1
|
Jirmo AC, Rossdam C, Grychtol R, Happle C, Gerardy‐Schahn R, Buettner FFR, Hansen G. Differential expression patterns of glycosphingolipids and C-type lectin receptors on immune cells in absence of functional regulatory T cells. IMMUNITY INFLAMMATION AND DISEASE 2020; 8:512-522. [PMID: 32737949 PMCID: PMC7654419 DOI: 10.1002/iid3.334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/03/2020] [Accepted: 07/20/2020] [Indexed: 02/05/2023]
Abstract
Background Glycosylation is a common and complex type of protein posttranslational modification. Altered glycosylation of immunoglobulins in autoimmune diseases has led to the “altered glycan hypothesis” postulating existence of a unique glycan signature on immune cells and extracellular proteins characterized by site‐specific relative abundances of individual glycan structures and glycosylation patterns. However, it is not clear how glycosylation on leukocyte subpopulations differ between states of health or inflammation. Hypothesis Glycosphingolipid patterns on immune cells of forkhead‐box‐P3‐deficient scurfy mice differs from those on wild‐type immune cells. Methods T cells and dendritic cells were isolated from spleens of either wild‐type or age‐matched scurfy mice. Glycosphingolipids of CD4+ T cells and splenic dendritic cells from wild‐type and scurfy mice were then analyzed by multiplexed capillary gel electrophoresis coupled to laser‐induced fluorescence detection (xCGE‐LIF). In addition, flow cytometry and ChipCytometry were used to access expression patterns of various C‐type lectin receptors on antigen‐presenting cells from various organs of both wild‐type and scurfy mice. Results We, hereby report differential expression of glycosphingolipids in health and under inflammatory conditions as reflected in wild‐type and scurfy mice. Furthermore, we observed that the absence of functional regulatory T cells correlated with elevated expression of CLEC‐7A and CD205 but a reduction in levels of CLEC12A and CD206 on antigen‐presenting cells. Conclusion We hereby show that the absence of functional regulatory T cells affects expression pattern and quantities of glycosphingolipids on immune cells. Thus, glycosphingolipids could serve as biomarkers for mapping genetical and homeostatic perturbances such as those resulting from a diseased condition.
Collapse
Affiliation(s)
- Adan C. Jirmo
- Department of Pediatric Pneumology, Allergology and NeonatologyHannover Medical SchoolHannoverGermany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH)German Center for Lung Research (DZL)HannoverGermany
| | - Charlotte Rossdam
- Institute of Clinical BiochemistryHannover Medical SchoolHannoverGermany
| | - Ruth Grychtol
- Department of Pediatric Pneumology, Allergology and NeonatologyHannover Medical SchoolHannoverGermany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH)German Center for Lung Research (DZL)HannoverGermany
| | - Christine Happle
- Department of Pediatric Pneumology, Allergology and NeonatologyHannover Medical SchoolHannoverGermany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH)German Center for Lung Research (DZL)HannoverGermany
| | - Rita Gerardy‐Schahn
- Institute of Clinical BiochemistryHannover Medical SchoolHannoverGermany
- Excellence Cluster RESIST (EXC 2155)Hannover Medical SchoolHannoverGermany
| | | | - Gesine Hansen
- Department of Pediatric Pneumology, Allergology and NeonatologyHannover Medical SchoolHannoverGermany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH)German Center for Lung Research (DZL)HannoverGermany
- Excellence Cluster RESIST (EXC 2155)Hannover Medical SchoolHannoverGermany
| |
Collapse
|
2
|
Wang H, Leeming MG, Ho J, Donald WA. Origin and Prediction of Highly Specific Bond Cleavage Sites in the Thermal Activation of Intact Protein Ions. Chemistry 2018; 25:823-834. [DOI: 10.1002/chem.201804668] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Huixin Wang
- School of Chemistry University of New South Wales Sydney New South Wales Australia
| | - Michael G. Leeming
- School of Chemistry, Bio21 Institute of Molecular Science and Biotechnology The University of Melbourne Melbourne Victoria Australia
| | - Junming Ho
- School of Chemistry University of New South Wales Sydney New South Wales Australia
| | - William A. Donald
- School of Chemistry University of New South Wales Sydney New South Wales Australia
| |
Collapse
|
3
|
Narimatsu H, Kaji H, Vakhrushev SY, Clausen H, Zhang H, Noro E, Togayachi A, Nagai-Okatani C, Kuno A, Zou X, Cheng L, Tao SC, Sun Y. Current Technologies for Complex Glycoproteomics and Their Applications to Biology/Disease-Driven Glycoproteomics. J Proteome Res 2018; 17:4097-4112. [PMID: 30359034 DOI: 10.1021/acs.jproteome.8b00515] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glycoproteomics is an important recent advance in the field of glycoscience. In glycomics, glycan structures are comprehensively analyzed after glycans are released from glycoproteins. However, a major limitation of glycomics is the lack of insight into glycoprotein functions. The Biology/Disease-driven Human Proteome Project has a particular focus on biological and medical applications. Glycoproteomics technologies aimed at obtaining a comprehensive understanding of intact glycoproteins, i.e., the kind of glycan structures that are attached to particular amino acids and proteins, have been developed. This Review focuses on the recent progress of the technologies and their applications. First, the methods for large-scale identification of both N- and O-glycosylated proteins are summarized. Next, the progress of analytical methods for intact glycopeptides is outlined. MS/MS-based methods were developed for improving the sensitivity and speed of the mass spectrometer, in parallel with the software for complex spectrum assignment. In addition, a unique approach to identify intact glycopeptides using MS1-based accurate masses is introduced. Finally, as an advance of glycomics, two approaches to provide the spatial distribution of glycans in cells are described, i.e., MS imaging and lectin microarray. These methods allow rapid glycomic profiling of different types of biological samples and thus facilitate glycoproteomics.
