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Yamada K, Asada K, Hanzawa K, Aoki Y, Nakajima K, Kinoshita M. Developing Method for Minor Acidic O-Glycan Analysis in Mucin and Cancer Cell Samples. J Proteome Res 2024. [PMID: 39255405 DOI: 10.1021/acs.jproteome.4c00240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Minor acidic glycans, such as sulfated and phosphorylated glycans, constitute only a small fraction of biological glycome, making their analysis a considerable challenge. In this study, we developed a technique to analyze minor acidic O-glycans in biological samples. First, efficient reaction conditions for the release of O-glycans from the proteins were determined. Next, a high-throughput method was established for the recovery of minor acidic glycans using NH2 spin columns. The performance of the established method was evaluated using mucin samples, and sulfated O-glycans were successfully detected in bovine submaxillary gland mucin and porcine stomach mucin. We also analyzed the minor acidic O-glycans in cultured cancer cells. In addition to trifucosylated sulfated O-glycans and disulfated O-glycans, sulfated O-glycans with KDN were detected in LS174T cells. The relative amount of sulfated glycans in LS174T cells was almost 10-fold higher than that in the other cells. Moreover, a large polylactosamine-type sulfated O-glycan with a molecular weight >3500 was detected in MKN45 cells. Interestingly, phosphorylated ribose, possibly bound to serine/threonine, was observed in all the cells used in this study. Thus, our established analytical method allows for the analysis of minor acidic O-glycans that cannot be detected using existing glycomics methods.
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Affiliation(s)
- Keita Yamada
- The Laboratory of Toxicology, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka 584-8540, Japan
| | - Kosuke Asada
- The Laboratory of Toxicology, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka 584-8540, Japan
| | - Ken Hanzawa
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yuma Aoki
- The Laboratory of Toxicology, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka 584-8540, Japan
| | - Kazuki Nakajima
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Mitsuhiro Kinoshita
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Higashi, Osaka 577-8502, Japan
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2
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Hanamatsu H, Yokota I, Kurogochi M, Akasaka-Manya K, Miura N, Manya H, Endo T, Nishikaze T, Furukawa JI, Tanaka K. Direct derivatization of sialic acids and mild β-elimination for linkage-specific sialyl O-glycan analysis. Anal Chim Acta 2024; 1318:342945. [PMID: 39067924 DOI: 10.1016/j.aca.2024.342945] [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: 04/13/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND In sharp contrast with analysis of N-glycan that can be prepared by PNGase F, O-glycan analysis remains challenging due to a lack of versatile and simple procedures, especially those mediating cleavage of O-glycans from proteins. Most N-glycans and O-glycans are modified with sialic acids at the non-reducing end and their glycosidic linkages are labile, making it difficult to measure glycans by mass spectrometric analysis. In addition, sialic acid residues present on glycan chains via α2,3-, α2,6-, and α2,8-linkages as structural isomers. RESULTS In this study, we firstly established a direct and linkage-specific derivatization method for sialylated O-glycans on proteins via linkage-specific lactone-opening aminolysis. In this procedure, labile sialylated glycans were not only stabilized, but also allowed distinguishing between sialyl linkages. Furthermore, we revealed that general reductive β-elimination was not useful for O-glycan cleavages with undesirable degradations of resulting methyl amides. Using β-elimination in the presence of pyrazolone (PMP), with low pH despite alkali base concentration, SALSA-derivatized O-glycans could be cleaved with minimal degradations. Cleaved and PMP-labeled O-glycans could be efficiently prepared in an open reaction system at high temperature (evaporative BEP reaction) and detected by simple liquid-phase extraction. Moreover, in the evaporative BEP reaction by changing the alkali solution with LiOH, the lithiated O-glycans could be observed and provided a lot of fragment information reflecting the complex structure of the O-glycans. SIGNIFICANCE Direct sialic acid linkage-specific derivatization of O-glycans on glycoproteins is simple protocol containing in-solution aminolysis-SALSA and acetonitrile precipitation for removal of excess reagents. Evaporative β-elimination with pyrazolone makes possible intact O-linked glycan analysis just by liquid-phase extraction. These analytical methods established by the appropriate combination of direct-SALSA and evaporative β-elimination will facilitate O-glycomic studies in various biological samples.
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Affiliation(s)
- Hisatoshi Hanamatsu
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan
| | - Ikuko Yokota
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan
| | - Masaki Kurogochi
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan; Laboratory of Glyco-Organic Chemistry, The Noguchi Institute, Tokyo, 173-0003, Japan
| | - Keiko Akasaka-Manya
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, 173-0015, Japan
| | - Nobuaki Miura
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan
| | - Hiroshi Manya
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, 173-0015, Japan
| | - Tamao Endo
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, 173-0015, Japan
| | - Takashi Nishikaze
- Solutions COE, Analytical & Measuring Instruments Division, Shimadzu Corporation, Kyoto, 604-8511, Japan.
| | - Jun-Ichi Furukawa
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan; Department of Orthopaedic Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638, Japan.
