Eradicating mass spectrometric glycan rearrangement by utilizing free radicals

Desai, Nikunj; Thomas, Daniel A.; Lee, Jung-Eun; Gao, Jinshan; Beauchamp, J. L.

doi:10.1039/c6sc01371f

Cited by 33 publications

(67 citation statements)

References 58 publications

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“…However, the prevailing glycan fragmentation method to date, CID, often fails to produce a complete series of glycosidic cleavages. Lately, a number of radical-induced dissociation methods have been applied to structural analysis of glycans, many of which were capable of producing more extensive sequence information than CID [33–43]. Among them, the recently developed EED is a particularly powerful method, as it can generate rich structural information for glycan characterization, including linkage differentiation, for a wide variety of glycans, with or without derivatization [40–41,44–45].…”

Section: Resultsmentioning

confidence: 99%

GlycoDeNovo – an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra

Hong

Sun

Sha

et al. 2017

J. Am. Soc. Mass Spectrom.

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A major challenge in glycomics is the characterization of complex glycan structures that are essential for understanding their diverse roles in many biological processes. We present a novel efficient computational approach, named GlycoDeNovo, for accurate elucidation of the glycan topologies from their tandem mass spectra. Given a spectrum, GlycoDeNovo first builds an interpretation-graph specifying how to interpret each peak using preceding interpreted peaks. It then reconstructs the topologies of peaks that contribute to interpreting the precursor ion. We theoretically prove that GlycoDeNovo is highly efficient. A major innovative feature added to GlycoDeNovo is a data-driven IonClassifier which can be used to effectively rank candidate topologies. IonClassifier is automatically learned from experimental spectra of known glycans to distinguish B- and C-type ions from all other ion types. Our results showed that GlycoDeNovo is robust and accurate for topology reconstruction of glycans from their tandem mass spectra.

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Section: Resultsmentioning

confidence: 99%

GlycoDeNovo – an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra

Hong

Sun

Sha

et al. 2017

J. Am. Soc. Mass Spectrom.

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“…The formation of these three types of ions are proposed to result from hydrogen abstraction, initiated by the nascent free radical, followed by a series of β-eliminations. 26,52 The free radical activated glycan dissociation is systematic and predictable due to the narrow range of the C−H bond dissociation enthalpies (BDEs) of the glycan. 26,52 Figure 3) is observed only at the branch site, providing the information to confirm the presence and location of the branch structure.…”

Section: Glycan Characterizationmentioning

confidence: 99%

“…26,52 The free radical activated glycan dissociation is systematic and predictable due to the narrow range of the C−H bond dissociation enthalpies (BDEs) of the glycan. 26,52 Figure 3) is observed only at the branch site, providing the information to confirm the presence and location of the branch structure. It is essential to note that the two glycosidic linkages need to be adjacent to each other to observe the unique Z α +Z β ion.…”

Section: Glycan Characterizationmentioning

confidence: 99%

“…[47][48][49][50][51] Inspired by the achievement of electron activated dissociation (ExD) for glycan structure analysis, which usually involve fragmentation via low energy free radical dissociation pathways, we recently developed a novel free radical activation glycan sequencing reagent (FRAGS), along with a methylated free radical activated glycan sequencing reagent (Me-FRAGS) for glycan structural characterization. 26,52 Free radical-directed systematic glycan dissociation with high fragmentation efficiency has been obtained using these two free radical reagents. Moreover, the use of these free radical glycan sequencing reagents does not require multiply charged precursor ions.…”

Section: Introductionmentioning

confidence: 99%

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Resin and Magnetic Nanoparticle-Based Free Radical Probes for Glycan Capture, Isolation, and Structural Characterization

et al. 2019

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By combing the merits of solid supports and free radical activated glycan sequencing (FRAGS) reagents, we develop a multi-functional solid-supported free radical probe (SS-FRAGS), which enables glycan enrichment and characterization. SS-FRAGS comprises a solid support, free radical precursor, disulfide bond, pyridyl, and hydrazine moieties. Thioactivated resin and magnetic nanoparticles (MNPs) are chosen as the solid support to selectively capture free glycans via the hydrazine moiety, allowing for their enrichment and isolation. The disulfide bond acts as a temporary covalent linkage between the solid support and the captured glycan, allowing the release of glycans via the cleavage of the disulfide bond by dithiothreitol. The basic pyridyl functional group provides a site for the formation of a fixed charge, enabling detection by mass spectrometry and avoiding glycan rearrangement during collisional activation. The free radical precursor generates a nascent free radical upon collisional activation and thus simultaneously induces systematic and predictable fragmentation for glycan structure elucidation. A radical-driven glycan deconstruction diagram (R-DECON) is developed to visually summarize the MS 2 results and thus allow for the assembly of the glycan skeleton, making the differentiation of isobaric glycan isomers unambiguous. For application to a real-world sample, we demonstrate the efficacy of the SS-FRAGS by analyzing glycan structures enzymatically cleaved from RNase-B.

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“…Conventionally, Fourier transform infrared spectroscopy, X‐ray photoelectron spectroscopy and nuclear magnetic resonance spectroscopy have been demonstrated to identify alkyl/aromatic positions for heteroatoms at the bulk property level . Mass spectrometry (MS) is a powerful tool to analyze complex mixtures including crude oils and coals . However, the differentiation of alkyl/aromatic positions for heteroatoms in molecules of coal cannot be addressed by routine MS methods.…”

Section: Introductionmentioning

confidence: 99%

A Novel Evaluation Method Developed for the Denitrogenation and Deoxygenation on Molecules in Coal during Catalytic Treatments

et al. 2019

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In‐depth understanding of coal conversion processes is a key step for clean and efficient utilization of coals in chemical industry. Currently, most analytic methods aim to evaluate heteroatom release on the entire molecules. However, the production of value‐added chemicals from complex mixtures like coals are technically demanding which inevitably requires in‐depth fundamental knowledge of the treatment processes for coals. In‐source collision‐activated dissociation (ISCAD), a mass spectrometric method, can obtain details of aromatic cores and was employed in this work to provide in‐depth understanding of the catalytic conversion process of a low‐rank coal under different solvent conditions. Different heteroatom release patterns on aromatic and alkyl locations were observed for the solvents. Each solvent exhibited a characteristic preference over deoxygenation/denitrogenation on aromatic versus alkyl positions. Such preference is important for developing a desired catalytic treatment for a targeted heteroatom release. Overall, this study provides novel insights in catalytic heteroatom release processes during coal conversion that may be critical for the production of value‐added chemicals from coals.

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Eradicating mass spectrometric glycan rearrangement by utilizing free radicals

Abstract: We designed and synthesized a methylated free radical activated glycan sequencing reagent (Me-FRAGS) for eliminating mass spectrometric glycan rearrangement.

Cited by 33 publications

References 58 publications

GlycoDeNovo – an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra

GlycoDeNovo – an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra

Resin and Magnetic Nanoparticle-Based Free Radical Probes for Glycan Capture, Isolation, and Structural Characterization

A Novel Evaluation Method Developed for the Denitrogenation and Deoxygenation on Molecules in Coal during Catalytic Treatments

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