Collapse
Affiliation(s)
- Hisashi Narimatsu
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Hiroyuki Kaji
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics , University of Copenhagen , Blegdamsvej 3 , Copenhagen 2200 , Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics , University of Copenhagen , Blegdamsvej 3 , Copenhagen 2200 , Denmark
| | - Hui Zhang
- Center for Biomarker Discovery and Translation , Johns Hopkins University , 400 North Broadway , Baltimore , Maryland 21205 , United States
| | - Erika Noro
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Akira Togayachi
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Chiaki Nagai-Okatani
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Atsushi Kuno
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Xia Zou
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan.,Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Li Cheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Yangyang Sun
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| |
Collapse
|
4
|
Videira PAQ, Castro-Caldas M. Linking Glycation and Glycosylation With Inflammation and Mitochondrial Dysfunction in Parkinson's Disease. Front Neurosci 2018; 12:381. [PMID: 29930494 PMCID: PMC5999786 DOI: 10.3389/fnins.2018.00381] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/18/2018] [Indexed: 01/08/2023] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disorder, affecting about 6.3 million people worldwide. PD is characterized by the progressive degeneration of dopaminergic neurons in the Substantia nigra pars compacta, resulting into severe motor symptoms. The cellular mechanisms underlying dopaminergic cell death in PD are still not fully understood, but mitochondrial dysfunction, oxidative stress and inflammation are strongly implicated in the pathogenesis of both familial and sporadic PD cases. Aberrant post-translational modifications, namely glycation and glycosylation, together with age-dependent insufficient endogenous scavengers and quality control systems, lead to cellular overload of dysfunctional proteins. Such injuries accumulate with time and may lead to mitochondrial dysfunction and exacerbated inflammatory responses, culminating in neuronal cell death. Here, we will discuss how PD-linked protein mutations, aging, impaired quality control mechanisms and sugar metabolism lead to up-regulated abnormal post-translational modifications in proteins. Abnormal glycation and glycosylation seem to be more common than previously thought in PD and may underlie mitochondria-induced oxidative stress and inflammation in a feed-forward mechanism. Moreover, the stress-induced post-translational modifications that directly affect parkin and/or its substrates, deeply impairing its ability to regulate mitochondrial dynamics or to suppress inflammation will also be discussed. Together, these represent still unexplored deleterious mechanisms implicated in neurodegeneration in PD, which may be used for a more in-depth knowledge of the pathogenic mechanisms, or as biomarkers of the disease.
Collapse
Affiliation(s)
- Paula A Q Videira
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal.,CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Margarida Castro-Caldas
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal.,Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
5
|
Yamagaki T, Makino Y. Fragmentation of Oligosaccharides from Sodium Adduct Molecules Depends on the Position of N-Acetyl Hexosamine Residue in Their Sequences in Mass Spectrometry. ACTA ACUST UNITED AC 2017; 6:S0073. [PMID: 28959518 DOI: 10.5702/massspectrometry.s0073] [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] [Received: 04/15/2017] [Accepted: 08/05/2017] [Indexed: 11/23/2022]
Abstract
Six different sequences of hexasaccharides, pyridylaminated malto-hexaoses containing one N-acetyl hexosamine (HexNAc) residue, were analyzed using matrix-assisted laser desorption/ionization (MALDI) tandem time-of-flight (TOF) mass spectrometry (MS). Based on the product ion spectra of sodium adducts [M+Na]+, the chemical species of the observed product ions contained a HexNAc residue and had high ion abundance, indicating that the HexNAc residue had a higher affinity to sodium atom than glucopyranose. The acetamide group coordinated easily to sodium atom. This general rule of product ion generation was useful to predict the structure of the oligosaccharides based on the MS/MS product ion spectra.
Collapse
Affiliation(s)
- Tohru Yamagaki
- Bioorganic Research Institute, Suntory Foundation for Life Sciences
| | - Yasushi Makino
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University
| |
Collapse
|
6
|
Hu H, Khatri K, Zaia J. Algorithms and design strategies towards automated glycoproteomics analysis. MASS SPECTROMETRY REVIEWS 2017; 36:475-498. [PMID: 26728195 PMCID: PMC4931994 DOI: 10.1002/mas.21487] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/30/2015] [Indexed: 05/09/2023]
Abstract
Glycoproteomics involves the study of glycosylation events on protein sequences ranging from purified proteins to whole proteome scales. Understanding these complex post-translational modification (PTM) events requires elucidation of the glycan moieties (monosaccharide sequences and glycosidic linkages between residues), protein sequences, as well as site-specific attachment of glycan moieties onto protein sequences, in a spatial and temporal manner in a variety of biological contexts. Compared with proteomics, bioinformatics for glycoproteomics is immature and many researchers still rely on tedious manual interpretation of glycoproteomics data. As sample preparation protocols and analysis techniques have matured, the number of publications on glycoproteomics and bioinformatics has increased substantially; however, the lack of consensus on tool development and code reuse limits the dissemination of bioinformatics tools because it requires significant effort to migrate a computational tool tailored for one method design to alternative methods. This review discusses algorithms and methods in glycoproteomics, and refers to the general proteomics field for potential solutions. It also introduces general strategies for tool integration and pipeline construction in order to better serve the glycoproteomics community. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:475-498, 2017.
Collapse
Affiliation(s)
- Han Hu
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Kshitij Khatri
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| |
Collapse
|
7
|
Sumner LW, Lei Z, Nikolau BJ, Saito K. Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects. Nat Prod Rep 2015; 32:212-29. [PMID: 25342293 DOI: 10.1039/c4np00072b] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plant metabolomics has matured and modern plant metabolomics has accelerated gene discoveries and the elucidation of a variety of plant natural product biosynthetic pathways. This review covers the approximate period of 2000 to 2014, and highlights specific examples of the discovery and characterization of novel genes and enzymes associated with the biosynthesis of natural products such as flavonoids, glucosinolates, terpenoids, and alkaloids. Additional examples of the integration of metabolomics with genome-based functional characterizations of plant natural products that are important to modern pharmaceutical technology are also reviewed. This article also provides a substantial review of recent technical advances in mass spectrometry imaging, nuclear magnetic resonance imaging, integrated LC-MS-SPE-NMR for metabolite identifications, and X-ray crystallography of microgram quantities for structural determinations. The review closes with a discussion on the future prospects of metabolomics related to crop species and herbal medicine.