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, 604-8511, Japan
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3
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Zhang T, Wang W, Wuhrer M, de Haan N. Comprehensive O-Glycan Analysis by Porous Graphitized Carbon Nanoliquid Chromatography-Mass Spectrometry. Anal Chem 2024; 96:8942-8948. [PMID: 38758656 PMCID: PMC11154684 DOI: 10.1021/acs.analchem.3c05826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024]
Abstract
The diverse and unpredictable structures of O-GalNAc-type protein glycosylation present a challenge for its structural and functional characterization in a biological system. Porous graphitized carbon (PGC) liquid chromatography (LC) coupled to mass spectrometry (MS) has become one of the most powerful methods for the global analysis of glycans in complex biological samples, mainly due to the extensive chromatographic separation of (isomeric) glycan structures and the information delivered by collision induced fragmentation in negative mode MS for structural elucidation. However, current PGC-based methodologies fail to detect the smaller glycan species consisting of one or two monosaccharides, such as the Tn (single GalNAc) antigen, which is broadly implicated in cancer biology. This limitation is caused by the loss of small saccharides during sample preparation and LC. Here, we improved the conventional PGC nano-LC-MS/MS-based strategy for O-glycan analysis, enabling the detection of truncated O-glycan species and improving isomer separation. This was achieved by the implementation of 2.7 μm PGC particles in both the trap and analytical LC columns, which provided an enhanced binding capacity and isomer separation for O-glycans. Furthermore, a novel mixed-mode PGC-boronic acid-solid phase extraction during sample preparation was established to purify a broad range of glycans in an unbiased manner, including the previously missed mono- and disaccharides. Taken together, the optimized PGC nano-LC-MS/MS platform presents a powerful component of the toolbox for comprehensive O-glycan characterization.
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Affiliation(s)
- Tao Zhang
- Center for Proteomics and
Metabolomics, Leiden University Medical
Center, P.O. Box 9600, Leiden 2300 RC, The Netherlands
| | - Wenjun Wang
- Center for Proteomics and
Metabolomics, Leiden University Medical
Center, P.O. Box 9600, Leiden 2300 RC, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and
Metabolomics, Leiden University Medical
Center, P.O. Box 9600, Leiden 2300 RC, The Netherlands
| | - Noortje de Haan
- Center for Proteomics and
Metabolomics, Leiden University Medical
Center, P.O. Box 9600, Leiden 2300 RC, The Netherlands
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4
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Xie Y, Liu X, Zhao C, Chen S, Wang S, Lin Z, Robison FM, George BM, Flynn RA, Lebrilla CB, Garcia BA. Development and application of GlycanDIA workflow for glycomic analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584702. [PMID: 38559279 PMCID: PMC10980037 DOI: 10.1101/2024.03.12.584702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Glycans modify protein, lipid, and even RNA molecules to form the regulatory outer coat on cells called the glycocalyx. The changes in glycosylation have been linked to the initiation and progression of many diseases. Thus, while the significance of glycosylation is well established, a lack of accessible methods to characterize glycans has hindered the ability to understand their biological functions. Mass spectrometry (MS)-based methods have generally been at the core of most glycan profiling efforts; however, modern data-independent acquisition (DIA), which could increase sensitivity and simplify workflows, has not been benchmarked for analyzing glycans. Herein, we developed a DIA-based glycomic workflow, termed GlycanDIA, to identify and quantify glycans with high sensitivity and accuracy. The GlycanDIA workflow combined higher energy collisional dissociation (HCD)-MS/MS and staggered windows for glycomic analysis, which facilitates the sensitivity in identification and the accuracy in quantification compared to conventional data-dependent acquisition (DDA)-based glycomics. To facilitate its use, we also developed a generic search engine, GlycanDIA Finder, incorporating an iterative decoy searching for confident glycan identification and quantification from DIA data. The results showed that GlycanDIA can distinguish glycan composition and isomers from N-glycans, O-glycans, and human milk oligosaccharides (HMOs), while it also reveals information on low-abundant modified glycans. With the improved sensitivity, we performed experiments to profile N-glycans from RNA samples, which have been underrepresented due to their low abundance. Using this integrative workflow to unravel the N-glycan profile in cellular and tissue glycoRNA samples, we found that RNA-glycans have specific forms as compared to protein-glycans and are also tissue-specific differences, suggesting distinct functions in biological processes. Overall, GlycanDIA can provide comprehensive information for glycan identification and quantification, enabling researchers to obtain in-depth and refined details on the biological roles of glycosylation.
