51
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Palmisano G, Larsen MR, Packer NH, Thaysen-Andersen M. Structural analysis of glycoprotein sialylation – part II: LC-MS based detection. RSC Adv 2013. [DOI: 10.1039/c3ra42969e] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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52
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Abstract
Extracellular glycoproteins frequently carry terminal sialic acids on their N-linked and/or O-linked glycan structures. In this chapter a sialic acid specific capture-and-release protocol for the enrichment of N- and O-glycopeptides originating from glycoproteins in complex biological samples is described. The enriched glycopeptides are subjected to reversed phase liquid chromatography (LC) interfaced with electrospray ionization and multistage tandem mass spectrometry (MS(n)). The glycopeptide precursor ions are fragmented by collision-induced dissociation (CID) for analysis of the glycan parts in the MS(2) spectra. Further fragmentation (i.e., MS(3)) of deglycosylated peptide ions results in peptide backbone fragmentation, which is used in protein database searches to identify protein sequences. For O-glycopeptides the use of both CID and electron capture dissociation (ECD) fragmentation of the peptide backbone with intact glycans still attached are used to pinpoint the glycosylation sites of glycopeptides containing several Ser/Thr residues. The step-by-step protocols for fragmentation analyses of O- and N-glycopeptides enriched from human cerebrospinal fluid are described.
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Affiliation(s)
- Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.
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53
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Schjoldager KTBG, Clausen H. Site-specific protein O-glycosylation modulates proprotein processing - deciphering specific functions of the large polypeptide GalNAc-transferase gene family. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1820:2079-94. [PMID: 23022508 DOI: 10.1016/j.bbagen.2012.09.014] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 09/17/2012] [Accepted: 09/19/2012] [Indexed: 01/18/2023]
Abstract
BACKGROUND Posttranslational modifications (PTMs) greatly expand the function and regulation of proteins, and glycosylation is the most abundant and diverse PTM. Of the many different types of protein glycosylation, one is quite unique; GalNAc-type (or mucin-type) O-glycosylation, where biosynthesis is initiated in the Golgi by up to twenty distinct UDP-N-acetyl-α-d-galactosamine:polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts). These GalNAc-Ts are differentially expressed in cells and have different (although partly overlapping) substrate specificities, which provide for both unique functions and considerable redundancy. Recently we have begun to uncover human diseases associated with deficiencies in GalNAc-T genes (GALNTs). Thus deficiencies in individual GALNTs produce cell and protein specific effects and subtle distinct phenotypes such as hyperphosphatemia with hyperostosis (GALNT3) and dysregulated lipid metabolism (GALNT2). These phenotypes appear to be caused by deficient site-specific O-glycosylation that co-regulates proprotein convertase (PC) processing of FGF23 and ANGPTL3, respectively. SCOPE OF REVIEW Here we summarize recent progress in uncovering the interplay between human O-glycosylation and protease regulated processing and describes other important functions of site-specific O-glycosylation in health and disease. MAJOR CONCLUSIONS Site-specific O-glycosylation modifies pro-protein processing and other proteolytic events such as ADAM processing and thus emerges as an important co-regulator of limited proteolytic processing events. GENERAL SIGNIFICANCE Our appreciation of this function may have been hampered by our sparse knowledge of the O-glycoproteome and in particular sites of O-glycosylation. New strategies for identification of O-glycoproteins have emerged and recently the concept of SimpleCells, i.e. human cell lines made deficient in O-glycan extension by zinc finger nuclease gene targeting, was introduced for broad O-glycoproteome analysis.
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54
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Dodds ED. Gas-phase dissociation of glycosylated peptide ions. MASS SPECTROMETRY REVIEWS 2012; 31:666-82. [PMID: 22407588 DOI: 10.1002/mas.21344] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 12/22/2011] [Accepted: 12/27/2011] [Indexed: 05/15/2023]
Abstract
Among the myriad of protein post-translational modifications (PTMs), glycosylation presents a singular analytical challenge. On account of the extraordinary diversity of protein-linked carbohydrates and the great complexity with which they decorate glycoproteins, the rigorous establishment of glycan-protein connectivity is often an arduous experimental venture. Consequently, elaborating the interplay between structures of oligosaccharides and functions of proteins they modify is usually not a straightforward task. A more mature biochemical appreciation of carbohydrates as PTMs will significantly hinge upon analytical advances in the field of glycoproteomics. Undoubtedly, the analysis of glycosylated peptides by tandem mass spectrometry (MS/MS) will play a pivotal role in this regard. The goal of this review is to summarize, from an analytical and tutorial perspective, the present state of knowledge regarding the dissociation of glycopeptide ions as accomplished by various MS/MS methods. In addition, this review will endeavor to harmonize some seemingly disparate findings to provide a more complete and broadly applicable description of glycopeptide ion fragmentation. A fuller understanding of the rich variety of glycopeptide dissociation behaviors will allow glycoproteomic researchers to maximize the information yielded by MS/MS experiments, while also paving the way to new innovations in MS-based glycoproteomics.