Collapse
Affiliation(s)
- Lloyd W Sumner
- The Samuel Roberts Noble Foundation, Plant Biology Division, 2510 Sam Noble Parkway, Ardmore, OK, USA.
| | | | | | | |
Collapse
|
8
|
Narimatsu H. Development of M2BPGi: a novel fibrosis serum glyco-biomarker for chronic hepatitis/cirrhosis diagnostics. Expert Rev Proteomics 2015; 12:683-93. [PMID: 26394846 DOI: 10.1586/14789450.2015.1084874] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many proteins in the living body are glycoproteins, which present glycans linked on their surface. Glycan structures reflect the degree of cell differentiation or canceration and are cell specific. These characteristics are advantageous in the development of various disease biomarkers. Glycoprotein-based biomarkers (glyco-biomarkers) are developed by utilizing the specific changes in the glycan structure on a glycoprotein secreted from the diseased cells of interest. Therefore, quantification of the altered glycan structures is the key to developing a new glyco-biomarker. Glycoscience is a relatively new area of molecular science, and recent advancement of glycotechnologies is remarkable. In the author's institute, new glycoscience technologies have been designed to be efficiently utilized for the development of new diagnostic agents. This paper introduces a strategy for glyco-biomarker development, which was successfully applied in the development of Wisteria floribunda agglutinin-positive Mac-2 binding protein M2BPGi, a liver fibrosis marker now commercially available for clinical use.
Collapse
Affiliation(s)
- Hisashi Narimatsu
- a Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
| |
Collapse
|
9
|
KAMEYAMA A, KIKUCHI N, NAKAYA S, FUNATSU S. Development of a rapid analytical system for glycans using a multistage tandem mass spectral database. ACTA ACUST UNITED AC 2015. [DOI: 10.5571/syntheng.8.4_196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
| | - Norihiro KIKUCHI
- Business Development Division, Mitsui Knowledge Industry Co., Ltd
| | - Shuuichi NAKAYA
- Analytical & Measuring Instruments Division, Shimadzu Corporation
| | - Shinji FUNATSU
- Analytical & Measuring Instruments Division, Shimadzu Corporation
| |
Collapse
|
10
|
Xue J, Laine RA, Matta KL. Enhancing MS(n) mass spectrometry strategy for carbohydrate analysis: A b2 ion spectral library. J Proteomics 2014; 112:224-49. [PMID: 25175058 DOI: 10.1016/j.jprot.2014.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/24/2014] [Accepted: 07/12/2014] [Indexed: 11/24/2022]
Abstract
UNLABELLED Searchable mass spectral libraries for glycans may be enhanced using a B2 ion library. Using a quadrupole ion-trap mass spectrometer, successive fragmentations of sodiated oligosaccharides were carried out in the positive ion mode. In B,Y-type fragmentation, disaccharide B2 ions are generated which correspond to specific glycosidic linkages using progressive MS stages. Fragmentation of "B2 ions" corresponding to glycosidic linkages such as Hex-Fuc, Hex-Hex, Hex-HexNAc, HexNAc-Hex and HexNAc-HexNAc, were systematically studied in low energy CID and collected to form a "B2 library". Linkages produce characteristic fragmentation patterns in the absence of cross-ring fragmentation. Patterns of "B2 ions" rely on relative stability of glycosidic bonds and carbohydrate-metal complexes in the gas phase. MS(n) studies of linear, branched trisaccharides and tetrasaccharides show that isomers for which B2 ion information is not available are rarely a problem in practice by their absence in an isomeric sequence or by their scarcity in nature. This MS strategy for linkage determination of carbohydrates aided by a "B2 library" was developed with a scope for expansion, providing an improved tool for glycomics. We validated this method examining levels of expressed activities of two glycosyl transferases in cancer cell lines: β3(B3GALNT2) and β4GalNAcT(B4GALNT3&4) that generate GalNAcβ3GlcNAcβ and GalNAcβ4GlcNAcβ. BIOLOGICAL SIGNIFICANCE Glycosylation is an important class of the "postranslationome", which includes manifold aspects of post-translational protein modification, affecting protein conformation, providing ligands for protein receptors [1-5], and encoding unique haptenic [6,7] or antigenic markers for oncology [8-11] and other applications. Identification of individual monomeric units, linkages, ring size, branching and anomerity has posed significant challenges to mass spectrometrists. MS(n) is a growing key instrumental method to differentiate among isomers [12]. While the potential isomers in oligosaccharides are impossibly large [12], likely possibilities can be limited by the biological system, including the expressed glycosyl transferases [13-20]. Mass spectra from sequential stages of collision activation (MS(n)) can supply structural details for precise characterization of linkage, monomer ID, substitutions, anomerity and branching [21-25]. There is a fundamental need for high throughput tools in glycomics to complement proteome studies. In that regard, nothing could be more important than searchable spectral library files for structural confirmation. The National Academy of Science (NAS) report (http://glyco.nas.edu) recommends the need of more than 10,000 synthetic structures of carbohydrates to advance the field of glycomics. This study demonstrates that the general reproducibility of ion trap spectra, and energy independence from modes of ionization and collisional activation, make compiling an MS(n) library for carbohydrate identification an achievable research target [26]. We intend to use the new B2 library for carbohydrate differences found on cancers, where we profile the glycosyltransferases to predict classes of potential structures, and use the library for MS identification of the expected cohort of altered structures.