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Affiliation(s)
- Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
- Department of Chemistry, University of California, Davis, Davis, California, United States
| | - Xingyu Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Chenfeng Zhao
- Department of Computer Science & Engineering, Washington University, St. Louis, Missouri, United States
| | - Siyu Chen
- Department of Chemistry, University of California, Davis, Davis, California, United States
| | - Shunyang Wang
- Department of Chemistry, University of California, Davis, Davis, California, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Faith M Robison
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Benson M George
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, California, United States
- Department of Biochemistry, University of California, Davis, Davis, California, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
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5
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Abikhodr AH, Warnke S, Ben Faleh A, Rizzo TR. Combining Liquid Chromatography and Cryogenic IR Spectroscopy in Real Time for the Analysis of Oligosaccharides. Anal Chem 2024; 96:1462-1467. [PMID: 38211954 PMCID: PMC10831784 DOI: 10.1021/acs.analchem.3c03578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/13/2024]
Abstract
While the combination of liquid chromatography (LC) and mass spectrometry (MS) serves as a robust approach for oligosaccharide analysis, it has difficulty distinguishing the smallest differences between isomers. The integration of infrared (IR) spectroscopy within a mass spectrometer as an additional analytical dimension can effectively address this limitation by providing a molecular fingerprint that is unique to each isomer. However, the direct interfacing of LC-MS with IR spectroscopy presents a technical challenge arising from the mismatch in the operational time scale of each method. In previous studies, this temporal incompatibility was mitigated by employing strategies designed to slow down or broaden the LC elution peaks of interest, but this workaround is applicable only for a few species at a time, necessitating multiple LC runs for comprehensive analysis. In the current work, we directly couple LC with cryogenic IR spectroscopy by acquiring a spectrum in as little as 10 s. This allows us to generate an orthogonal data dimension for molecular identification in the same amount of time that it normally takes for LC analysis. We successfully demonstrate this approach on a commercially available human milk oligosaccharide product, acquiring spectral information on the eluting peaks in real time and using it to identify both the specified constituents and nonspecified product impurities.
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Affiliation(s)
- Ali H Abikhodr
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Stephan Warnke
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Ahmed Ben Faleh
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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6
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Su Y, Li Y, Meng T, Xu B, Zhu H, Zhang L, Wang X, Liu X, Sun H. AANL6 is a new efficient tool to probe non-reducing N-acetylglucosamine of N-linked glycans. Carbohydr Res 2023; 530:108858. [PMID: 37276662 DOI: 10.1016/j.carres.2023.108858] [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: 02/09/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/07/2023]
Abstract
Terminal N-acetylglucosamine (GlcNAc) N-linked glycosylation is a truncated N-glycosylated modification that has been reported to be involved in various diseases, such as autoimmune diseases, cancers, and neurodegenerative diseases. New and simple tools will be always valuable for further characterization of the functions of this kind of glycosylation. Our previous paper proved that an optimized lectin created from Agrocybe aegerita GlcNAc selective lectin (AANL) named AANL6, can effectively identify O-GlcNAcylation, which is terminal GlcNAc O-linked glycosylation. We speculated that AANL6 could also be used to identify terminal GlcNAc N-linked glycosylation. Using therapeutic monoclonal antibodies as a model of terminal GlcNAc N-glycosylated proteins, we proved that AANL6 could selectively identify terminal GlcNAc N-linked glycosylation. The ratio of terminal GlcNAc N-linked glycosylation was increased by enrichment with AANL6 in human serum. Using cell membrane proteins as a complex sample, we found that AANL6 bound to the sperm surface, which expresses abundant terminal GlcNAc N-glycans, but did not bind to some tumor cell surfaces such A549 and MCF-7 cells, which is rich in high mannose glycoforms. In conclusion, AANL6 was identified as a powerful tool to probe terminal GlcNAc N-linked glycosylation and would be valuable for uncovering the function of this glycosylation.
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Affiliation(s)
- Yanting Su
- School of Basic Medical Sciences, Xianning Medical Colloge, Hubei University of Science and Technology, Xianning, 437100, PR China
| | - Yang Li
- College of Life Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Tianqing Meng
- Hubei Province Human Sperm Bank, Center of Reproductive Medicine, Wuhan Tongji Reproductive Medicine Hospital, Wuhan, PR China
| | - Bo Xu
- College of Life Sciences, Wuhan University, Wuhan, 430072, PR China
| | - He Zhu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Li Zhang
- Wuhan Huayang Animal Pharmaceutical Co., Ltd, Wuhan, PR China
| | - Xueqing Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Xiaomei Liu
- College of Life Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Hui Sun
- College of Life Sciences, Wuhan University, Wuhan, 430072, PR China; Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, 430072, PR China.