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Affiliation(s)
- Eric D Dodds
- Department of Chemistry, University of Nebraska-Lincoln, 711 Hamilton Hall, Lincoln, Nebraska 68588-0304, USA.
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55
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Zauner G, Hoffmann M, Rapp E, Koeleman CAM, Dragan I, Deelder AM, Wuhrer M, Hensbergen PJ. Glycoproteomic Analysis of Human Fibrinogen Reveals Novel Regions of O-Glycosylation. J Proteome Res 2012; 11:5804-14. [DOI: 10.1021/pr3005937] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gerhild Zauner
- Department
of Parasitology, Biomolecular Mass Spectrometry Unit, Leiden University Medical Center, The Netherlands
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg,
Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg,
Germany
| | - Carolien A. M. Koeleman
- Department
of Parasitology, Biomolecular Mass Spectrometry Unit, Leiden University Medical Center, The Netherlands
| | - Irina Dragan
- Department
of Parasitology, Biomolecular Mass Spectrometry Unit, Leiden University Medical Center, The Netherlands
| | - André M. Deelder
- Department
of Parasitology, Biomolecular Mass Spectrometry Unit, Leiden University Medical Center, The Netherlands
| | - Manfred Wuhrer
- Department
of Parasitology, Biomolecular Mass Spectrometry Unit, Leiden University Medical Center, The Netherlands
| | - Paul J. Hensbergen
- Department
of Parasitology, Biomolecular Mass Spectrometry Unit, Leiden University Medical Center, The Netherlands
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56
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Ongay S, Boichenko A, Govorukhina N, Bischoff R. Glycopeptide enrichment and separation for protein glycosylation analysis. J Sep Sci 2012; 35:2341-72. [DOI: 10.1002/jssc.201200434] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | | | | | - Rainer Bischoff
- Department of Analytical Biochemistry; University of Groningen; Groningen The Netherlands
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57
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Nilsson J, Halim A, Grahn A, Larson G. Targeting the glycoproteome. Glycoconj J 2012; 30:119-36. [PMID: 22886069 PMCID: PMC3552370 DOI: 10.1007/s10719-012-9438-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 07/06/2012] [Accepted: 07/26/2012] [Indexed: 12/12/2022]
Abstract
Despite numerous original publications describing the structural complexity of N- and O-linked glycans on glycoproteins, only very few answer the basic question of which particular glycans are linked to which amino acid residues along the polypeptide chain. Such structural information is of fundamental importance for understanding the biological roles of complex glycosylations as well as deciphering their non-template driven biosynthesis. This review focuses on presenting and commenting on recent strategies, specifically aimed at identifying the glycoproteome of cultured cells and biological samples, using targeted and global enrichment procedures and utilizing the high resolution power, high through-put capacity and complementary fragmentation techniques of tandem mass spectrometry. The goal is to give an update of this emerging field of protein and glyco-sciences and suggest routes to bridge the data gap between the two aspects of glycoprotein characteristics, i.e. glycan structures and their attachment sites.
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Affiliation(s)
- Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg 413 45, Sweden
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58
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Zhou K, Ai C, Dong P, Fan X, Yang L. A novel model to predict O-glycosylation sites using a highly unbalanced dataset. Glycoconj J 2012; 29:551-64. [DOI: 10.1007/s10719-012-9434-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 07/11/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
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59
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Darula Z, Sherman J, Medzihradszky KF. How to dig deeper? Improved enrichment methods for mucin core-1 type glycopeptides. Mol Cell Proteomics 2012; 11:O111.016774. [PMID: 22393263 DOI: 10.1074/mcp.o111.016774] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two different workflows were tested in order to develop methods that provide deeper insight into the secreted O-glycoproteome. Bovine serum samples were subjected to lectin affinity-chromatography both at the protein- and peptide-level in order to selectively isolate glycopeptides with the most common, mucin core-1 sugar. This enrichment step was implemented with either protein-level mixed-bed ion-exchange chromatography or with peptide-level electrostatic repulsion hydrophilic interaction chromatography. Both methods led to at least 65% of the identified products being glycopeptides, in comparison to ≈ 25% without the additional chromatography steps [Darula, Z., and Medzihradszky, K. F. (2009) Affinity enrichment and characterization of mucin core-1 type glycopeptides from bovine serum. Mol. Cell. Proteomics 8, 2515-2526]. In order to improve not only the isolation but also the characterization of the glycopeptides exoglycosidases were used to eliminate carbohydrate extensions from the directly peptide-bound GalNAc units. Consequent tandem MS analysis of the mixtures using higher-energy collision-dissociation and electron-transfer dissociation led to the identification of 124 glycosylation sites in 51 proteins. While the electron-transfer dissociation data provided the bulk of the information for both modified sequence and modification site assignment, the higher-energy collision-dissociation data frequently yielded confirmation of the peptide identity, and revealed the presence of some core-2 or core-3 oligosaccharides. More than two-thirds of the sites as well as the proteins have never been reported modified.
