Glycoproteomics: Past, present and future

Morris, Howard R.; Chalabi, Sara; Panico, Maria; Sutton-Smith, Mark; Clark, Gary F.; Goldberg, David; Dell, Anne

doi:10.1016/j.ijms.2006.09.002

Cited by 19 publications

(20 citation statements)

References 74 publications

(23 reference statements)

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“…The digestion was terminated by lyophilization. Digests were analyzed by nanoscale liquid chromatography-electrospray-MS (nano-LC-ES-MS) and tandem MS (MS/MS) using a reversed-phase nano-HPLC system (Dionex, Sunnyvale, CA) connected to a quadrupole TOF mass spectrometer (Q-STAR Pulsar I; MDS Sciex) as previously described (18).…”

Section: Transient Transfection Immunoprecipitation and Western Blomentioning

confidence: 99%

A Filovirus-Unique Region of Ebola Virus Nucleoprotein Confers Aberrant Migration and Mediates Its Incorporation into Virions

Shi

Huang

Sutton-Smith

et al. 2008

J Virol

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The Ebola virus nucleoprotein (NP) is an essential component of the nucleocapsid, required for filovirus particle formation and replication. Together with virion protein 35 (VP35) and VP24, this gene product gives rise to the filamentous nucleocapsid within transfected cells. Ebola virus NP migrates aberrantly, with an apparent molecular mass of 115 kDa, although it is predicted to encode an ϳ85-kDa protein. In this report, we show that two domains of this protein determine this aberrant migration and that this region mediates its incorporation into virions. These regions, amino acids 439 to 492 and amino acids 589 to 739, alter the mobility of Ebola virus NP by sodium dodecyl sulfate-polyacrylamide gel electrophoresis by 5 and 15 kDa, respectively, and confer similar effects on a heterologous protein, LacZ, in a position-independent fashion. Furthermore, when coexpressed with VP40, VP35, and VP24, this region mediated incorporation of NP into released viruslike particles. When fused to chimeric paramyxovirus NPs derived from measles or respiratory syncytial virus, this domain directed these proteins into the viruslike particle. The COOH-terminal NP domain comprises a conserved highly acidic region of NP with predicted disorder, distinguishing Ebola virus NPs from paramyxovirus NPs. The acidic character of this domain is likely responsible for its aberrant biochemical properties. These findings demonstrate that this region is essential for the assembly of the filamentous nucleocapsids that give rise to filoviruses.Ebola virus is a member of the family Filoviridae, most closely related to the paramyxoviruses among the negativestranded RNA viruses. Filoviruses are characterized by their enveloped, nonsegmented, and filamentous forms, and these viruses replicate rapidly in monocytes/macrophages, fibroblasts, and endothelial cells during acute infection (7,10,24). Ebola virions are characterized by their longitudinal fibers, with forms ϳ970 nm in length displaying optimal infectivity (9). They otherwise show a uniform diameter. In previous studies, three viral proteins-Ebola virus nucleoprotein (NP), virion protein 35 (VP35), and VP24-were shown to be necessary and sufficient for the formation of nucleocapsid-containing viruslike structures in transfected cells (13). Although expression of VP40 gives rise to filamentous vesicles when expressed in cells, it does not by itself allow formation of nucleocapsid-containing viruslike particles (2,11,15,19,26). Transfection of these genes gave rise to nucleocapsids confirmed by transmission electron microscopy, and they appear to be necessary and sufficient for the formation of these particles within cells. In a previous study, NP was found to interact with glycan-binding proteins (lectins) (13), and it was suggested that this posttranslational modification may account for its aberrant migration. A subsequent investigation provided further insight into the structure-function relationship within NP, including the role of the first 450 amino acids in NP-NP interactions and vi...