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7
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Peng W, Reyes CDG, Gautam S, Yu A, Cho BG, Goli M, Donohoo K, Mondello S, Kobeissy F, Mechref Y. MS-based glycomics and glycoproteomics methods enabling isomeric characterization. MASS SPECTROMETRY REVIEWS 2023; 42:577-616. [PMID: 34159615 PMCID: PMC8692493 DOI: 10.1002/mas.21713] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
Glycosylation is one of the most significant and abundant posttranslational modifications in mammalian cells. It mediates a wide range of biofunctions, including cell adhesion, cell communication, immune cell trafficking, and protein stability. Also, aberrant glycosylation has been associated with various diseases such as diabetes, Alzheimer's disease, inflammation, immune deficiencies, congenital disorders, and cancers. The alterations in the distributions of glycan and glycopeptide isomers are involved in the development and progression of several human diseases. However, the microheterogeneity of glycosylation brings a great challenge to glycomic and glycoproteomic analysis, including the characterization of isomers. Over several decades, different methods and approaches have been developed to facilitate the characterization of glycan and glycopeptide isomers. Mass spectrometry (MS) has been a powerful tool utilized for glycomic and glycoproteomic isomeric analysis due to its high sensitivity and rich structural information using different fragmentation techniques. However, a comprehensive characterization of glycan and glycopeptide isomers remains a challenge when utilizing MS alone. Therefore, various separation methods, including liquid chromatography, capillary electrophoresis, and ion mobility, were developed to resolve glycan and glycopeptide isomers before MS. These separation techniques were coupled to MS for a better identification and quantitation of glycan and glycopeptide isomers. Additionally, bioinformatic tools are essential for the automated processing of glycan and glycopeptide isomeric data to facilitate isomeric studies in biological cohorts. Here in this review, we discuss commonly employed MS-based techniques, separation hyphenated MS methods, and software, facilitating the separation, identification, and quantitation of glycan and glycopeptide isomers.
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Affiliation(s)
- Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | | | - Sakshi Gautam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Byeong Gwan Cho
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Kaitlyn Donohoo
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | | | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Departments of Emergency Medicine, University of Florida, Gainesville, Florida, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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8
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Madunić K, Luijkx YMCA, Mayboroda OA, Janssen GMC, van Veelen PA, Strijbis K, Wennekes T, Lageveen-Kammeijer GSM, Wuhrer M. O-Glycomic and Proteomic Signatures of Spontaneous and Butyrate-Stimulated Colorectal Cancer Cell Line Differentiation. Mol Cell Proteomics 2023; 22:100501. [PMID: 36669592 PMCID: PMC9999233 DOI: 10.1016/j.mcpro.2023.100501] [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: 03/13/2022] [Revised: 01/08/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Gut microbiota of the gastrointestinal tract provide health benefits to the human host via bacterial metabolites. Bacterial butyrate has beneficial effects on intestinal homeostasis and is the preferred energy source of intestinal epithelial cells, capable of inducing differentiation. It was previously observed that changes in the expression of specific proteins as well as protein glycosylation occur with differentiation. In this study, specific mucin O-glycans were identified that mark butyrate-induced epithelial differentiation of the intestinal cell line CaCo-2 (Cancer Coli-2), by applying porous graphitized carbon nano-liquid chromatography with electrospray ionization tandem mass spectrometry. Moreover, a quantitative proteomic approach was used to decipher changes in the cell proteome. It was found that the fully differentiated butyrate-stimulated cells are characterized by a higher expression of sialylated O-glycan structures, whereas fucosylation is downregulated with differentiation. By performing an integrative approach, we generated hypotheses about the origin of the observed O-glycome changes. These insights pave the way for future endeavors to study the dynamic O-glycosylation patterns in the gut, either produced via cellular biosynthesis or through the action of bacterial glycosidases as well as the functional role of these patterns in homeostasis and dysbiosis at the gut-microbiota interface.
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Affiliation(s)
- K Madunić
- Center for Proteomics and Metabolomics, Leiden University, The Netherlands
| | - Y M C A Luijkx
- Department Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands; Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - O A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University, The Netherlands
| | - G M C Janssen
- Center for Proteomics and Metabolomics, Leiden University, The Netherlands
| | - P A van Veelen
- Center for Proteomics and Metabolomics, Leiden University, The Netherlands
| | - K Strijbis
- Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - T Wennekes
- Department Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | | | - M Wuhrer
- Center for Proteomics and Metabolomics, Leiden University, The Netherlands.