Collapse
Affiliation(s)
- Jun Xue
- Department of Cancer Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Roger A Laine
- Departments of Biological Sciences and Chemistry, Louisiana State University and A&M College, Baton Rouge, LA 70803, USA; TumorEnd, LLC, Louisiana Emerging Technology Center, Baton Rouge, LA 70803, USA.
| | - Khushi L Matta
- Department of Cancer Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA; TumorEnd, LLC, Louisiana Emerging Technology Center, Baton Rouge, LA 70803, USA.
| |
Collapse
|
11
|
Yamagaki T, Sugahara K, Watanabe T. Amino and acetamide functional group effects on the ionization and fragmentation of sugar chains in positive-ion mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:95-103. [PMID: 24154946 PMCID: PMC3880478 DOI: 10.1007/s13361-013-0739-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 07/31/2013] [Accepted: 08/07/2013] [Indexed: 06/02/2023]
Abstract
To elucidate the influence of amino (-NH2) and acetamide (-NHCOCH3, -NAc) groups in sugar chains on their ionization and fragmentation, cycloamyloses (cyclodextrins, CyDs) and lacto-oligosaccharide are analyzed by MALDI TOF/TOF and ESI Q-TOF mass spectrometry. CyD derivatives substituted by amino or acetamide groups are ideal analytes to extract the function group effects, which are amino-CyD with one hexosamine (HexNH2) and acetamide-CyD with one N-acetyl hexosamine (HexNAc). Interestingly, the relative ion intensities and isotope-like patterns in their product ion spectra depend on the functional groups and ion forms of sugar chains. Consequently, the results indicate that a proton (H(+)) localizes on the amino group of the amino sugar, and that the proton (H(+)) induces their fragmentation. Sodium cation (Na(+)) attachment is independent from amino group and exerts no influence on their fragmentation patterns in amino group except for mono- and disaccharide fragment ions because there is the possibility of the reducing end effect. In contrast, a sodium cation localizes much more frequently on the acetamide group in acetamide-CyDs because the chemical species with HexNAc are stable. Thus, their ions with HexNAc are abundant. These results are consistent with the fragmentation of lacto-neo-N-tetraose and maltotetraose, suggesting that a sodium cation generally localizes much more frequently on the acetamide group in sugar chains.
Collapse
Affiliation(s)
- Tohru Yamagaki
- Suntory Institute for Bioorganic Research, Mishima, Osaka, 618-8503, Japan,
| | | | | |
Collapse
|
12
|
Leung KSY, Fong BMW. LC–MS/MS in the routine clinical laboratory: has its time come? Anal Bioanal Chem 2013; 406:2289-301. [DOI: 10.1007/s00216-013-7542-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/18/2013] [Accepted: 11/28/2013] [Indexed: 11/30/2022]
|
13
|
Scheubert K, Hufsky F, Böcker S. Computational mass spectrometry for small molecules. J Cheminform 2013; 5:12. [PMID: 23453222 PMCID: PMC3648359 DOI: 10.1186/1758-2946-5-12] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 02/01/2013] [Indexed: 12/29/2022] Open
Abstract
: The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from the identification of a compound searching a reference spectral library, to the structural elucidation of unknowns. In detail, we describe the basic principles and pitfalls of searching mass spectral reference libraries. Determining the molecular formula of the compound can serve as a basis for subsequent structural elucidation; consequently, we cover different methods for molecular formula identification, focussing on isotope pattern analysis. We then discuss automated methods to deal with mass spectra of compounds that are not present in spectral libraries, and provide an insight into de novo analysis of fragmentation spectra using fragmentation trees. In addition, this review shortly covers the reconstruction of metabolic networks using MS data. Finally, we list available software for different steps of the analysis pipeline.
Collapse
Affiliation(s)
- Kerstin Scheubert
- Chair of Bioinformatics, Friedrich Schiller University, Ernst-Abbe-Platz 2, Jena, Germany.
| | | | | |
Collapse
|
14
|
Toyama A, Nakagawa H, Matsuda K, Sato TA, Nakamura Y, Ueda K. Quantitative structural characterization of local N-glycan microheterogeneity in therapeutic antibodies by energy-resolved oxonium ion monitoring. Anal Chem 2012; 84:9655-62. [PMID: 23004563 DOI: 10.1021/ac3023372] [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
Site-specific characterization of glycoform heterogeneity currently requires glycan structure assignment and glycopeptide quantification in two independent experiments. We present here a new method combining multiple reaction monitoring mass spectrometry with energy-resolved structural analysis, which we termed "energy-resolved oxonium ion monitoring". We demonstrated that monitoring the yields of oligosaccharide-derived fragment ions (oxonium ions) over a wide range of collision induced dissociation (CID) energy applied to a glycopeptide precursor exhibits a glycan structure-unique fragmentation pattern. In the analysis of purified immunoglobulin glycopeptides, the energy-resolved oxonium ion profile was shown to clearly distinguish between isomeric glycopeptides. Moreover, limit of detection (LOD) of glycopeptide detection was 30 attomole injection, and quantitative dynamic range spanned 4 orders magnitude. Therefore, both quantification of glycopeptides and assignment of their glycan structures were achieved by a simple analysis procedure. We assessed the utility of this method for characterizing site-specific N-glycan microheterogeneity on therapeutic antibodies, including validation of lot-to-lot glycoform variability. A significant change in the degree of terminal galactosylation was observed in different production lots of trastuzumab and bevacizumab. Cetuximab Fab glycosylation, previously known to cause anaphylaxis, was also analyzed, and several causative antigens including Lewis X motifs were quantitatively detected. The data suggests that energy-resolved oxonium ion monitoring could fulfill the regulatory requirement on the routine quality control analysis of forthcoming biosimilar therapeutics.
Collapse
Affiliation(s)
- Atsuhiko Toyama
- Life Science Research Center, Shimadzu Corporation, Kanda-Nishikicho 1, Chiyoda-ku, Tokyo, Japan
| | | | | | | | | | | |
Collapse
|
15
|
Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005-2006. MASS SPECTROMETRY REVIEWS 2011; 30:1-100. [PMID: 20222147 DOI: 10.1002/mas.20265] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This review is the fourth update of the original review, 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 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI-MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate-protein complexes and glycodendrimers are highlighted in this final section.
