity admitting only the glycans into the pores and excluding proteins. Immobilization of lectins onto porous materials of suitable pore size allows for the use of lectin-carbohydrate interactions in capture or separation of glycoproteins. Porous material surfaces modified with carbohydrates can be used for the selective capture of lectins. Controlled release of therapeutics from porous materials mediated by glycans has been reported, and so has therapeutic targeting using carbohydrate-modified porous particles. Additional applications of porous materials in glycoscience include their use in the supported synthesis of oligosaccharides and in the development of biosensors for glycans.
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21
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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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22
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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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23
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Wang Y, Wang J, Gao M, Zhang X. A novel carbon material with nanopores prepared using a metal-organic framework as precursor for highly selective enrichment of N-linked glycans. Anal Bioanal Chem 2016; 409:431-438. [PMID: 27485625 DOI: 10.1007/s00216-016-9796-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/07/2016] [Accepted: 07/14/2016] [Indexed: 12/28/2022]
Abstract
Protein glycosylation plays a key role in many biological processes. In this study, a novel carbon material with nanopores was prepared by carbonization of metal-organic framework (MOF) Mil-101(Cr). The parent MOF assembled from metal ions with bridging organic linkers had many fascinating properties, such as ultrahigh surface area, suitable nanopore structure, and especially a large amount of carbon after being calcined. Due to the strong interactions between carbon and glycans as well as the size-exclusion effect of pore against protein, the N-linked glycans from standard glycoprotein or complex human serum proteins could be identified with high efficiency. The simple synthesis method as well as good enrichment efficiency made this novel carbon material a promising tool for glycosylation research.
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Affiliation(s)
- Yanan Wang
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Jiaxi Wang
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Mingxia Gao
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
| | - Xiangmin Zhang
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China
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Hu Y, Shihab T, Zhou S, Wooding K, Mechref Y. LC-MS/MS of permethylated N-glycans derived from model and human blood serum glycoproteins. Electrophoresis 2016; 37:1498-505. [PMID: 26959726 PMCID: PMC4964794 DOI: 10.1002/elps.201500560] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/17/2016] [Accepted: 02/17/2016] [Indexed: 12/24/2022]
Abstract
LC-MS/MS is one of the most powerful tools for N-glycan structure elucidation; however, it is still challenging to identify some glycan structures with low abundance. In this study, we investigated the chromatographic behavior of permethylated N-glycans. The relationship between retention times versus molecular weight of dextran, dextrin, and model glycans was investigated. Also, the nonpolar surface area of glycans was calculated and compared to their experimental retention times. Both retention time and nonpolar surface area trends are similar when the intermolecular interaction is included in the calculation. Moreover, retention time corresponds to glycan types and branch types. The N-glycans analysis model, which combines high mass accuracy and retention time, was applied to confirm serum N-glycans. In total, there were 78 N-glycan compositions identified. A linear relationship between retention times and molecular weights were observed for each subgroup of glycan structures, for example, R(2) value for complex N-glycans was determined to be > 0.98. Moreover, the retention time could be further applied to distinguish between structural isomers as well as linkage isomers. MS/MS data were used to confirm the structural isomers.
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Affiliation(s)
- Yunli Hu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Tarek Shihab
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Shiyue Zhou
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Kerry Wooding
- 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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Microfluidic Chip-LC/MS-based Glycomic Analysis Revealed Distinct N-glycan Profile of Rat Serum. Sci Rep 2015; 5:12844. [PMID: 26248949 PMCID: PMC4650694 DOI: 10.1038/srep12844] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 07/03/2015] [Indexed: 12/30/2022] Open
Abstract
The rat is an important alternative for studying human pathology owing to certain similarities to humans. Glycomic studies on rat serum have revealed that variations in the N-glycans of glycoproteins correlated with disease progression, which is consistent with the findings in human serum. Therefore, we comprehensively characterized the rat serum N-glycome using microfluidic chip-LC-ESI-QTOF MS and MS/MS techniques. In total, 282 N-glycans, including isomers, were identified. This study is the first to present comprehensive profiling of N-glycans containing O-acetylated sialic acid, among which 27 N-glycans are novel. In addition, the co-existence of N-acetylneuraminic acid (NeuAc) and N-glycolylneuraminic acid (NeuGc) in a single N-glycan ('mixed' N-glycan) was detected and represents a new type of N-glycan in rat serum. The existence of O-acetylated sialic acid is the characteristic feature of rat serum that distinguishes it from mouse and human sera. Comparisons between the rat, mouse, and human serum glycomes revealed that the rat glycome is more similar to that of human sera than to that of mouse sera. Our findings highlight the similarities between the glycomic profile of rat and human sera and provided important selection criteria for choosing an appropriate animal model for pathological and pharmacological studies.
