Fragmentation of negative ions from N-linked carbohydrates: Part 6. Glycans containing one<i>N</i>-acetylglucosamine in the core

Harvey, David J.; Edgeworth, Matthew; Krishna, Benjamin A.; Bonomelli, Camille; Allman, Sarah; Crispin, Max; Scrivens, James H.

doi:10.1002/rcm.6980

Cited by 25 publications

(24 citation statements)

References 43 publications

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“…(a) to one in which the spectrum lacks the diagnostic fragments and is dominated by a series of (mannose) n ‐CH = CH‐O − cross‐ring fragments (Fig. (d)) in a similar way to ions from endoglycosidase H‐released glycans reported earlier . For Man 5 GlcNAc 2 ( 17 ), for example, shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

Travelling‐wave ion mobility and negative ion fragmentation of high‐mannose N‐glycans

et al. 2016

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The isomeric structure of high-mannose N-glycans can significantly impact biological recognition events. Here, the utility of travelling-wave ion mobility-mass spectrometry (TW IM-MS)for isomer separation of high-mannose N-glycans is investigated. Negative ion fragmentation using collision-induced dissociation (CID) gave more informative spectra than positive ion spectra with mass-different fragment ions characterizing many of the isomers. Isomer separation by ion mobility in both ionization modes was generally limited, with the arrival time distributions (ATD) often showing little sign of isomers. However, isomers could be partially resolved by plotting extracted fragment ATDs of the diagnostic fragment ions from the negative ion spectra and the fragmentation spectra of the isomers could be extracted by using ions from limited areas of the ATD peak. In some cases, asymmetric ATDs were observed but no isomers could be detected by fragmentation. In these cases, it was assumed that conformers were being separated. Collision cross sections (CCSs) of the isomers in positive and negative fragmentation mode were estimated from TW IM-MS data using dextran glycans as calibrant. More complete CCS data were achieved in negative ion mode by utilizing the diagnostic fragment ions. Examples of isomer separations are shown for N-glycans released from the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. In addition to the cross sectional data, details of the negative ion collision-induced dissociation (CID) spectra of all resolved isomers are discussed.

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Section: Resultsmentioning

confidence: 99%

Travelling‐wave ion mobility and negative ion fragmentation of high‐mannose N‐glycans

et al. 2016

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“…152 Even more interesting, as it relates to the negative ion mode CID fragmentation of N-glycans, is the result that glycans released via endoH and endoS provide the same diagnostic fragment ions and thus structural information as those intact glycans released by the much more commonly used PNGase F discussed earlier. 152 In a separate study that utilized the negative ion mode for glycoproteomics and low collision energies, the peptide sequence had a tremendous impact on the fragment ions that were observed. 153 Specifically, glycan fragment ions were detected when short peptide sequences were present, and interestingly, these fragment ions were only seen in the negative ion mode from a deprotonated precursor ion and not in the positive ion mode, while secondary cleavage ions were seen when long peptide sequences were present.…”

Section: Advances In Mass Spectrometrymentioning

confidence: 99%

Recent Advances in the Analysis of Complex Glycoproteins

et al. 2016

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“…Other notable recent progresses in MS-based instrumentations for glycoprotein characterization are as follows: development of spectral libraries of sodiated oligosaccharides by sequential MS fragmentation in the positive-ion mode [122]; introduction of novel fragmentation method such as ultraviolet photodissociation (UVPD) for the improved spectral data of glycans [123]; employing negative-ion mode in glycan fragmentation in order to obtain more diagnostic cross-ring fragments [124]; development of promising applications of IM-MS in the discrimination of linkage and position isomers, identification of glycosylation sites, and information on potential conformational changes that are induced from protein-glycan interactions; introduction of CID prior to ion mobility separation for the discrimination of epimeric oxonium ions from D-GalNAc and D-GlcNAc glycoforms; discrimination of sialic acid linkage isomers (α-2-3 and α-2-6 linked sialic acid) by the use of traveling-wave ion mobility spectrometry (TW-IM-MS) [125]; and finally, increased use of capillary zone electrophoresis for the unprecedented separation efficiencies, resolution, and sensitivities in the characterization of glycoconjugates from charged biomolecules [88]. …”

Section: Step-by-step Description Of Workflowsmentioning

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Glycomic and glycoproteomic analysis of glycoproteins—a tutorial

et al. 2017

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The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.

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Fragmentation of negative ions from N-linked carbohydrates: Part 6. Glycans containing oneN-acetylglucosamine in the core

Abstract: The results show that the CID spectra of endoH- and endoS-released glycans are as useful as the corresponding spectra of the intact glycans (as released by PNGase F) in providing structural information on N-glycans.

Cited by 25 publications

References 43 publications

Travelling‐wave ion mobility and negative ion fragmentation of high‐mannose N‐glycans

Travelling‐wave ion mobility and negative ion fragmentation of high‐mannose N‐glycans

Recent Advances in the Analysis of Complex Glycoproteins

Glycomic and glycoproteomic analysis of glycoproteins—a tutorial

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