Collapse
Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK.
| |
Collapse
|
16
|
Cortes DF, Kabulski JL, Lazar AC, Lazar IM. Recent advances in the MS analysis of glycoproteins: Capillary and microfluidic workflows. Electrophoresis 2011; 32:14-29. [PMID: 21171110 PMCID: PMC3717299 DOI: 10.1002/elps.201000394] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/21/2010] [Accepted: 09/21/2010] [Indexed: 12/26/2022]
Abstract
Recent developments in bioanalytical instrumentation, MS detection, and computational data analysis approaches have provided researchers with capabilities for interrogating the complex cellular glycoproteome, to help gain a better insight into the cellular and physiological processes that are associated with a disease and to facilitate the efforts centered on identifying disease-specific biomarkers. This review describes the progress achieved in the characterization of protein glycosylation by using advanced capillary and microfluidic MS technologies. The major steps involved in large-scale glycoproteomic analysis approaches are discussed, with special emphasis given to workflows that have evolved around complex MS detection functions. In addition, quantitative analysis strategies are assessed, and the bioinformatics aspects of glycoproteomic data processing are summarized. The developments in commercial and custom fabricated microfluidic front-end platforms to ESI- and MALDI-MS instrumentation, for addressing major challenges in carbohydrate analysis such as sensitivity, throughput, and ability to perform structural characterization, are further evaluated and illustrated with relevant examples.
Collapse
Affiliation(s)
- Diego F. Cortes
- Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University Washington St. Bio II/283, Blacksburg, VA 24061
| | - Jarod L. Kabulski
- Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University Washington St. Bio II/283, Blacksburg, VA 24061
| | | | - Iulia M. Lazar
- Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University Washington St. Bio II/283, Blacksburg, VA 24061
- Department of Biological Sciences, Virginia Polytechnic Institute and State University Washington St. Bio II/283, Blacksburg, VA 24061
| |
Collapse
|
17
|
Kind T, Fiehn O. Advances in structure elucidation of small molecules using mass spectrometry. BIOANALYTICAL REVIEWS 2010; 2:23-60. [PMID: 21289855 PMCID: PMC3015162 DOI: 10.1007/s12566-010-0015-9] [Citation(s) in RCA: 303] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 08/03/2010] [Indexed: 12/22/2022]
Abstract
The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tobias Kind
- Genome Center–Metabolomics, University of California Davis, Davis, CA 95616 USA
| | - Oliver Fiehn
- Genome Center–Metabolomics, University of California Davis, Davis, CA 95616 USA
| |
Collapse
|
18
|
Chiba Y, Ito H, Sato T, Takahashi Y, Jigami Y, Narimatsu H. Expression System for Human Glycosyltransferases and Its Application. J Appl Glycosci (1999) 2010. [DOI: 10.5458/jag.57.131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Yasunori Chiba
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hiromi Ito
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Takashi Sato
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yoshie Takahashi
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yoshifumi Jigami
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hisashi Narimatsu
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST)
| |
Collapse
|
19
|
Hwang H, Zhang J, Chung KA, Leverenz JB, Zabetian CP, Peskind ER, Jankovic J, Su Z, Hancock AM, Pan C, Montine TJ, Pan S, Nutt J, Albin R, Gearing M, Beyer RP, Shi M, Zhang J. Glycoproteomics in neurodegenerative diseases. MASS SPECTROMETRY REVIEWS 2010; 29:79-125. [PMID: 19358229 PMCID: PMC2799547 DOI: 10.1002/mas.20221] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protein glycosylation regulates protein function and cellular distribution. Additionally, aberrant protein glycosylations have been recognized to play major roles in human disorders, including neurodegenerative diseases. Glycoproteomics, a branch of proteomics that catalogs and quantifies glycoproteins, provides a powerful means to systematically profile the glycopeptides or glycoproteins of a complex mixture that are highly enriched in body fluids, and therefore, carry great potential to be diagnostic and/or prognostic markers. Application of this mass spectrometry-based technology to the study of neurodegenerative disorders (e.g., Alzheimer's disease and Parkinson's disease) is relatively new, and is expected to provide insight into the biochemical pathogenesis of neurodegeneration, as well as biomarker discovery. In this review, we have summarized the current understanding of glycoproteins in biology and neurodegenerative disease, and have discussed existing proteomic technologies that are utilized to characterize glycoproteins. Some of the ongoing studies, where glycoproteins isolated from cerebrospinal fluid and human brain are being characterized in Parkinson's disease at different stages versus controls, are presented, along with future applications of targeted validation of brain specific glycoproteins in body fluids.
Collapse
Affiliation(s)
- Hyejin Hwang
- Department of Pathology, University of Washington, Seattle, Washington
| | - Jianpeng Zhang
- Department of Pathology, University of Washington, Seattle, Washington
| | - Kathryn A. Chung
- Department of Neurology, Oregon Health and Science University, Portland, Oregon
| | - James B. Leverenz
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington
| | - Cyrus P. Zabetian
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington
| | - Elaine R. Peskind
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington
| | - Joseph Jankovic
- Department of Neurology, Baylor College of Medicine, Houston, Texas
| | - Zhen Su
- Department of Pathology, University of Washington, Seattle, Washington
| | - Aneeka M. Hancock
- Department of Pathology, University of Washington, Seattle, Washington
| | - Catherine Pan
- Department of Pathology, University of Washington, Seattle, Washington
| | - Thomas J. Montine
- Department of Pathology, University of Washington, Seattle, Washington
| | - Sheng Pan
- Department of Pathology, University of Washington, Seattle, Washington
| | - John Nutt
- Department of Neurology, Oregon Health and Science University, Portland, Oregon
| | - Roger Albin
- Ann Arbor VAMC GRECC and Department of Neurology, University of Michigan, Ann Arbor, Michigan
| | - Marla Gearing
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Richard P. Beyer
- Department of Environmental & Occupational Health Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Min Shi
- Department of Pathology, University of Washington, Seattle, Washington
| | - Jing Zhang
- Department of Pathology, University of Washington, Seattle, Washington
| |
Collapse
|
20
|
Strategies for analysis of the glycosylation of proteins: current status and future perspectives. Mol Biotechnol 2009; 43:76-88. [PMID: 19507069 DOI: 10.1007/s12033-009-9184-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 04/30/2009] [Indexed: 01/27/2023]
Abstract
More than half of human proteins are glycosylated by a bewildering array of complex and heterogeneous N- and O-linked glycans. They function in myriad biological processes, including cell adhesion and signalling and influence the physical characteristics, stability, function, activity and immunogenicity of soluble glycoproteins. A single protein may be glycosylated differently to yield heterogenous glycoforms. Glycosylation analysis is of increasing interest in biomedical and biological research, the pharmaceutical and healthcare industry and biotechnology. This is because it is increasingly apparent that glycosylation changes in diseases, such as cancer, making it a promising target for development of clinically useful biomarkers and therapeutics. Furthermore, as the non-human cells employed in expression systems glycosylate their proteins very differently to human cells, and as glycosylation changes unpredictably under changing environmental conditions, glycans analysis for quality control, optimum efficacy and safety of recombinant glycoproteins destined for human therapeutic use is paramount. The complexities of carbohydrate chemistry make analysis challenging and while there are a variety of robust methodologies available for glycan analysis, there is currently a pressing need for the development of new, streamlined, high throughput approaches accessible to non-specialist laboratories.