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A MALDI-MS-based quantitative targeted glycomics (MALDI-QTaG) for total N-glycan analysis. Biotechnol Lett 2015; 37:2019-25. [PMID: 26063621 DOI: 10.1007/s10529-015-1881-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/03/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVES To develop a sensitive and quantitative method for monitoring the abnormal glycosylation of clinical and biopharmaceutical products. RESULTS MALDI-MS-based quantitative targeted glycomics (MALDI-QTaG) was proposed for sensitive and quantitative analysis of total N-glycans. The derivatization reactions (i.e., amidation of sialic acid and incorporation of a positive charge moiety into the reducing end) dramatically increased the linearity (R(2) > 0.99) and sensitivity (limit of detection is 0.5 pmol/glycoprotein) relative to underivatized glycans. In addition, the analytical strategy was chromatographic purification-free and non-laborious process accessible to the high-throughput analyses. We used MALDI-QTaG to analyze the N-glycans of α-fetoprotein (AFP) purified from normal cord blood and HCC cell line (Huh7 cells). The total percentages of core-fucosylated AFP N-glycans from Huh7 cells and normal cord blood were 98 and 18%, respectively. CONCLUSIONS This MALDI-MS-based glycomics technology has wide applications in many clinical and bioengineering fields requiring sensitive, quantitative and fast N-glycosylation validation.
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2009-2010. MASS SPECTROMETRY REVIEWS 2015; 34:268-422. [PMID: 24863367 PMCID: PMC7168572 DOI: 10.1002/mas.21411] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/16/2013] [Accepted: 07/16/2013] [Indexed: 05/07/2023]
Abstract
This review is the sixth 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 2010. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, arrays and fragmentation are covered in the first part of the review and applications to various structural typed constitutes the remainder. The main groups of compound that are discussed in this section are oligo and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Many of these applications are presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis.
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Affiliation(s)
- David J. Harvey
- Department of BiochemistryOxford Glycobiology InstituteUniversity of OxfordOxfordOX1 3QUUK
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28
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Ali F, Cheong WJ. Open tubular capillary electrochromatography with an N
-phenylacrylamide-styrene copolymer-based stationary phase for the separation of anomers of glucose and structural isomers of maltotriose. J Sep Sci 2015; 38:1763-70. [DOI: 10.1002/jssc.201401356] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Faiz Ali
- Department of Chemistry; Inha University; Namku Incheon South Korea
| | - Won Jo Cheong
- Department of Chemistry; Inha University; Namku Incheon South Korea
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29
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Ji IJ, Hua S, Shin DH, Seo N, Hwang JY, Jang IS, Kang MG, Choi JS, An HJ. Spatially-Resolved Exploration of the Mouse Brain Glycome by Tissue Glyco-Capture (TGC) and Nano-LC/MS. Anal Chem 2015; 87:2869-77. [DOI: 10.1021/ac504339t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- In Jung Ji
- Asia Glycomics Reference Site, Daejeon 305-764, Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Serenus Hua
- Asia Glycomics Reference Site, Daejeon 305-764, Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Dong Hee Shin
- Asia Glycomics Reference Site, Daejeon 305-764, Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Nari Seo
- Asia Glycomics Reference Site, Daejeon 305-764, Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Jae Yun Hwang
- Asia Glycomics Reference Site, Daejeon 305-764, Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Ik-Soon Jang
- Division
of Life Science, Korea Basic Science Institute, Daejeon 305-764, Korea
| | - Myoung-Goo Kang
- Center
for Cognition and Sociality, Institute for Basic Science, Daejeon 305-764, Korea
| | - Jong-Soon Choi
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
- Division
of Life Science, Korea Basic Science Institute, Daejeon 305-764, Korea
| | - Hyun Joo An
- Asia Glycomics Reference Site, Daejeon 305-764, Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
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30
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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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31