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Affiliation(s)
- Z Darula
- Proteomics Research Group, Biological Research Center of Hungarian Academy of Sciences, Szeged, H-6701, Szeged, POB 521, Hungary
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60
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Takahashi K, Smith AD, Poulsen K, Kilian M, Julian BA, Mestecky J, Novak J, Renfrow MB. Naturally occurring structural isomers in serum IgA1 o-glycosylation. J Proteome Res 2011; 11:692-702. [PMID: 22067045 DOI: 10.1021/pr200608q] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
IgA is the most abundantly produced antibody and plays an important role in the mucosal immune system. Human IgA is represented by two isotypes, IgA1 and IgA2. The major structural difference between these two subclasses is the presence of nine potential sites of O-glycosylation in the hinge region between the first and second constant region domains of the heavy chain. Thr(225), Thr(228), Ser(230), Ser(232) and Thr(236) have been identified as the predominant sites of O-glycan attachment. The range and distribution of O-glycan chains at each site within the context of adjacent sites in this clustered region create a complex heterogeneity of surface epitopes that is incompletely defined. We previously described the analysis of IgA1 O-glycan heterogeneity by use of high resolution LC-MS and electron capture dissociation tandem MS to unambiguously localize all amino acid attachment sites in IgA1 (Ale) myeloma protein. Here, we report the identification and elucidation of IgA1 O-glycopeptide structural isomers that occur based on amino acid position of the attached glycans (positional isomers) and the structure of the O-glycan chains at individual sites (glycan isomers). These isomers are present in a model IgA1 (Mce1) myeloma protein and occur naturally in normal human serum IgA1. Variable O-glycan chains attached to Ser(230), Thr(233) or Thr(236) produce the predominant positional isomers, including O-glycans composed of a single GalNAc residue. These findings represent the first definitive identification of structural isomeric IgA1 O-glycoforms, define the single-site heterogeneity for all O-glycan sites in a single sample, and have implications for defining epitopes based on clustered O-glycan variability.
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Affiliation(s)
- Kazuo Takahashi
- UAB Biomedical FT-ICR MS Laboratory, MCLM 570, 1530 3rd Avenue South, Birmingham, AL 35294, USA
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61
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Halfinger B, Sarg B, Lindner HH. Evaluation of non-reductive β-elimination/Michael addition for glycosylation site determination in mucin-like O-glycopeptides. Electrophoresis 2011; 32:3546-53. [DOI: 10.1002/elps.201100393] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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62
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Halim A, Nilsson J, Rüetschi U, Hesse C, Larson G. Human urinary glycoproteomics; attachment site specific analysis of N- and O-linked glycosylations by CID and ECD. Mol Cell Proteomics 2011; 11:M111.013649. [PMID: 22171320 DOI: 10.1074/mcp.m111.013649] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Urine is a complex mixture of proteins and waste products and a challenging biological fluid for biomarker discovery. Previous proteomic studies have identified more than 2800 urinary proteins but analyses aimed at unraveling glycan structures and glycosylation sites of urinary glycoproteins are lacking. Glycoproteomic characterization remains difficult because of the complexity of glycan structures found mainly on asparagine (N-linked) or serine/threonine (O-linked) residues. We have developed a glycoproteomic approach that combines efficient purification of urinary glycoproteins/glycopeptides with complementary MS-fragmentation techniques for glycopeptide analysis. Starting from clinical sample size, we eliminated interfering urinary compounds by dialysis and concentrated the purified urinary proteins by lyophilization. Sialylated urinary glycoproteins were conjugated to a solid support by hydrazide chemistry and trypsin digested. Desialylated glycopeptides, released through mild acid hydrolysis, were characterized by tandem MS experiments utilizing collision induced dissociation (CID) and electron capture dissociation fragmentation techniques. In CID-MS(2), Hex(5)HexNAc(4)-N-Asn and HexHexNAc-O-Ser/Thr were typically observed, in agreement with known N-linked biantennary complex-type and O-linked core 1-like structures, respectively. Additional glycoforms for specific N- and O-linked glycopeptides were also identified, e.g. tetra-antennary N-glycans and fucosylated core 2-like O-glycans. Subsequent CID-MS(3), of selected fragment-ions from the CID-MS(2) analysis, generated peptide specific b- and y-ions that were used for peptide identification. In total, 58 N- and 63 O-linked glycopeptides from 53 glycoproteins were characterized with respect to glycan- and peptide sequences. The combination of CID and electron capture dissociation techniques allowed for the exact identification of Ser/Thr attachment site(s) for 40 of 57 putative O-glycosylation sites. We defined 29 O-glycosylation sites which have, to our knowledge, not been previously reported. This is the first study of human urinary glycoproteins where "intact" glycopeptides were studied, i.e. the presence of glycans and their attachment sites were proven without doubt.