Collapse
|
21
|
Sato M, Ito Y, Arima N, Baba M, Sobel M, Wakao M, Suda Y. High-sensitivity analysis of naturally occurring sugar chains, using a novel fluorescent linker molecule. J Biochem 2009; 146:33-41. [PMID: 19270055 DOI: 10.1093/jb/mvp041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To analyse the binding of sugar chains to proteins, viruses and cells, the surface plasmon resonance (SPR) technique is very convenient and effective because it is a real-time, non-destructive detection system. Key to this method is linker compounds for immobilization of the sugar chains to the gold-coated chip for SPR. Also, well-designed fluorescent labelling reagents are essential when analysing the structure of trace amounts of sugar chains derived from natural sources, such as glycoproteins on the surface of specific cells. In this report, we developed a novel linker molecule, named 'f-mono', which has both of these properties: simple immobilization chemistry and a fluorescent label. Since the molecule contains a 2,5-diaminopyridyl group and a thioctic acid group, conjugation with sugar chains can be achieved using the well-established reductive amination reaction. This conjugate of sugar chain and fluorescent linker (fluorescent ligand-conjugate, FLC) has fluorescent properties (ex. 335 nm, em. 380 nm), and as little as 1 microg of FLC can be easily purified using HPLC with a fluorescent detector. MS and MS/MS analysis of the FLC is also possible. As a +2 Da larger MS peak ([M + H + 2](+) ion) was always associated with the theoretical MS peak ([M + H](+)) (due to the reduction of the thioctic acid moiety), the MS peaks of the FLC were easily found, even using unfractionated crude samples. Immobilization of the FLC onto gold-coated chips, and their subsequent SPR analyses were successively accomplished, as had been performed previously using non-fluorescent ligand conjugates.
Collapse
Affiliation(s)
- Masaki Sato
- Department of Nanostructure and Advanced Materials, Kagoshima University, Kohrimoto, Japan
| | | | | | | | | | | | | |
Collapse
|
22
|
Suzuki H, Kameyama A, Tachibana K, Narimatsu H, Fukui K. Computationally and Experimentally Derived General Rules for Fragmentation of Various Glycosyl Bonds in Sodium Adduct Oligosaccharides. Anal Chem 2008; 81:1108-20. [DOI: 10.1021/ac802230a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroaki Suzuki
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto, Tokyo 135-0064, Japan, Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Akihiko Kameyama
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto, Tokyo 135-0064, Japan, Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kazuo Tachibana
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto, Tokyo 135-0064, Japan, Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Hisashi Narimatsu
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto, Tokyo 135-0064, Japan, Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kazuhiko Fukui
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto, Tokyo 135-0064, Japan, Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan
| |
Collapse
|
23
|
Tajiri M, Kadoya M, Wada Y. Dissociation Profile of Protonated Fucosyl Glycopeptides and Quantitation of Fucosylation Levels of Glycoproteins by Mass Spectrometry. J Proteome Res 2008; 8:688-93. [DOI: 10.1021/pr800727w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michiko Tajiri
- Department of Molecular Medicine, Osaka Medical Center and Research Institute for Maternal and Child Health, 840 Murodo-cho Izumi, Osaka 594-1101, Japan, and CREST, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Machiko Kadoya
- Department of Molecular Medicine, Osaka Medical Center and Research Institute for Maternal and Child Health, 840 Murodo-cho Izumi, Osaka 594-1101, Japan, and CREST, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Yoshinao Wada
- Department of Molecular Medicine, Osaka Medical Center and Research Institute for Maternal and Child Health, 840 Murodo-cho Izumi, Osaka 594-1101, Japan, and CREST, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
24
|
Hirabayashi J. Concept, Strategy and Realization of Lectin-based Glycan Profiling. J Biochem 2008; 144:139-47. [DOI: 10.1093/jb/mvn043] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
25
|
Deguchi K. TRENDS GLYCOSCI GLYC 2008; 20:81-95. [DOI: 10.4052/tigg.20.81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
26
|
|
27
|
Kimura S, Kameyama A, Nakaya S, Ito H, Narimatsu H. Direct On-Membrane Glycoproteomic Approach Using MALDI-TOF Mass Spectrometry Coupled with Microdispensing of Multiple Enzymes. J Proteome Res 2007; 6:2488-94. [PMID: 17523613 DOI: 10.1021/pr070067m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a novel approach for direct on-membrane glycoproteomics by digestion of membrane-blotted glycoproteins with multiple enzymes using piezoelectric chemical inkjet printing technology and on-membrane direct MALDI-TOF mass spectrometry. With this approach, both N-linked glycan analyses and peptide mass fingerprinting of several standard glycoproteins were successfully performed using PNGase F and trypsin microscale digestions of the blotted spots on membrane from an SDS-PAGE gel. In addition, we performed a similar analysis for 2-DE separated serum glycoproteins as a demonstration of how the system could be used in human plasma glycoproteomics.