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Pan Y, Bai H, Ma C, Deng Y, Qin W, Qian X. Brush polymer modified and lectin immobilized core-shell microparticle for highly efficient glycoprotein/glycopeptide enrichment. Talanta 2013; 115:842-8. [PMID: 24054672 DOI: 10.1016/j.talanta.2013.06.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 06/16/2013] [Accepted: 06/20/2013] [Indexed: 12/12/2022]
Abstract
Protein glycosylation regulates numerous important biological processes and plays key roles in many diseases including cancer, diabetes and inflammation. The ability to efficiently profile variation of protein glycosylation in biological samples is very useful for identifying new diagnostic biomarkers or developing new therapeutic approaches. Due to the low availability of glycoprotein/glycopeptide from natural sources, enrichment before mass spectrometry (MS) analysis is usually a prerequisite. Affinity enrichment using lectins is currently one of the most widely adopted approaches. Conventionally, lectins are immobilized on solid supporting materials for sample recovery. However, the limited specific surface area, high steric hindrance and rigid nature of such supporting materials restricts lectin loading amount and results in low flexibility as well as accessibility of the immobilized lectins. Therefore, we proposed using core-shell microparticles composed of silica core and brush-like polymer chains shell for improved lectin immobilization. The surface bound brush-like polymer are synthesized by in situ growth of polymer chains from microparticle surface using surface initiated atom transfer radical polymerization (SI-ATRP). The flexible non-crosslinked polymer chains not only provide numerous binding sites, but also work as three-dimensional support for lectin immobilization, which leads to high loading amount and good accessibility of the immobilized lectin. Successful enrichment which facilitated glycoprotein/glycopeptide identification is demonstrated.
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Affiliation(s)
- Yiting Pan
- School of Life Science and Technology, Beijing Institute of Technology, Beijing 100081, PR China; National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, PR China
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32
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Gama MR, Collins CH, Bottoli CBG. Nano-Liquid Chromatography in Pharmaceutical and Biomedical Research. J Chromatogr Sci 2013; 51:694-703. [DOI: 10.1093/chromsci/bmt023] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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33
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Alley WR, Mann BF, Novotny MV. High-sensitivity analytical approaches for the structural characterization of glycoproteins. Chem Rev 2013; 113:2668-732. [PMID: 23531120 PMCID: PMC3992972 DOI: 10.1021/cr3003714] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- William R. Alley
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
| | - Benjamin F. Mann
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
- Indiana University School of Medicine, Indiana University, Indianapolis, Indiana, United States
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34
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Hua S, Williams CC, Dimapasoc LM, Ro GS, Ozcan S, Miyamoto S, Lebrilla CB, An HJ, Leiserowitz GS. Isomer-specific chromatographic profiling yields highly sensitive and specific potential N-glycan biomarkers for epithelial ovarian cancer. J Chromatogr A 2013; 1279:58-67. [PMID: 23380366 PMCID: PMC5628020 DOI: 10.1016/j.chroma.2012.12.079] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 12/17/2012] [Accepted: 12/26/2012] [Indexed: 12/13/2022]
Abstract
Aberrant glycosylation has been observed for decades in essentially all types of cancer, and is now well established as an indicator of carcinogenesis. Mining the glycome for biomarkers, however, requires analytical methods that can rapidly separate, identify, and quantify isomeric glycans. We have developed a rapid-throughput method for chromatographic glycan profiling using microfluidic chip-based nanoflow liquid chromatography (nano-LC)/mass spectrometry. To demonstrate the utility of this method, we analyzed and compared serum samples from epithelial ovarian cancer cases (n=46) and healthy control individuals (n=48). Over 250 N-linked glycan compound peaks with over 100 distinct N-linked glycan compositions were identified. Statistical testing identified 26 potential glycan biomarkers based on both compositional and structure-specific analyses. Using these results, an optimized model was created incorporating the combined abundances of seven potential glycan biomarkers. The receiver operating characteristic (ROC) curve of this optimized model had an area under the curve (AUC) of 0.96, indicating robust discrimination between cancer cases and healthy controls. Rapid-throughput chromatographic glycan profiling was found to be an effective platform for structure-specific biomarker discovery.