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Affiliation(s)
- Adnan Halim
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Sweden
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63
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Abstract
As drastic structural changes in cell-surface glycans of glycoproteins and glycosphingolipids, as well as serum glycoproteins, are often observed during cell differentiation and cancer progression, it is considered that glycans can be potential candidates for novel diagnostic and therapeutic biomarkers. Although there have been substantial advances in our understanding of the effects of glycosylation on some biological systems, we still do not fully understand the significance and mechanism of glycoform alteration that is widely observed in many human diseases. This is due to the highly complicated structures of the glycans and the extremely tedious and time-consuming processes required for their separation from complex mixtures and their subsequent analysis. As a result, with a few notable exceptions, the therapeutic potential of complex glycans has not been well exploited. This article is focused on the state of the art and current advances in glycomics, and efforts for the development of automated glycan analysis, which should greatly accelerate functional glycobiology and its medical/pharmaceutical applications. The "glycoblotting method" is the only method currently available that allows rapid and large-scale clinical glycomics of human whole-serum glycoproteins, because it requires very little material and, when combined with an automated system "SweetBlot," takes only ∼14h to complete whole glycan profiling by mass spectrometry. The upcoming goal is to combine glycoblotting methods and various MS-based platforms for the development of a fully automated glycan analytical system and accelerating research to discover highly sensitive and clinically important biomarker molecules.
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Affiliation(s)
- Shin-Ichiro Nishimura
- Field of Drug Discovery Research, Faculty of Advanced Life Science, Hokkaido University, Kita-ku, Sapporo, Japan
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64
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Steentoft C, Vakhrushev SY, Vester-Christensen MB, Schjoldager KTBG, Kong Y, Bennett EP, Mandel U, Wandall H, Levery SB, Clausen H. Mining the O-glycoproteome using zinc-finger nuclease-glycoengineered SimpleCell lines. Nat Methods 2011; 8:977-82. [PMID: 21983924 DOI: 10.1038/nmeth.1731] [Citation(s) in RCA: 285] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 09/09/2011] [Indexed: 11/09/2022]
Abstract
Zinc-finger nuclease (ZFN) gene targeting is emerging as a versatile tool for engineering of multiallelic gene deficiencies. A longstanding obstacle for detailed analysis of glycoproteomes has been the extensive heterogeneities in glycan structures and attachment sites. Here we applied ZFN targeting to truncate the O-glycan elongation pathway in human cells, generating stable 'SimpleCell' lines with homogenous O-glycosylation. Three SimpleCell lines expressing only truncated GalNAcα or NeuAcα2-6GalNAcα O-glycans were produced, allowing straightforward isolation and sequencing of GalNAc O-glycopeptides from total cell lysates using lectin chromatography and nanoflow liquid chromatography-mass spectrometry (nLC-MS/MS) with electron transfer dissociation fragmentation. We identified >100 O-glycoproteins with >350 O-glycan sites (the great majority previously unidentified), including a GalNAc O-glycan linkage to a tyrosine residue. The SimpleCell method should facilitate analyses of important functions of protein glycosylation. The strategy is also applicable to other O-glycoproteomes.
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Affiliation(s)
- Catharina Steentoft
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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65
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Glycoproteomics-based identification of cancer biomarkers. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011:601937. [PMID: 22084691 PMCID: PMC3195811 DOI: 10.1155/2011/601937] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 07/16/2011] [Indexed: 01/06/2023]
Abstract
Protein glycosylation is one of the most common posttranslational modifications in mammalian cells. It is involved in many biological pathways and molecular functions and is well suited for proteomics-based disease investigations. Aberrant protein glycosylation may be associated with disease processes. Specific glycoforms of glycoproteins may serve as potential biomarkers for the early detection of disease or as biomarkers for the evaluation of therapeutic efficacy for treatment of cancer, diabetes, and other diseases. Recent technological developments, including lectin affinity chromatography and mass spectrometry, have provided researchers the ability to obtain detailed information concerning protein glycosylation. These in-depth investigations, including profiling and quantifying glycoprotein expression, as well as comprehensive glycan structural analyses may provide important information leading to the development of disease-related biomarkers. This paper describes methodologies for the detection of cancer-related glycoprotein and glycan structural alterations and briefly summarizes several current cancer-related findings.