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9
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Peng W, Kobeissy F, Mondello S, Barsa C, Mechref Y. MS-based glycomics: An analytical tool to assess nervous system diseases. Front Neurosci 2022; 16:1000179. [PMID: 36408389 PMCID: PMC9671362 DOI: 10.3389/fnins.2022.1000179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/05/2022] [Indexed: 08/27/2023] Open
Abstract
Neurological diseases affect millions of peopleochemistryorldwide and are continuously increasing due to the globe's aging population. Such diseases affect the nervous system and are characterized by a progressive decline in brain function and progressive cognitive impairment, decreasing the quality of life for those with the disease as well as for their families and loved ones. The increased burden of nervous system diseases demands a deeper insight into the biomolecular mechanisms at work during disease development in order to improve clinical diagnosis and drug design. Recently, evidence has related glycosylation to nervous system diseases. Glycosylation is a vital post-translational modification that mediates many biological functions, and aberrant glycosylation has been associated with a variety of diseases. Thus, the investigation of glycosylation in neurological diseases could provide novel biomarkers and information for disease pathology. During the last decades, many techniques have been developed for facilitation of reliable and efficient glycomic analysis. Among these, mass spectrometry (MS) is considered the most powerful tool for glycan analysis due to its high resolution, high sensitivity, and the ability to acquire adequate structural information for glycan identification. Along with MS, a variety of approaches and strategies are employed to enhance the MS-based identification and quantitation of glycans in neurological samples. Here, we review the advanced glycomic tools used in nervous system disease studies, including separation techniques prior to MS, fragmentation techniques in MS, and corresponding strategies. The glycan markers in common clinical nervous system diseases discovered by utilizing such MS-based glycomic tools are also summarized and discussed.
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Affiliation(s)
- Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL, United States
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Chloe Barsa
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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10
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Lageveen‐Kammeijer GSM, Kuster B, Reusch D, Wuhrer M. High sensitivity glycomics in biomedicine. MASS SPECTROMETRY REVIEWS 2022; 41:1014-1039. [PMID: 34494287 PMCID: PMC9788051 DOI: 10.1002/mas.21730] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 05/15/2023]
Abstract
Many analytical challenges in biomedicine arise from the generally high heterogeneity and complexity of glycan- and glycoconjugate-containing samples, which are often only available in minute amounts. Therefore, highly sensitive workflows and detection methods are required. In this review mass spectrometric workflows and detection methods are evaluated for glycans and glycoproteins. Furthermore, glycomic methodologies and innovations that are tailored for enzymatic treatments, chemical derivatization, purification, separation, and detection at high sensitivity are highlighted. The discussion is focused on the analysis of mammalian N-linked and GalNAc-type O-linked glycans.
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Affiliation(s)
| | - Bernhard Kuster
- Chair for Proteomics and BioanalyticsTechnical University of MunichFreisingGermany
| | - Dietmar Reusch
- Pharma Technical Development EuropeRoche Diagnostics GmbHPenzbergGermany
| | - Manfred Wuhrer
- Leiden University Medical CenterCenter for Proteomics and MetabolomicsLeidenThe Netherlands
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11
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Wang J, Dong X, Yu A, Huang Y, Peng W, Mechref Y. Isomeric separation of permethylated glycans by extra-long reversed-phase liquid chromatography (RPLC)-MS/MS. Analyst 2022; 147:2048-2059. [PMID: 35311852 PMCID: PMC9117491 DOI: 10.1039/d2an00010e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Glycosylation is known as a critical biological process that can largely affect the properties and the functions of proteins. Glycan isomers have been shown to be involved in a variety of disease progressions. However, the separation and identification of glycan isomers has been a challenge for years due to the microheterogeneity of glycan isomeric structures. Therefore, effective and stable techniques have been investigated over the last few decades to improve isomeric separations of glycans. RPLC has been widely used in biomolecule analysis because of its extraordinary reproducibility and reliability in retention time and separation resolution. However, so far, no studies have achieved high resolution of glycan isomers using this technique. In this study, we focused on further boosting the isomeric separation of permethylated glycans using a 500 mm reversed-phase LC column. To achieve better resolutions on permethylated glycans, different LC conditions were optimized using glycan standards, including core- and branch-fucosylated N-glycan isomers and sialic acid linked isomers, which were both successfully separated. Then, the optimal separation strategy was applied to achieve separations of N- and O-glycan isomers derived from model glycoproteins, including bovine fetuin, ribonuclease B and κ-casein. Baseline separations were observed on multiple sialylated linkage isomers. However, the separation performance of high-mannose isomers needs further improvement. The reproducibility and stability of this long C18 column was also tested by doing run-to-run, day-to-day and month-to-month comparisons of retention times on multiple glycans and the %RSD was found less than 0.92%. Finally, we applied this approach to separate glycan isomers derived from complex biological samples, including blood serum and cell lines, where baseline separations were attained on several isomeric structures. Compared to the separation efficiency of PGC and MGC columns, the RPLC C18 column provides lower resolution but more robust reproducibility, which makes it a good complementary alternative for isomeric separations of glycans.