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Affiliation(s)
- Serenus Hua
- Department of Chemistry, University of California, Davis, CA, USA
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35
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Zhang W, Han H, Bai H, Tong W, Zhang Y, Ying W, Qin W, Qian X. A Highly Efficient and Visualized Method for Glycan Enrichment by Self-Assembling Pyrene Derivative Functionalized Free Graphene Oxide. Anal Chem 2013; 85:2703-9. [DOI: 10.1021/ac303101t] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Wanjun Zhang
- National
Center for Protein Sciences Beijing, State
Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
P.R. China
| | - Huanhuan Han
- National
Center for Protein Sciences Beijing, State
Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
P.R. China
| | - Haihong Bai
- National
Center for Protein Sciences Beijing, State
Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
P.R. China
| | - Wei Tong
- National
Center for Protein Sciences Beijing, State
Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
P.R. China
| | - Yangjun Zhang
- National
Center for Protein Sciences Beijing, State
Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
P.R. China
| | - Wantao Ying
- National
Center for Protein Sciences Beijing, State
Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
P.R. China
| | - Weijie Qin
- National
Center for Protein Sciences Beijing, State
Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
P.R. China
| | - Xiaohong Qian
- National
Center for Protein Sciences Beijing, State
Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
P.R. China
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Gaye MM, Valentine SJ, Hu Y, Mirjankar N, Hammoud ZT, Mechref Y, Lavine BK, Clemmer DE. Ion mobility-mass spectrometry analysis of serum N-linked glycans from esophageal adenocarcinoma phenotypes. J Proteome Res 2012; 11:6102-10. [PMID: 23126309 DOI: 10.1021/pr300756e] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three disease phenotypes, Barrett's esophagus (BE), high-grade dysplasia (HGD), esophageal adenocarcinoma (EAC), and a set of normal control (NC) serum samples are examined using a combination of ion mobility spectrometry (IMS), mass spectrometry (MS), and principal component analysis (PCA) techniques. Samples from a total of 136 individuals were examined, including 7 characterized as BE, 12 as HGD, 56 as EAC, and 61 as NC. In typical data sets, it was possible to assign ∼20 to 30 glycan ions based on MS measurements. Ion mobility distributions for these ions show multiple features. In some cases, such as the [S1H5N4+3Na]3+ and [S1F1H5N4+3Na]3+ glycan ions, the ratio of intensities of high-mobility features to low-mobility features vary significantly for different groups. The degree to which such variations in mobility profiles can be used to distinguish phenotypes is evaluated for 11 N-linked glycan ions. An outlier analysis on each sample class followed by an unsupervised PCA using a genetic algorithm for pattern recognition reveals that EAC samples are separated from NC samples based on 46 features originating from the 11-glycan composite IMS distribution.
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Affiliation(s)
- M M Gaye
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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37
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Hu Y, Mechref Y. Comparing MALDI-MS, RP-LC-MALDI-MS and RP-LC-ESI-MS glycomic profiles of permethylated N-glycans derived from model glycoproteins and human blood serum. Electrophoresis 2012; 33:1768-77. [PMID: 22740465 DOI: 10.1002/elps.201100703] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The glycomic profiling of purified glycoproteins and biological specimen is routinely achieved through different analytical methods, but mainly through MS and LC-MS. The enhanced ionization efficiency and improved tandem MS interpretation of permethylated glycans have prompted the popularity of this approach. This study focuses on comparing the glycomic profiling of permethylated N-glycans derived from model glycoproteins and human blood serum using MALDI-MS as well as RP-LC-MALDI-MS and RP-LC-ESI-MS. In the case of model glycoproteins, the glycomic profiles acquired using the three methods were very comparable. However, this was not completely true in the case of glycans derived from blood serum. RP-LC-ESI-MS analysis of reduced and permethylated N-glycans derived from 250 nl of blood serum allowed the confident detection of 73 glycans (the structures of which were confirmed by mass accuracy and tandem MS), while 53 and 43 structures were identified in the case of RP-LC-MALDI-MS and MALDI-MS analyses of the same sample, respectively. RP-LC-ESI-MS analysis facilitates automated and sensitive tandem MS acquisitions. The glycan structures that were detected only in the RP-LC-ESI-MS analysis were glycans existing at low abundances. This is suggesting the higher detection sensitivity of RP-LC-ESI-MS analysis, originating from both reduced competitive ionization and saturation of detectors, facilitated by the chromatographic separation. The latter also permitted the separation of several structural isomers; however, isomeric separations pertaining to linkages were not detected.