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66
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Hanisch FG. Top-down sequencing of O-glycoproteins by in-source decay matrix-assisted laser desorption ionization mass spectrometry for glycosylation site analysis. Anal Chem 2011; 83:4829-37. [PMID: 21526855 DOI: 10.1021/ac200493c] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The sites of mucin-type O-glycosylation are largely unpredictable, making structural analysis by mass spectrometry (MS) indispensible. On the peptide level, a site localization and characterization of O-linked glycans in situ using tandem MS with electron-transfer dissociation or matrix-assisted laser desorption ionization (MALDI) MS with postsource decay have been reported. The top-down sequencing on the protein level by MALDI-MS is based on the in-source decay (ISD) of intact glycoproteins induced by hydrogen radical transfer from the matrix. It allows a ladder sequencing from both termini with assignment of O-glycosylation sites based on intense c-, y-, and z-type ions. The feasibility of ISD-MALDI-MS in the localization of O-glycosylation sites was demonstrated with synthetic O-glycopeptides, the tandem repeat domain of recombinant MUC1, and the natural bovine glycoproteins asialofetuin and desialylated κ-casein. Ladder sequencing of the 17-18.5 kD MUC1 hexarepeat domains revealed (1) cell-specific glycosylation site patterns on comparison of probes expressed in human HEK-293 or Drosophila S2 cells, and (2) a site-specific microheterogeneity at the Thr/Ser sites with variations of the glycan compositions from zero to four monosaccharides. Novel O-glycosylation sites in the C-terminal domains of fetuin (T334) and κ-caseinoglycopeptide (S154 and T156) were assigned, the former representing a sequence conflict with the published T154.
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Affiliation(s)
- Franz-Georg Hanisch
- Institute of Biochemistry II, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Köln, Germany.
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67
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Scott NE, Parker BL, Connolly AM, Paulech J, Edwards AVG, Crossett B, Falconer L, Kolarich D, Djordjevic SP, Højrup P, Packer NH, Larsen MR, Cordwell SJ. Simultaneous glycan-peptide characterization using hydrophilic interaction chromatography and parallel fragmentation by CID, higher energy collisional dissociation, and electron transfer dissociation MS applied to the N-linked glycoproteome of Campylobacter jejuni. Mol Cell Proteomics 2011; 10:M000031-MCP201. [PMID: 20360033 PMCID: PMC3033663 DOI: 10.1074/mcp.m000031-mcp201] [Citation(s) in RCA: 237] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 03/29/2010] [Indexed: 11/06/2022] Open
Abstract
Campylobacter jejuni is a gastrointestinal pathogen that is able to modify membrane and periplasmic proteins by the N-linked addition of a 7-residue glycan at the strict attachment motif (D/E)XNX(S/T). Strategies for a comprehensive analysis of the targets of glycosylation, however, are hampered by the resistance of the glycan-peptide bond to enzymatic digestion or β-elimination and have previously concentrated on soluble glycoproteins compatible with lectin affinity and gel-based approaches. We developed strategies for enriching C. jejuni HB93-13 glycopeptides using zwitterionic hydrophilic interaction chromatography and examined novel fragmentation, including collision-induced dissociation (CID) and higher energy collisional (C-trap) dissociation (HCD) as well as CID/electron transfer dissociation (ETD) mass spectrometry. CID/HCD enabled the identification of glycan structure and peptide backbone, allowing glycopeptide identification, whereas CID/ETD enabled the elucidation of glycosylation sites by maintaining the glycan-peptide linkage. A total of 130 glycopeptides, representing 75 glycosylation sites, were identified from LC-MS/MS using zwitterionic hydrophilic interaction chromatography coupled to CID/HCD and CID/ETD. CID/HCD provided the majority of the identifications (73 sites) compared with ETD (26 sites). We also examined soluble glycoproteins by soybean agglutinin affinity and two-dimensional electrophoresis and identified a further six glycosylation sites. This study more than doubles the number of confirmed N-linked glycosylation sites in C. jejuni and is the first to utilize HCD fragmentation for glycopeptide identification with intact glycan. We also show that hydrophobic integral membrane proteins are significant targets of glycosylation in this organism. Our data demonstrate that peptide-centric approaches coupled to novel mass spectrometric fragmentation techniques may be suitable for application to eukaryotic glycoproteins for simultaneous elucidation of glycan structures and peptide sequence.