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Affiliation(s)
- Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, USA.
| | - Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University, USA.
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, USA.
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, USA.
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, USA.
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, USA.
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12
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Sea Cucumber Body Vesicular Syndrome Is Driven by the Pond Water Microbiome via an Altered Gut Microbiota. mSystems 2022; 7:e0135721. [PMID: 35418244 PMCID: PMC9239130 DOI: 10.1128/msystems.01357-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Apostichopus japonicus (sea cucumber) is one of the most valuable aquaculture species in China; however, different diseases can limit its economic development. Recently, a novel disease, body vesicular syndrome (BVS), was observed in A. japonicus aquaculture. Diseased animals displayed no obvious phenotypic characteristics; however, after boiling at the postharvest stage, blisters, lysis, and body ruptures appeared. In this study, a multiomics strategy incorporating analysis of the gut microbiota, the pond microbiome, and A. japonicus genotype was established to investigate BVS. Detailed analyses of differentially expressed proteins (DEPs) and metabolites suggested that changes in cell adhesion structures, caused by disordered fatty acid β-oxidation mediated by vitamin B5 deficiency, could be a putative BVS mechanism. Furthermore, intestinal dysbacteriosis due to microbiome variations in pond water was considered a potential reason for vitamin B5 deficiency. Our BVS index, based on biomarkers identified from the A. japonicus gut microbiota, was a useful tool for BVS diagnosis. Finally, vitamin B5 supplementation was successfully used to treat BVS, suggesting an association with BVS etiology. IMPORTANCE Body vesicular syndrome (BVS) is a novel disease in sea cucumber aquaculture. As no phenotypic features are visible, BVS is difficult to confirm during aquaculture and postharvest activities, until animals are boiled. Therefore, BVS could lead to severe economic losses compared with other diseases in sea cucumber aquaculture. In this study, for the first time, we systematically investigated BVS pathogenesis and proposed an effective treatment for the condition. Moreover, based on the gut microbiota, we established a noninvasive diagnostic method for BVS in sea cucumber.
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13
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Tang W, Liu D, Nie SP. Food glycomics in food science: recent advances and future perspectives. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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14
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Wu E, Guo X, Teng X, Zhang R, Li F, Cui Y, Zhang D, Liu Q, Luo J, Wang J, Chen R. Discovery of Plasma Membrane-Associated RNAs through APEX-seq. Cell Biochem Biophys 2021; 79:905-917. [PMID: 34028638 DOI: 10.1007/s12013-021-00991-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2021] [Indexed: 02/08/2023]
Abstract
In addition to nucleic acids, a variety of other biomolecules have also been found on the plasma membrane. Although researchers have realized that RNA has the ability to bind to membrane vesicles in vitro, little is known about whether and how RNA connects to the plasma membrane of the cell. The combination of high-throughput sequencing and in situ labeling methods provides an innovative approach for large-scale identification of subcellular RNAs. Here, we applied the recently published method APEX-seq and identified 75 RNAs related to the plasma membrane, in which lncRNA PMAR72 (plasma membrane-associated RNA AL121772.1) has a considerable affinity with sphingomyelin (SM) and localizes within distinct membrane foci. Our findings will provide some new evidence to elaborate the relationship between RNA and the plasma membrane of mammalian cells.
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Affiliation(s)
- Erzhong Wu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xuzhen Guo
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xueyi Teng
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Ruijin Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Fahui Li
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ya Cui
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Dongdong Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Qinghua Liu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jianjun Luo
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Jiangyun Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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15
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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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16
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Donohoo KB, Wang J, Goli M, Yu A, Peng W, Hakim MA, Mechref Y. Advances in mass spectrometry-based glycomics-An update covering the period 2017-2021. Electrophoresis 2021; 43:119-142. [PMID: 34505713 DOI: 10.1002/elps.202100199] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/21/2022]
Abstract
The wide variety of chemical properties and biological functions found in proteins is attained via post-translational modifications like glycosylation. Covalently bonded to proteins, glycans play a critical role in cell activity. Complex structures with microheterogeneity, the glycan structures that are associated with proteins are difficult to analyze comprehensively. Recent advances in sample preparation methods, separation techniques, and MS have facilitated the quantitation and structural elucidation of glycans. This review focuses on highlighting advances in MS-based techniques for glycomic analysis that occurred over the last 5 years (2017-2021) as an update to the previous review on the subject. The topics of discussion will include progress in glycomic workflow such as glycan release, purification, derivatization, and separation as well as the topics of ionization, tandem MS, and separation techniques that can be coupled with MS. Additionally, bioinformatics tools used for the analysis of glycans will be described.