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Affiliation(s)
- Yunli Hu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
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Walker SH, Carlisle BC, Muddiman DC. Systematic comparison of reverse phase and hydrophilic interaction liquid chromatography platforms for the analysis of N-linked glycans. Anal Chem 2012; 84:8198-206. [PMID: 22954204 PMCID: PMC3689152 DOI: 10.1021/ac3012494] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Due to the hydrophilic nature of glycans, reverse phase chromatography has not been widely used as a glycomic separation technique coupled to mass spectrometry. Other approaches such as hydrophilic interaction chromatography and porous graphitized carbon chromatography are often employed, though these strategies frequently suffer from decreased chromatographic resolution, long equilibration times, indefinite retention, and column bleed. Herein, it is shown that, through an efficient hydrazone formation derivatization of N-linked glycans (~4 h of additional sample preparation time which is carried out in parallel), numerous experimental and practical advantages are gained when analyzing the glycans by online reverse phase chromatography. These benefits include an increased number of glycans detected, increased peak capacity of the separation, and the ability to analyze glycans on the identical liquid chromatography-mass spectrometry platform commonly used for proteomic analyses. The data presented show that separation of derivatized N-linked glycans by reverse phase chromatography significantly out-performs traditional separation of native or derivatized glycans by hydrophilic interaction chromatography. Furthermore, the movement to a more ubiquitous separation technique will afford numerous research groups the opportunity to analyze both proteomic and glycomic samples on the same platform with minimal time and physical change between experiments, increasing the efficiency of "multiomic" biological approaches.
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Affiliation(s)
- S. Hunter Walker
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - Brandon C. Carlisle
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - David C. Muddiman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
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Dallas DC, Martin WF, Hua S, German JB. Automated glycopeptide analysis--review of current state and future directions. Brief Bioinform 2012; 14:361-74. [PMID: 22843980 DOI: 10.1093/bib/bbs045] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glycosylation of proteins is involved in immune defense, cell-cell adhesion, cellular recognition and pathogen binding and is one of the most common and complex post-translational modifications. Science is still struggling to assign detailed mechanisms and functions to this form of conjugation. Even the structural analysis of glycoproteins-glycoproteomics-remains in its infancy due to the scarcity of high-throughput analytical platforms capable of determining glycopeptide composition and structure, especially platforms for complex biological mixtures. Glycopeptide composition and structure can be determined with high mass-accuracy mass spectrometry, particularly when combined with chromatographic separation, but the sheer volume of generated data necessitates computational software for interpretation. This review discusses the current state of glycopeptide assignment software-advances made to date and issues that remain to be addressed. The various software and algorithms developed so far provide important insights into glycoproteomics. However, there is currently no freely available software that can analyze spectral data in batch and unambiguously determine glycopeptide compositions for N- and O-linked glycopeptides from relevant biological sources such as human milk and serum. Few programs are capable of aiding in structural determination of the glycan component. To significantly advance the field of glycoproteomics, analytical software and algorithms are required that: (i) solve for both N- and O-linked glycopeptide compositions, structures and glycosites in biological mixtures; (ii) are high-throughput and process data in batches; (iii) can interpret mass spectral data from a variety of sources and (iv) are open source and freely available.