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Affiliation(s)
| | - Benjamin L. Parker
- ¶Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney 2006, Australia
| | | | - Jana Paulech
- From the ‡School of Molecular and Microbial Biosciences and
| | - Alistair V. G. Edwards
- ¶Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney 2006, Australia
| | - Ben Crossett
- From the ‡School of Molecular and Microbial Biosciences and
| | - Linda Falconer
- **New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Camden 2570, Australia
| | - Daniel Kolarich
- ‡‡Department of Chemistry and Biomolecular Sciences, Macquarie University, 2109, Australia
| | - Steven P. Djordjevic
- **New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Camden 2570, Australia
- §§Institute for the Biotechnology of Infectious Diseases, University of Technology, Sydney 2007, Australia, and
| | - Peter Højrup
- ¶¶Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5000 Odense, Denmark
| | - Nicolle H. Packer
- ‡‡Department of Chemistry and Biomolecular Sciences, Macquarie University, 2109, Australia
| | - Martin R. Larsen
- ¶¶Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5000 Odense, Denmark
| | - Stuart J. Cordwell
- From the ‡School of Molecular and Microbial Biosciences and
- ¶Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney 2006, Australia
- ¶¶Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5000 Odense, Denmark
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68
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Hashimoto R, Fujitani N, Takegawa Y, Kurogochi M, Matsushita T, Naruchi K, Ohyabu N, Hinou H, Gao XD, Manri N, Satake H, Kaneko A, Sakamoto T, Nishimura SI. An Efficient Approach for the Characterization of Mucin-Type Glycopeptides: The Effect of O-Glycosylation on the Conformation of Synthetic Mucin Peptides. Chemistry 2011; 17:2393-404. [DOI: 10.1002/chem.201002754] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Indexed: 01/19/2023]
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69
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Pan S, Chen R, Aebersold R, Brentnall TA. Mass spectrometry based glycoproteomics--from a proteomics perspective. Mol Cell Proteomics 2011. [PMID: 20736408 DOI: 10.1074/mc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Glycosylation is one of the most important and common forms of protein post-translational modification that is involved in many physiological functions and biological pathways. Altered glycosylation has been associated with a variety of diseases, including cancer, inflammatory and degenerative diseases. Glycoproteins are becoming important targets for the development of biomarkers for disease diagnosis, prognosis, and therapeutic response to drugs. The emerging technology of glycoproteomics, which focuses on glycoproteome analysis, is increasingly becoming an important tool for biomarker discovery. An in-depth, comprehensive identification of aberrant glycoproteins, and further, quantitative detection of specific glycosylation abnormalities in a complex environment require a concerted approach drawing from a variety of techniques. This report provides an overview of the recent advances in mass spectrometry based glycoproteomic methods and technology, in the context of biomarker discovery and clinical application.
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Affiliation(s)
- Sheng Pan
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
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70
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Miura Y, Kato K, Takegawa Y, Kurogochi M, Furukawa JI, Shinohara Y, Nagahori N, Amano M, Hinou H, Nishimura SI. Glycoblotting-Assisted O-Glycomics: Ammonium Carbamate Allows for Highly Efficient O-Glycan Release from Glycoproteins. Anal Chem 2010; 82:10021-9. [DOI: 10.1021/ac101599p] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yoshiaki Miura
- Ezose Sciences, Inc., 25 Riverside Drive Pine Brook, New Jersey 07058, United States, Graduate School of Life Science, and Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan, and Division of Quantification of Health State (Feel Fine Corporation), Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan
| | - Kentaro Kato
- Ezose Sciences, Inc., 25 Riverside Drive Pine Brook, New Jersey 07058, United States, Graduate School of Life Science, and Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan, and Division of Quantification of Health State (Feel Fine Corporation), Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan
| | - Yasuhiro Takegawa
- Ezose Sciences, Inc., 25 Riverside Drive Pine Brook, New Jersey 07058, United States, Graduate School of Life Science, and Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan, and Division of Quantification of Health State (Feel Fine Corporation), Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan
| | - Masaki Kurogochi
- Ezose Sciences, Inc., 25 Riverside Drive Pine Brook, New Jersey 07058, United States, Graduate School of Life Science, and Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan, and Division of Quantification of Health State (Feel Fine Corporation), Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan
| | - Jun-ichi Furukawa
- Ezose Sciences, Inc., 25 Riverside Drive Pine Brook, New Jersey 07058, United States, Graduate School of Life Science, and Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan, and Division of Quantification of Health State (Feel Fine Corporation), Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan
| | - Yasuro Shinohara