Collapse
Affiliation(s)
- Satoshi Kimura
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | | | | | | | | |
Collapse
|
28
|
Korekane H, Tsuji S, Noura S, Ohue M, Sasaki Y, Imaoka S, Miyamoto Y. Novel fucogangliosides found in human colon adenocarcinoma tissues by means of glycomic analysis. Anal Biochem 2007; 364:37-50. [PMID: 17350584 DOI: 10.1016/j.ab.2007.01.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 01/24/2007] [Accepted: 01/25/2007] [Indexed: 11/24/2022]
Abstract
The structures of acidic glycosphingolipids in colon adenocarcinoma have been analyzed extensively using a number of conventional methods, such as thin-layer chromatography and methylation analysis, and a variety of acidic glycosphingolipids present in the tissues have been reported. However, because of a number of limitations in the techniques used in previous studies in terms of resolution, quantification, and sensitivity, we employed a different method that could be applied to small amounts of tissue. In this technique, the carbohydrate moieties of acidic glycosphingolipids from approximately 20mg of colon adenocarcinoma were released by endoglycoceramidase II and were labeled by pyridylamination. They were separated and structurally characterized by a two-dimensional HPLC mapping technique, electrospray ionization tandem mass spectrometry (ESI-MS/MS), and enzymatic cleavage. A total of 22 major acidic glycosphingolipid structures were identified, and their relative quantities were revealed in detail. They are composed of 1 sulfated (SM3), 1 lacto-series (SLe(a)), 6 kinds of ganglio-series, and 14 kinds of neolacto-series glycosphingolipids. They include most of the acidic glycosphingolipids previously reported to be present in the tissues and two previously unknown fucogangliosides sharing the same terminal structure: NeuAcalpha2-6(Fucalpha1-2)Galbeta1-4GlcNAcbeta1-3Galbeta1-4Glc, and NeuAcalpha2-6(Fucalpha1-2)Galbeta1-4GlcNAcbeta1-3Galbeta1-4(Fucalpha1-3)GlcNAcbeta1-3-Galbeta1-4Glc. Thus, this highly sensitive, high-resolution analysis enabled the identification of novel structures of acidic glycosphingolipids from small amounts of already comprehensively studied cancerous tissues. This method is a powerful tool for microanalysis of glycosphingolipid structures from small quantities of cancerous tissues and should be applicable to different types of malignant tissues.
Collapse
Affiliation(s)
- Hiroaki Korekane
- Department of Immunology, Osaka Medical Center for Cancer and Cardiovascular Diseases, 1-3-2 Nakamichi, Higashinari-ku, Osaka 537-8511, Japan
| | | | | | | | | | | | | |
Collapse
|
29
|
Kaji H, Yamauchi Y, Takahashi N, Isobe T. Mass spectrometric identification of N-linked glycopeptides using lectin-mediated affinity capture and glycosylation site–specific stable isotope tagging. Nat Protoc 2007; 1:3019-27. [PMID: 17406563 DOI: 10.1038/nprot.2006.444] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein post-translational modifications (PTMs), such as glycosylation and phosphorylation, are crucial for various signaling and regulatory events, and are therefore an important objective of proteomics research. We describe here a protocol for isotope-coded glycosylation site-specific tagging (IGOT), a method for the large-scale identification of N-linked glycoproteins from complex biological samples. The steps of this approach are: (1) lectin column-mediated affinity capture of glycopeptides generated by protease digestion of protein mixtures; (2) purification of the enriched glycopeptides by hydrophilic interaction chromatography (HIC); (3) peptide-N-glycanase-mediated incorporation of a stable isotope tag, 18O18O, specifically at the N-glycosylation site; and (4) identification of 18O-tagged peptides by liquid chromatography-coupled mass spectrometry (LC/MS)-based proteomics technology. The application of this protocol to the characterization of N-linked glycoproteins from crude extracts of the nematode Caenorhabditis elegans or mouse liver provides a list of hundreds to a thousand glycoproteins and their sites of glycosylation within a week.
Collapse
Affiliation(s)
- Hiroyuki Kaji
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji, Tokyo 192-0397, Japan
| | | | | | | |
Collapse
|
30
|
Deguchi K, Ito H, Baba T, Hirabayashi A, Nakagawa H, Fumoto M, Hinou H, Nishimura SI. Structural analysis of O-glycopeptides employing negative- and positive-ion multi-stage mass spectra obtained by collision-induced and electron-capture dissociations in linear ion trap time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:691-8. [PMID: 17279605 DOI: 10.1002/rcm.2885] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Structural analyses of various glycans attached to proteins and peptides are highly desirable for elucidating their biological roles. An approach based on mass spectrometry (MS) combining both collision-induced dissociation (CID) and electron-capture dissociation (ECD) in the positive- and negative-ion modes has been proposed as a simple and direct method of assigning an O-glycan without releasing it from the peptide and of determining the amino acid sequence of the peptide and glycosylation site. The instrument used is an electrospray ionization (ESI) linear ion trap (LIT) time-of-flight (TOF) mass spectrometer with tandem LITs for CID by He gas and ECD. The proposed approach was tested with two synthetic O-glycopeptides binding a sialyl Lewis x (sLe(x)) oligosaccharide and a 3'-sialyl N-acetyllactosamine (3'-SLN) on a serine (S) residue. In the negative-ion mode, the CID MS(2) spectra of O-glycopeptides showed a relatively abundant glycoside-bond cleavage between the core N-acetylglucosamine (GlcNAc) and serine (S) that yields deprotonated C(3)-type fragment ions of O-glycan and deprotonated Z(0)-type peptide ions. The structure of the sLe(x) (3'-SLN) oligosaccharide was simply assigned by comparing the CID MS(3) spectrum derived from the C(3)-type fragment ion with the CID MS(2) spectra of the sLe(x) and sLe(a) (3'- and 6'-SLN) standards (i.e., negative-ion MS(n) spectral matching). The amino acid sequence of the peptide including the glycosylation site was determined from the ECD MS(2) spectrum in the positive-ion mode.