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40
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Resolving the problem of chromatographic overlap by 3D cross correlation (3DCC) processing of LC, MS and NMR data for characterization of complex glycan mixtures. Anal Bioanal Chem 2012; 404:1427-37. [DOI: 10.1007/s00216-012-6241-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 06/26/2012] [Accepted: 06/29/2012] [Indexed: 12/18/2022]
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Abstract
The glycome, that is, the glycan components of a biological source, has been widely reported to change with disease states. However, mining the glycome for biomarkers is complicated by glycan structural heterogeneity. Nanoflow LC, or nano-LC, significantly addresses the problem by providing a highly sensitive and quantitative method of separating and profiling glycans. This review summarizes recent advances in analytical technology and methodology that enhance and augment the advantages offered by nano-LC. (e.g., reversed phase, hydrophilic interaction and porous graphitized carbon chromatography, as well as associated derivatization strategies), detectors (e.g., fluorescence and MS), and technology platforms (particularly chip-based nano-LC) are examined in detail, along with their application to biomarker discovery. Particular emphasis is placed on methods and technologies that allow structure-specific glycan profiling.
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42
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Zauner G, Deelder AM, Wuhrer M. Recent advances in hydrophilic interaction liquid chromatography (HILIC) for structural glycomics. Electrophoresis 2012; 32:3456-66. [PMID: 22180202 DOI: 10.1002/elps.201100247] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review presents recent progress in employing hydrophilic interaction liquid chromatography (HILIC) for glycan and glycopeptides analysis. After an introduction of this technique, the following themes are addressed: (i) implementation of HILIC in large-scale studies for analyzing the human plasma N-glycome; (ii) the use of HILIC UPLC (ultrahigh pressure liquid chromatography) for fast high-resolution runs and its successful application with online MS for glycan and glycopeptide analysis; (iii) high-throughput profiling using HILIC solid-phase extraction in combination with MS detection; (iv) HILIC sample preparation for CE and CGE; (v) the latest glycoproteomic approaches implementing HILIC separation; (vi) future perspectives of HILIC including its use in large-scale glycoproteomics studies such as the analysis of entire glycoproteomes at the glycopeptide level.
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Affiliation(s)
- Gerhild Zauner
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
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43
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Isailovic D, Plasencia MD, Gaye MM, Stokes ST, Kurulugama RT, Pungpapong V, Zhang M, Kyselova Z, Goldman R, Mechref Y, Novotny MV, Clemmer DE. Delineating diseases by IMS-MS profiling of serum N-linked glycans. J Proteome Res 2012; 11:576-85. [PMID: 22148953 PMCID: PMC3337085 DOI: 10.1021/pr200777u] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Altered branching and aberrant expression of N-linked glycans is known to be associated with disease states such as cancer. However, the complexity of determining such variations hinders the development of specific glycomic approaches for assessing disease states. Here, we examine a combination of ion mobility spectrometry (IMS) and mass spectrometry (MS) measurements, with principal component analysis (PCA) for characterizing serum N-linked glycans from 81 individuals: 28 with cirrhosis of the liver, 25 with liver cancer, and 28 apparently healthy. Supervised PCA of combined ion-mobility profiles for several, to as many as 10 different mass-to-charge ratios for glycan ions, improves the delineation of diseased states. This extends an earlier study [J. Proteome Res.2008, 7, 1109-1117] of isomers associated with a single glycan (S(1)H(5)N(4)) in which PCA analysis of the IMS profiles appeared to differentiate the liver cancer group from the other samples. Although performed on a limited number of test subjects, the combination of IMS-MS for different combinations of ions and multivariate PCA analysis shows promise for characterizing disease states.
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Affiliation(s)
- Dragan Isailovic
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | - Maissa M. Gaye
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Sarah T. Stokes
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | - Vitara Pungpapong
- Department of Statistics, Purdue University, West Lafayette, IN 47907-2068
| | - Min Zhang
- Department of Statistics, Purdue University, West Lafayette, IN 47907-2068
| | - Zuzana Kyselova
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Radoslav Goldman
- Department of Oncology, Georgetown Univ. Medical Center, Washington, DC 20057
| | - Yehia Mechref
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405
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44
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Zhou W, Håkansson K. Structural Characterization of Carbohydrates by Fourier Transform Tandem Mass Spectrometry. CURR PROTEOMICS 2011; 8:297-308. [PMID: 22389641 PMCID: PMC3289259 DOI: 10.2174/157016411798220826] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fourier transform tandem mass spectrometry (MS/MS) provides high mass accuracy, high sensitivity, and analytical versatility and has therefore emerged as an indispensable tool for structural elucidation of biomolecules. Glycosylation is one of the most common posttranslational modifications, occurring in ~50% of proteins. However, due to the structural diversity of carbohydrates, arising from non-template driven biosynthesis, achievement of detailed structural insight is highly challenging. This review briefly discusses carbohydrate sample preparation and ionization methods, and highlights recent developments in alternative high-resolution MS/MS strategies, including infrared multiphoton dissociation (IRMPD), electron capture dissociation (ECD), and electron detachment dissociation (EDD), for carbohydrates with a focus on glycans and proteoglycans from mammalian glycoproteins.