- Ezose Sciences, Inc., 25 Riverside Drive Pine Brook, New Jersey 07058, United States, Graduate School of Life Science, and Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan, and Division of Quantification of Health State (Feel Fine Corporation), Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan
| | - Noriko Nagahori
- Ezose Sciences, Inc., 25 Riverside Drive Pine Brook, New Jersey 07058, United States, Graduate School of Life Science, and Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan, and Division of Quantification of Health State (Feel Fine Corporation), Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan
| | - Maho Amano
- Ezose Sciences, Inc., 25 Riverside Drive Pine Brook, New Jersey 07058, United States, Graduate School of Life Science, and Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan, and Division of Quantification of Health State (Feel Fine Corporation), Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan
| | - Hiroshi Hinou
- Ezose Sciences, Inc., 25 Riverside Drive Pine Brook, New Jersey 07058, United States, Graduate School of Life Science, and Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan, and Division of Quantification of Health State (Feel Fine Corporation), Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan
| | - Shin-Ichiro Nishimura
- Ezose Sciences, Inc., 25 Riverside Drive Pine Brook, New Jersey 07058, United States, Graduate School of Life Science, and Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan, and Division of Quantification of Health State (Feel Fine Corporation), Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo, Japan
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71
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Wiśniewski JR. Tools for phospho- and glycoproteomics of plasma membranes. Amino Acids 2010; 41:223-33. [DOI: 10.1007/s00726-010-0796-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 10/22/2010] [Indexed: 12/15/2022]
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72
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Takahashi K, Wall SB, Suzuki H, Smith AD, Hall S, Poulsen K, Kilian M, Mobley JA, Julian BA, Mestecky J, Novak J, Renfrow MB. Clustered O-glycans of IgA1: defining macro- and microheterogeneity by use of electron capture/transfer dissociation. Mol Cell Proteomics 2010; 9:2545-57. [PMID: 20823119 DOI: 10.1074/mcp.m110.001834] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
IgA nephropathy (IgAN) is the most common primary glomerulonephritis in the world. Aberrantly glycosylated IgA1, with galactose (Gal)-deficient hinge region (HR) O-glycans, plays a pivotal role in the pathogenesis of the disease. It is not known whether the glycosylation defect occurs randomly or preferentially at specific sites. We have described the utility of activated ion-electron capture dissociation (AI-ECD) mass spectrometric analysis of IgA1 O-glycosylation. However, locating and characterizing the entire range of O-glycan attachment sites are analytically challenging due to the clustered serine and threonine residues in the HR of IgA1 heavy chain. To address this problem, we analyzed all glycoforms of the HR glycopeptides of a Gal-deficient IgA1 myeloma protein, mimicking the aberrant IgA1 in patients with IgAN, by use of a combination of IgA-specific proteases + trypsin and AI-ECD Fourier transform ion cyclotron resonance (FT-ICR) tandem mass spectrometry (MS/MS). The IgA-specific proteases provided a variety of IgA1 HR fragments that allowed unambiguous localization of all O-glycosylation sites in the six most abundant glycoforms, including the sites deficient in Gal. Additionally, this protocol was adapted for on-line liquid chromatography (LC)-AI-ECD MS/MS and LC-electron transfer dissociation MS/MS analysis. Our results thus represent a new clinically relevant approach that requires ECD/electron transfer dissociation-type fragmentation to define the molecular events leading to pathogenesis of a chronic kidney disease. Furthermore, this work offers generally applicable principles for the analysis of clustered sites of O-glycosylation.
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Affiliation(s)
- Kazuo Takahashi
- Biomedical FT-ICR MS Laboratory, Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama 35294-0005, USA
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73
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Pan S, Chen R, Aebersold R, Brentnall TA. Mass spectrometry based glycoproteomics--from a proteomics perspective. Mol Cell Proteomics 2010; 10:R110.003251. [PMID: 20736408 DOI: 10.1074/mcp.r110.003251] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Glycosylation is one of the most important and common forms of protein post-translational modification that is involved in many physiological functions and biological pathways. Altered glycosylation has been associated with a variety of diseases, including cancer, inflammatory and degenerative diseases. Glycoproteins are becoming important targets for the development of biomarkers for disease diagnosis, prognosis, and therapeutic response to drugs. The emerging technology of glycoproteomics, which focuses on glycoproteome analysis, is increasingly becoming an important tool for biomarker discovery. An in-depth, comprehensive identification of aberrant glycoproteins, and further, quantitative detection of specific glycosylation abnormalities in a complex environment require a concerted approach drawing from a variety of techniques. This report provides an overview of the recent advances in mass spectrometry based glycoproteomic methods and technology, in the context of biomarker discovery and clinical application.