Collapse
Affiliation(s)
- Kisaburo Deguchi
- Graduate School of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Ito H, Yamada K, Deguchi K, Nakagawa H, Nishimura SI. Structural assignment of disialylated biantennary N-glycan isomers derivatized with 2-aminopyridine using negative-ion multistage tandem mass spectral matching. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:212-8. [PMID: 17171781 DOI: 10.1002/rcm.2824] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
To investigate the possibility of structural assignment based on negative-ion multistage tandem mass (MS(n)) spectral matching, four isomers of disialylated biantennary N-glycans (alpha2-6 and/or alpha2-3 linked sialic acid on alpha1-6 and alpha1-3 antennae) derivatized with 2-aminopyridine (PA) were analyzed by employing high-performance liquid chromatography/electrospray ionization linear ion trap time-of-flight mass spectrometry (HPLC/ESI-LIT-TOFMS), which uses helium gas for ion trapping and collision-induced dissociation (CID). It is shown that the MS(2) spectra derived from each precursor ion [M-2H](2-) are reproducible and useful for distinguishing the four isomers. Thus, they can be assigned by negative-ion MS(2) spectral matching based on correlation coefficients. In addition, MS(3) spectra derived from D-type fragment ions clearly differentiate the alpha2-3- or alpha2-6-linked sialic acid on the alpha1-6 antenna due to their characteristic spectral patterns. The C(4)-type fragment ions, which are produced from both the alpha1-6 and alpha1-3 antennae, show the characteristic MS(3) spectra reflecting alpha2-3- or alpha2-6- linkage type or a mixture of both types. Thus, the differentiation and assignment of these disialylated biantennary N-glycan isomers can also be supported with the MS(3) spectra of C(4)- and D-type ions.
Collapse
Affiliation(s)
- Hiroki Ito
- Graduate School of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | | | | | | | | |
Collapse
|
32
|
Budnik BA, Lee RS, Steen JAJ. Global methods for protein glycosylation analysis by mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1870-80. [PMID: 17118724 DOI: 10.1016/j.bbapap.2006.10.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Revised: 10/01/2006] [Accepted: 10/10/2006] [Indexed: 12/14/2022]
Abstract
Mass spectrometry has been an analytical tool of choice for glycosylation analysis of individual proteins. Over the last 5 years several previously and newly developed mass spectrometry methods have been extended to global glycoprotein studies. In this review we discuss the importance of these global studies and the advances that have been made in enrichment analyses and fragmentation methods. We also briefly describe relevant sample preparation methods that have been used for the analysis of a single glycoprotein that could be extrapolated to global studies. Finally this review covers aspects of improvements and advances on the instrument front which are important to future global glycoproteomic studies.
Collapse
Affiliation(s)
- Bogdan A Budnik
- Department of Pathology, Children's Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
| | | | | |
Collapse
|
33
|
Wuhrer M, Catalina MI, Deelder AM, Hokke CH. Glycoproteomics based on tandem mass spectrometry of glycopeptides. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 849:115-28. [PMID: 17049937 DOI: 10.1016/j.jchromb.2006.09.041] [Citation(s) in RCA: 327] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 08/23/2006] [Accepted: 09/08/2006] [Indexed: 12/28/2022]
Abstract
Next to the identification of proteins and the determination of their expression levels, the analysis of post-translational modifications (PTM) is becoming an increasingly important aspect in proteomics. Here, we review mass spectrometric (MS) techniques for the study of protein glycosylation at the glycopeptide level. Enrichment and separation techniques for glycoproteins and glycopeptides from complex (glyco-)protein mixtures and digests are summarized. Various tandem MS (MS/MS) techniques for the analysis of glycopeptides are described and compared with respect to the information they provide on peptide sequence, glycan attachment site and glycan structure. Approaches using electrospray ionization and matrix-assisted laser desorption/ionization (MALDI) of glycopeptides are presented and the following fragmentation techniques in glycopeptide analysis are compared: collision-induced fragmentation on different types of instruments, metastable fragmentation after MALDI ionization, infrared multi-photon dissociation, electron-capture dissociation and electron-transfer dissociation. This review discusses the potential and limitations of tandem mass spectrometry of glycopeptides as a tool in structural glycoproteomics.
Collapse
Affiliation(s)
- Manfred Wuhrer
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
| | | | | | | |
Collapse
|
34
|
Ito H, Takegawa Y, Deguchi K, Nagai S, Nakagawa H, Shinohara Y, Nishimura SI. Direct structural assignment of neutral and sialylated N-glycans of glycopeptides using collision-induced dissociation MSn spectral matching. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:3557-65. [PMID: 17091533 DOI: 10.1002/rcm.2761] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Mass spectrometric analyses of various N-glycans binding to proteins and peptides are highly desirable for elucidating their biological roles. An approach based on collision-induced dissociation (CID) MS(n) spectra acquired by electrospray ionization linear ion trap time-of-flight mass spectrometry (ESI-LIT-TOFMS) in the positive- and negative-ion modes has been proposed as a direct method of assigning N-glycans without releasing them from N-glycopeptides. In the positive-ion mode of this approach, the MS(2) spectrum of N-glycopeptide was acquired so that a glycoside-bond cleavage occurs in the chitobiose residue (i.e., GlcNAcbeta1-4GlcNAc, GlcNAc: N-acetylglucosamine) attached to asparagine (N), and two charges on the [M+H+Na](2+) precursor ion are shared with both of the resulting fragments. These fragments are sodiated B(n)-type fragment ions of oligosaccharide (N-glycan) and a protonated peptide ion retaining one GlcNAc residue on the asparagine (N) residue. The structure of N-glycan was assigned by comparing MS(3) spectra derived from both the sodiated B(n)-type fragment ions of N-glycopeptide and the PA (2-aminopyridine) N-glycan standard (i.e., MS(n) spectral matching). In a similar manner, the structural assignment of sialylated N-glycan was performed by employing the negative-ion CID MS(n) spectra of deprotonated B(n)-type fragment ions of N-glycopeptide and the PA N-glycan standard. The efficacy of this approach was tested with chicken egg yolk glycopeptides with a neutral and a sialylated N-glycan, and human serum IgG glycopeptides with neutral N-glycan isomers. These results suggest that the approach based on MS(n) spectral matching is useful for the direct and simple structural assignment of neutral and sialylated N-glycans of glycopeptides.
Collapse
Affiliation(s)
- Hiroki Ito
- Graduate School of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | | | | | | | | | | | | |
Collapse
|