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Affiliation(s)
- Wen Zhou
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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45
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Zhang Y, Wen Z, Washburn MP, Florens L. Improving proteomics mass accuracy by dynamic offline lock mass. Anal Chem 2011; 83:9344-51. [PMID: 22044264 DOI: 10.1021/ac201867h] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several methods to obtain low-ppm mass accuracy have been described. In particular, online or offline lock mass approaches can use background ions, produced by electrospray under ambient conditions, as calibrants. However, background ions such as protonated and ammoniated polydimethylcyclosiloxane ions have relatively weak and fluctuating intensity. To address this issue, we implemented dynamic offline lock mass (DOLM). Within every MS1 survey spectrum, DOLM dynamically selected the strongest n background ions for statistical treatments and m/z recalibration. We systematically optimized the mass profile abstraction method to find one single m/z value to represent an ion and the number of calibrants. To assess the influence of the intensity of the analyte ions, we used tandem mass spectroscopy (MS/MS) datasets obtained from MudPIT analyses of two protein samples with different dynamic ranges. DOLM outperformed both external mass calibration and offline lock mass that used predetermined calibrant ions, especially in the low-ppm range. The unique dynamic feature of DOLM was able to adapt to wide variations in calibrant intensities, leading to averaged mass error center at 0.03 ± 0.50 ppm for precursor ions. Such consistently tight mass accuracies meant that a precursor mass tolerance as low as 1.5 ppm could be used to search or filter post-search DOLM-recalibrated MS/MS datasets.
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Affiliation(s)
- Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, United States
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46
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Glycoproteomics-based identification of cancer biomarkers. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011:601937. [PMID: 22084691 PMCID: PMC3195811 DOI: 10.1155/2011/601937] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 07/16/2011] [Indexed: 01/06/2023]
Abstract
Protein glycosylation is one of the most common posttranslational modifications in mammalian cells. It is involved in many biological pathways and molecular functions and is well suited for proteomics-based disease investigations. Aberrant protein glycosylation may be associated with disease processes. Specific glycoforms of glycoproteins may serve as potential biomarkers for the early detection of disease or as biomarkers for the evaluation of therapeutic efficacy for treatment of cancer, diabetes, and other diseases. Recent technological developments, including lectin affinity chromatography and mass spectrometry, have provided researchers the ability to obtain detailed information concerning protein glycosylation. These in-depth investigations, including profiling and quantifying glycoprotein expression, as well as comprehensive glycan structural analyses may provide important information leading to the development of disease-related biomarkers. This paper describes methodologies for the detection of cancer-related glycoprotein and glycan structural alterations and briefly summarizes several current cancer-related findings.
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47
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Hua S, An HJ, Ozcan S, Ro GS, Soares S, DeVere-White R, Lebrilla CB. Comprehensive native glycan profiling with isomer separation and quantitation for the discovery of cancer biomarkers. Analyst 2011; 136:3663-71. [PMID: 21776491 PMCID: PMC3331797 DOI: 10.1039/c1an15093f] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Glycosylation is highly sensitive to the biochemical environment and has been implicated in many diseases including cancer. Glycan compositional profiling of human serum with mass spectrometry has already identified potential biomarkers for several types of cancer and diseases; however, composition alone does not fully describe glycan stereo- and regioisomeric diversity. The vast structural heterogeneity of glycans presents a formidable analytical challenge. We have developed a method to identify and quantify isomeric native glycans using nanoflow liquid chromatography (nano-LC)/mass spectrometry. A microfluidic chip packed with graphitized carbon was used to chromatographically separate the glycans. To determine the utility of this method for structure-specific biomarker discovery, we analyzed serum samples from two groups of prostate cancer patients with different prognoses. More than 300 N-glycan species (including isomeric structures) were identified, corresponding to over 100 N-glycan compositions. Statistical tests established significant differences in glycan abundances between patient groups. This method provides comprehensive, selective, and quantitative glycan profiling.