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Affiliation(s)
- Kaitlyn B Donohoo
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Md Abdul Hakim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
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17
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Liu X, Song N, Qian D, Gu S, Pu J, Huang L, Liu J, Qian K. Porous Inorganic Materials for Bioanalysis and Diagnostic Applications. ACS Biomater Sci Eng 2021; 8:4092-4109. [PMID: 34494831 DOI: 10.1021/acsbiomaterials.1c00733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Porous inorganic materials play an important role in adsorbing targeted analytes and supporting efficient reactions in analytical science. The detection performance relies on the structural properties of porous materials, considering the tunable pore size, shape, connectivity, etc. Herein, we first clarify the enhancement mechanisms of porous materials for bioanalysis, concerning the detection sensitivity and selectivity. The diagnostic applications of porous material-assisted platforms by coupling with various analytical techniques, including electrochemical sensing, optical spectrometry, and mass spectrometry, etc., are then reviewed. We foresee that advanced porous materials will bring far-reaching implications in bioanalysis toward real-case applications, especially as diagnostic assays in clinical settings.
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Affiliation(s)
- Xun Liu
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Naikun Song
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Dahong Qian
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Sai Gu
- School of Engineering, University of Warwick, Coventry CV4 7AL, W Midlands, England.,Department of Chemical and Process Engineering, University of Surrey, Guildford, Surrey GU27XH, United Kingdom
| | - Jun Pu
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, P. R. China
| | - Lin Huang
- Stem Cell Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, P. R. China
| | - Jian Liu
- Department of Chemical and Process Engineering, University of Surrey, Guildford, Surrey GU27XH, United Kingdom.,Chinese Academy of Sciences, Dalian Institute of Chemical Physics, CAS State Key Laboratory of Catalysis, 568 Zhongshan Road, Dalian 116023, P. R. China
| | - Kun Qian
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, P. R. China.,Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, P. R. China
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18
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Castillo JJ, Galermo AG, Amicucci MJ, Nandita E, Couture G, Bacalzo N, Chen Y, Lebrilla CB. A Multidimensional Mass Spectrometry-Based Workflow for De Novo Structural Elucidation of Oligosaccharides from Polysaccharides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2175-2185. [PMID: 34261322 PMCID: PMC8344699 DOI: 10.1021/jasms.1c00133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/09/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Carbohydrates play essential roles in a variety of biological processes that are dictated by their structures. However, characterization of carbohydrate structures remains extremely difficult and generally unsolved. In this work, a de novo mass spectrometry-based workflow was developed to isolate and structurally elucidate oligosaccharides to provide sequence, monosaccharide compositions, and glycosidic linkage positions. The approach employs liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based methods in a 3-dimensional concept: one high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (HPLC-QTOF MS) analysis for oligosaccharide sequencing and two ultra high performance liquid chromatography-triple quadrupole mass spectrometry (UHPLC-QqQ MS) analyses on fractionated oligosaccharides to determine their monosaccharides and linkages compositions. The workflow was validated by applying the procedure to maltooligosaccharide standards. The approach was then used to determine the structures of oligosaccharides derived from polysaccharide standards and whole food products. The integrated LC-MS workflow will reveal the in-depth structures of oligosaccharides.
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Affiliation(s)
- Juan Jose Castillo
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
| | - Ace G. Galermo
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
| | - Matthew J. Amicucci
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
- Agricultural and Environmental Chemistry Graduate
Group, University of California Davis, Davis, California 95616,
United States
| | - Eshani Nandita
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
| | - Garret Couture
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
| | - Nikita Bacalzo
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
| | - Ye Chen
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of
California Davis, Davis, California 95616, United
States
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19
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A mass spectrometry-based glycotope-centric cellular glycomics is the more fruitful way forward to see the forest for the trees. Biochem Soc Trans 2021; 49:55-69. [PMID: 33492355 DOI: 10.1042/bst20190861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 02/08/2023]
Abstract
The nature of protein glycosylation renders cellular glycomics a very challenging task in having to deal with all the disparate glycans carried on membrane glycoproteins. Rapid mapping by mass spectrometry analysis provides only a coarse sketch of the glycomic complexity based primarily on glycosyl compositions, whereby the missing high-resolution structural details require a combination of multi-mode separations and multi-stages of induced fragmentation to gain sufficiently discriminative precision, often at the expenses of throughput and sensitivity. Given the available technology and foreseeable advances in the near future, homing in on resolving the terminal fucosylated, sialylated and/or sulfated structural units, or glycotopes, maybe a more pragmatic and ultimately more rewarding approach to gain insights into myriad biological processes mediated by these terminal coding units carried on important glycoproteins, to be decoded by a host of endogenous glycan-binding proteins and antibodies. A broad overview of recent technical advances and limitations in cellular glycomics is first provided as a backdrop to the propounded glycotope-centric approach based on advanced nanoLC-MS2/MS3 analysis of permethylated glycans. To prioritize analytical focus on the more tangible glycotopes is akin to first identifying the eye-catching and characteristic-defining flowers and fruits of the glyco-forest, to see the forest for the trees. It has the best prospects of attaining the much-needed balance in sensitivity, structural precision and analytical throughput to match advances in other omics.