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Section: Transient Transfection Immunoprecipitation and Western Blomentioning

confidence: 99%

A Filovirus-Unique Region of Ebola Virus Nucleoprotein Confers Aberrant Migration and Mediates Its Incorporation into Virions

Shi

Huang

Sutton-Smith

et al. 2008

J Virol

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“…The QqTOF, which can be regarded as a triple quadrupole (QqQ) instrument where the third quadrupole is replaced by an orthogonal TOF, was originally used for rapid de novo peptide sequencing (Shevchenko et al, 1997) but has found application in many areas of research including metabolite (Levsen et al, 2005), nucleic acid (Oberacher, Niederstatter, & Parson, 2005) and glycoprotein (Morris et al, 2007) analysis. However, for scan-types in which a single ion is monitored such as precursor ion and neutral loss scans (important experiments for structural characterization), the sensitivity of the QqTOF (5-30% duty cycle) is lower than QqQ instruments because more ions are lost in TOF compared with a third quadrupole.…”

Section: Introductionmentioning

confidence: 99%

Orbitrap mass spectrometry: Instrumentation, ion motion and applications

Perry

Cooks

Noll

2008

Mass Spectrometry Reviews

401

290

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Since its introduction, the orbitrap has proven to be a robust mass analyzer that can routinely deliver high resolving power and mass accuracy. Unlike conventional ion traps such as the Paul and Penning traps, the orbitrap uses only electrostatic fields to confine and to analyze injected ion populations. In addition, its relatively low cost, simple design and high space‐charge capacity make it suitable for tackling complex scientific problems in which high performance is required. This review begins with a brief account of the set of inventions that led to the orbitrap, followed by a qualitative description of ion capture, ion motion in the trap and modes of detection. Various orbitrap instruments, including the commercially available linear ion trap–orbitrap hybrid mass spectrometers, are also discussed with emphasis on the different methods used to inject ions into the trap. Figures of merit such as resolving power, mass accuracy, dynamic range and sensitivity of each type of instrument are compared. In addition, experimental techniques that allow mass‐selective manipulation of the motion of confined ions and their potential application in tandem mass spectrometry in the orbitrap are described. Finally, some specific applications are reviewed to illustrate the performance and versatility of the orbitrap mass spectrometers. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 27: 661–699, 2008

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“…Glycosylation is among the most important and common post-translational protein modifications (PTM) [2][3][4]. A given glycoprotein usually has a large number of glycoforms, having the same amino acid backbone, but differing in sugar composition.…”

Section: ) Introductionmentioning

confidence: 99%

Fragmentation characteristics of glycopeptides

Vékey

Ozohanics

Tóth

et al. 2013

International Journal of Mass Spectrometry

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Mass spectrometric analysis of glycopeptides is an emerging strategy for analysis of glycosylation patterns. Here we present an approach using energy resolved collision induced decomposition (CID) spectra to determine structural features of glycopeptides. Fragmentation of multiply protonated glycopeptides proceeds by a series of competing charge separation processes by cleavage of a glycosidic bond, each producing two charged products: a singly charged, "B" type sugar (oxonium) ion, and a complementary high mass fragment. Energy requirements (activation energies) of these processes are similar to each other, and are far less, than that required for peptide fragmentation. At higher collision energies these first generation products fragment further, yielding a complex fragmentation pattern. Analysis of low energy spectra (those corresponding to ca. 50% survival yield) are straightforward; the ions observed correspond to structural features present in the oligosaccharide, and are not complicated by consecutive reactions. This makes it feasible to identify and distinguish antenna-and core-fucosylated isomers; antenna fucosylation usually suggests presence of the Lewis-X antigen. In general, analysis of the triply protonated molecules are most advantageous, where neutral losses and monosaccharide oxonium ion formation are less abundant.

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Glycoproteomics: Past, present and future

Cited by 19 publications

References 74 publications

A Filovirus-Unique Region of Ebola Virus Nucleoprotein Confers Aberrant Migration and Mediates Its Incorporation into Virions

A Filovirus-Unique Region of Ebola Virus Nucleoprotein Confers Aberrant Migration and Mediates Its Incorporation into Virions

Orbitrap mass spectrometry: Instrumentation, ion motion and applications

Fragmentation characteristics of glycopeptides

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