GAGrank: Software for Glycosaminoglycan Sequence Ranking Using a Bipartite Graph Model

Hogan, John D.; Wu, Jiandong; Klein, Joshua; Lin, Cheng; Carvalho, Luís; Zaia, Joseph

doi:10.1016/j.mcpro.2021.100093

Cited by 3 publications

(1 citation statement)

References 46 publications

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“…MS is the essential tool to determine the molecular composition and sequence of GAG oligosaccharides. − Recent methodology studies have focused on automating the interpretation of MS and tandem MS data. , However, most previously reported methods are capable only of dealing with a single chain or relatively simple mixture of oligosaccharides obtained through tedious purification or chemical/biochemical synthesis. A completely different strategy is used in the current study.…”

Section: Resultsmentioning

confidence: 99%

A Cluster Sequencing Strategy To Determine the Consensus Affinity Domains in Heparin for Its Binding to Specific Proteins

Shi

Sheng

et al. 2022

Anal. Chem.

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Glycosaminoglycans (GAGs) have high negative charge and are biologically and pharmaceutically important because their high charge promotes a strong interaction with many proteins. Due to the inherent heterogeneity of GAGs, multiple oligosaccharides, containing certain common domains, often can interact with clusters of basic amino acid residues on a target protein. The specificity of many GAG–protein interactions remains undiscovered since there is insufficient structural information on the interacting GAGs. Herein, we establish a cluster sequencing strategy to simultaneously deduce all major sequences of the affinity GAG oligosaccharides, leading to a definition of the consensus sequence they share that corresponds to the specific binding domain for the target protein. As a proof of concept, antithrombin III-binding oligosaccharides were examined, resulting in a heptasaccharide domain containing the well-established anticoagulant pentasaccharide sequence. Repeating this approach, a new pentasaccharide domain was discovered corresponding to the heparin motif responsible for binding interferon-γ (IFNγ). Our strategy is fundamentally important for the discovery of saccharide sequences needed in the development of novel GAG-based therapeutics.

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Section: Resultsmentioning

confidence: 99%

A Cluster Sequencing Strategy To Determine the Consensus Affinity Domains in Heparin for Its Binding to Specific Proteins

Shi

Sheng

et al. 2022

Anal. Chem.

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Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2021–2022

Harvey

2024

Mass Spectrometry Reviews

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The use of matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well‐established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo‐ and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.

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Advanced Activation Techniques for the Determination of Glycan Structures Using Tandem Mass Spectrometry

Lin,

Costello

2024

Glycoprotein Analysis

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Structural analysis of glycans presents unique challenges due to their inherent complexity and the pervasive simultaneous presence of multiple isomers. The widely utilized slow-heating ion activation methods, such as collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD), often fail to provide sufficient structural details for delineation of the many glycan structural variables or for isomer differentiation. Recently, however, alternative ion activation methods, including ultraviolet photodissociation (UVPD), charge transfer dissociation (CTD), free radical-activated glycan sequencing (FRAGS), and a range of electron-activated dissociation (ExD) methods, have shown great promise for comprehensive glycan structural analysis. This chapter starts with a brief review of glycan structural analysis by the established slow-heating methods, followed by a discussion on the recent development of advanced ion activation methods and their applications to glycan sequencing. The current understanding of the fragmentation mechanism for each activation method, as well as their implementation with online separation modes for analysis of glycan mixtures, is presented.

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GAGrank: Software for Glycosaminoglycan Sequence Ranking Using a Bipartite Graph Model

Cited by 3 publications

References 46 publications

A Cluster Sequencing Strategy To Determine the Consensus Affinity Domains in Heparin for Its Binding to Specific Proteins

A Cluster Sequencing Strategy To Determine the Consensus Affinity Domains in Heparin for Its Binding to Specific Proteins

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2021–2022

Advanced Activation Techniques for the Determination of Glycan Structures Using Tandem Mass Spectrometry

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