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Affiliation(s)
- Sheng Pan
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
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74
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Darula Z, Chalkley RJ, Lynn A, Baker PR, Medzihradszky KF. Improved identification of O-linked glycopeptides from ETD data with optimized scoring for different charge states and cleavage specificities. Amino Acids 2010; 41:321-8. [PMID: 20652609 PMCID: PMC3102200 DOI: 10.1007/s00726-010-0692-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 07/07/2010] [Indexed: 12/03/2022]
Abstract
This article describes the effect of re-interrogation of electron-transfer dissociation (ETD) data with newly developed analytical tools. MS/MS-based characterization of O-linked glycopeptides is discussed using data acquired from a complex mixture of O-linked glycopeptides, featuring mucin core 1-type carbohydrates with and without sialic acid, as well as after partial deglycosylation to leave only the core GalNAc units (Darula and Medzihradszky in Mol Cell Proteomics 8:2515, 2009). Information content of collision-induced dissociation spectra generated in collision cell (in QqTOF instruments) and in ion traps is compared. Interpretation of the corresponding ETD data using Protein Prospector is also presented. Search results using scoring based on the frequency of different fragment ions occurring in ETD spectra of tryptic peptides are compared with results obtained after ion weightings were adjusted to accommodate differential ion frequencies in spectra of differing charge states or cleavage specificities. We show that the improved scoring is more than doubled the glycopeptide assignments under very strict acceptance criteria. This study illustrates that “old” proteomic data may yield significant new information when re-interrogated with new, improved tools.
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Affiliation(s)
- Zsuzsa Darula
- Proteomics Research Group, Biological Research Center, 62 Temesvari krt, Szeged, 6726, Hungary
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75
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Klement E, Lipinszki Z, Kupihár Z, Udvardy A, Medzihradszky KF. Enrichment of O-GlcNAc modified proteins by the periodate oxidation-hydrazide resin capture approach. J Proteome Res 2010; 9:2200-6. [PMID: 20146544 PMCID: PMC2866058 DOI: 10.1021/pr900984h] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A chemical derivatization approach has been developed for the enrichment of O-GlcNAc modified proteins. The procedure is based on the isolation technique used for N-glycoproteins with appropriate modifications because of the differences in the two types of glycosylation: a prolonged periodate oxidation is followed by hydrazide resin capture, on-resin proteolytic digestion, and release of the modified peptides by hydroxylamine. This enrichment strategy offers a fringe benefit in mass spectrometry analysis. Upon collisional activation, the presence of the open carbohydrate ring leads to characteristic fragmentation facilitating both glycopeptide identification and site assignment. The enrichment protocol was applied to the Drosophila proteasome complex previously described as O-GlcNAc modified. The O-GlcNAc modification was located on proteasome interacting proteins, deubiquitinating enzyme Faf (CG1945) and a ubiquitin-like domain containing protein (CG7546). Three other proteins were also found GlcNAc modified, a HSP70 homologue (CG2918), scribbled (CG5462) and the 205 kDa microtubule-associated protein (CG1483). Interestingly, in the HSP70 homologue the GlcNAc modification is attached to an asparagine residue of a N-glycosylation motif.
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Affiliation(s)
- Eva Klement
- Proteomics Research Group, Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Zoltán Lipinszki
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Zoltán Kupihár
- Department of Medical Chemistry, University of Szeged, Szeged, Hungary
| | - Andor Udvardy
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Katalin F. Medzihradszky
- Proteomics Research Group, Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
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76
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Darula Z, Chalkley RJ, Baker P, Burlingame AL, Medzihradszky KF. Mass spectrometric analysis, automated identification and complete annotation of O-linked glycopeptides. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:421-8. [PMID: 20530845 PMCID: PMC2963623 DOI: 10.1255/ejms.1028] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Complex mixtures containing O-linked glycopeptides bearing SA(1-0)GalGalNAc structures, or single GalNAc units were subjected to collision-induced dissociation (CID) and electron transfer dissociation (ETD) analysis on a linear ion trap-Orbitrap mass spectrometer and the resulting data was analyzed using the Protein Prospector software. An overview of the structural information provided by the different fragmentation techniques, as well as their limitations, is presented. We illustrate the importance of the complementary information in the mass spectrometry survey scans as well as the different tandem mass spectrometry techniques. We also present some unique features offered by Protein Prospector that are advantageous in glycopeptide analysis: (i) considering a modification that will produce a neutral loss, without "labeling" the original modification site; (ii) merging CID and ETD search results; (iii) permitting the comparison of different modification site-assignments. Although these data were obtained from secreted glycopeptides, the observations and conclusions are also valid for the intracellular regulatory O-GlcNAc modification.
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Affiliation(s)
- Zsuzsa Darula
- Proteomics Research Group, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
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