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20
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Lu L, Riley NM, Shortreed MR, Bertozzi CR, Smith LM. O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nat Methods 2020. [PMID: 33106676 DOI: 10.1101/2020.05.18.102327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
We report O-Pair Search, an approach to identify O-glycopeptides and localize O-glycosites. Using paired collision- and electron-based dissociation spectra, O-Pair Search identifies O-glycopeptides via an ion-indexed open modification search and localizes O-glycosites using graph theory and probability-based localization. O-Pair Search reduces search times more than 2,000-fold compared to current O-glycopeptide processing software, while defining O-glycosite localization confidence levels and generating more O-glycopeptide identifications. Beyond the mucin-type O-glycopeptides discussed here, O-Pair Search also accepts user-defined glycan databases, making it compatible with many types of O-glycosylation. O-Pair Search is freely available within the open-source MetaMorpheus platform at https://github.com/smith-chem-wisc/MetaMorpheus .
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Affiliation(s)
- Lei Lu
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Nicholas M Riley
- Department of Chemistry, University of Stanford, Stanford, CA, USA
| | | | - Carolyn R Bertozzi
- Department of Chemistry, University of Stanford, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI, USA.
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21
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Cho BG, Peng W, Mechref Y. Separation of Permethylated O-Glycans, Free Oligosaccharides, and Glycosphingolipid-Glycans Using Porous Graphitized Carbon (PGC) Column. Metabolites 2020; 10:metabo10110433. [PMID: 33121051 PMCID: PMC7692250 DOI: 10.3390/metabo10110433] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 01/01/2023] Open
Abstract
Glycosylation is one of the most common and complex post-translational modifications of proteins. However, there are other carbohydrates such as free oligosaccharides and glycosphingolipids-glycans that are associated with important biological and clinical roles. To analyze these molecules using liquid chromatography coupled with mass spectrometry (LC-MS), the permethylation approach was utilized. Although permethylation is a commonly utilized glycan derivatization technique, separation of permethylated glycans released from glycosphingolipid (GSL) by LC-MS has never been previously demonstrated. Here, a nanoflow porous graphitized carbon (PGC) column coupled with a high-resolution mass spectrometer was used to achieve isomeric separation of these permethylated glycans. We demonstrate the separation of free reducing end and reduced end O-glycans, free oligosaccharides derived from human milk, and GSL glycans derived from the MDA-MB-231BR cancer cell line using PGC-LC-MS.
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22
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Lu L, Riley NM, Shortreed MR, Bertozzi CR, Smith LM. O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nat Methods 2020; 17:1133-1138. [PMID: 33106676 PMCID: PMC7606753 DOI: 10.1038/s41592-020-00985-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/21/2020] [Indexed: 11/23/2022]
Abstract
We report O-Pair Search, a new approach to identify O-glycopeptides and localize O-glycosites. Using paired collision- and electron-based dissociation spectra, O-Pair Search identifies O-glycopeptides using an ion-indexed open modification search and localizes O-glycosites using graph theory and probability-based localization. O-Pair Search reduces search times more than 2,000-fold compared to current O-glycopeptide processing software, while defining O-glycosite localization confidence levels and generating more O-glycopeptide identifications. Beyond the mucin-type O-glycopeptides discussed here, O-Pair Search also accepts user-defined glycan databases, making it compatible with many types of O-glycosylation. O-Pair Search is freely available within the open-source MetaMorpheus platform at https://github.com/smith-chem-wisc/MetaMorpheus.
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Affiliation(s)
- Lei Lu
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Nicholas M Riley
- Department of Chemistry, University of Stanford, Stanford, CA, USA
| | | | - Carolyn R Bertozzi
- Department of Chemistry, University of Stanford, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford, CA, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI, USA.
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23
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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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