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Affiliation(s)
- Serenus Hua
- Department of Chemistry, University of California, Davis, 95616
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Sureyya Ozcan
- Department of Chemistry, University of California, Davis, 95616
| | - Grace S. Ro
- Department of Chemistry, University of California, Davis, 95616
| | | | | | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, 95616
- Department of Biochemistry and Molecular Medicine, University of California, Davis, 95616
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48
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Walker SH, Budhathoki-Uprety J, Novak BM, Muddiman DC. Stable-isotope labeled hydrophobic hydrazide reagents for the relative quantification of N-linked glycans by electrospray ionization mass spectrometry. Anal Chem 2011; 83:6738-45. [PMID: 21774516 PMCID: PMC3184603 DOI: 10.1021/ac201376q] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This study presents the development of stable-isotope labeled hydrophobic, hydrazide reagents for the relative quantification of N-linked glycans. The P2GPN "light" ((12)C) and "heavy" ((13)C(6)) pair are used to differentially label two N-linked glycan samples. The samples are combined 1:1, separated using HILIC, and then mass differentiated and quantified using mass spectrometry. These reagents have several benefits: (1) impart hydrophobic character to the glycans affording an increase in electrospray ionization efficiency and MS detection; (2) indistinguishable chromatographic, MS, and MS/MS performance of the "light" and "heavy" reagents affording relative quantification; and (3) analytical variability is significantly reduced due to the two samples being mixed together after sample preparation. Obtaining these analytical benefits only requires ~4 h of sample preparation time. It is shown that these reagents are capable of quantifying changes in glycosylation in simple mixtures, and the analytical variability of the reagents in pooled plasma samples is shown to be less than ±30%. Additionally, the incorporation of an internal standard allows one to account for the difference in systematic error between the two samples due to the samples being processed in parallel and not mixed until after derivatization.
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Affiliation(s)
- S. Hunter Walker
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, North Carolina State University, Raleigh, North Carolina 27695
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | | | - Bruce M. Novak
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - David C. Muddiman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, North Carolina State University, Raleigh, North Carolina 27695
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
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49
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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50
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Dixon RB, Bereman MS, Petitte JN, Hawkridge AM, Muddiman DC. One-Year Plasma N-linked Glycome Intra-individual and Inter-individual Variability in the Chicken Model of Spontaneous Ovarian Adenocarcinoma. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 305:79-86. [PMID: 21845070 PMCID: PMC3155253 DOI: 10.1016/j.ijms.2010.05.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Spontaneous epithelial ovarian cancer (EOC) in the chicken presents a similar pathogenesis compared with humans including CA-125 expression and genetic mutational frequencies (e.g., p53). The high prevalence of spontaneous EOC chickens also provides a unique experimental model for biomarker discovery at the genomic, proteomic, glycomic, and metabolomic level. In an effort to exploit this unique model for biomarker discovery, longitudinal plasma samples were collected from chickens at three month intervals for one year. The study described herein involved cleaving the N-glycans from these longitudinal chicken plasma samples and analyzing them via nanoLC-FTMS/MS. Glycans identified in this study were previously found in human plasma and this work provides a promising methodology to enable longitudinal studies of the N-linked plasma glycome profile during EOC progression. The structure, abundance, and intra-variability and inter-variability for 35 N-linked glycans identified in this study are reported. The full potential of the chicken model for biomarker discovery has yet to be realized, but the initial interrogation of longitudinally-procured samples provides evidence that supports the value of this strategy in the search for glycomic biomarkers.
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Affiliation(s)
- R. Brent Dixon
- W.M. Keck FT-ICR Mass Spectrometry Laboratory and Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - Michael S. Bereman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory and Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - James N. Petitte
- Department of Poultry Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Adam M. Hawkridge
- W.M. Keck FT-ICR Mass Spectrometry Laboratory and Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - David C. Muddiman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory and Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
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