Quantitative Glycomics

Veillon, Lucas; Zhou, Shiyue; Mechref, Yehia

doi:10.1016/bs.mie.2016.11.006

Cited by 13 publications

(11 citation statements)

References 210 publications

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“…Glycans serve a variety of structural and functional roles in membrane and secreted proteins. For instance, they may contribute to modulate immune responses and to impact processes such as adhesion or invasion ( Valguarnera et al, 2016 ; Stadlmann et al, 2017 ; Veillon et al, 2017 ). In ERG, approx.…”

Section: Discussionmentioning

confidence: 99%

Sweet and Sour Ehrlichia: Glycoproteomics and Phosphoproteomics Reveal New Players in Ehrlichia ruminantium Physiology and Pathogenesis

Marcelino

Colomé-Calls²,

Holzmüller

et al. 2019

Front. Microbiol.

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Unraveling which proteins and post-translational modifications (PTMs) affect bacterial pathogenesis and physiology in diverse environments is a tough challenge. Herein, we used mass spectrometry-based assays to study protein phosphorylation and glycosylation in Ehrlichia ruminantium Gardel virulent (ERGvir) and attenuated (ERGatt) variants and, how they can modulate Ehrlichia biological processes. The characterization of the S/T/Y phosphoproteome revealed that both strains share the same set of phosphoproteins (n = 58), 36% being overexpressed in ERGvir. The percentage of tyrosine phosphorylation is high (23%) and 66% of the identified peptides are multi-phosphorylated. Glycoproteomics revealed a high percentage of glycoproteins (67% in ERGvir) with a subset of glycoproteins being specific to ERGvir (n = 64/371) and ERGatt (n = 36/343). These glycoproteins are involved in key biological processes such as protein, amino-acid and purine biosynthesis, translation, virulence, DNA repair, and replication. Label-free quantitative analysis revealed over-expression in 31 proteins in ERGvir and 8 in ERGatt. While further PNGase digestion confidently localized 2 and 5 N-glycoproteins in ERGvir and ERGatt, respectively, western blotting suggests that many glycoproteins are O-GlcNAcylated. Twenty-three proteins were detected in both the phospho- and glycoproteome, for the two variants. This work represents the first comprehensive assessment of PTMs on Ehrlichia biology, rising interesting questions regarding ER–host interactions. Phosphoproteome characterization demonstrates an increased versatility of ER phosphoproteins to participate in different mechanisms. The high number of glycoproteins and the lack of glycosyltransferases-coding genes highlight ER dependence on the host and/or vector cellular machinery for its own protein glycosylation. Moreover, these glycoproteins could be crucial to interact and respond to changes in ER environment. PTMs crosstalk between of O-GlcNAcylation and phosphorylation could be used as a major cellular signaling mechanism in ER. As little is known about the Ehrlichia proteins/proteome and its signaling biology, the results presented herein provide a useful resource for further hypothesis-driven exploration of Ehrlichia protein regulation by phosphorylation and glycosylation events. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD012589.

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Section: Discussionmentioning

confidence: 99%

Sweet and Sour Ehrlichia: Glycoproteomics and Phosphoproteomics Reveal New Players in Ehrlichia ruminantium Physiology and Pathogenesis

Marcelino

Colomé-Calls²,

Holzmüller

et al. 2019

Front. Microbiol.

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“…Furthermore, several quantitative glycomics methods are based on derivatization approaches and heavy labelled isotopes (reviewed in refs. 22–24 ). Quantification using stable isotope standards and MS has been shown to provide excellent precision in glycomics 25–27 and glycoproteomics 28 .…”

Section: Methods and Reporting Standards For Ms-based Glycomicsmentioning

confidence: 99%

Towards a standardized bioinformatics infrastructure for N- and O-glycomics

et al. 2019

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The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.

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“…Sensitive quantitative glycomics for low abundance structures in complex biological samples is still challenging . The reliability and sensitivity of glycan analysis can be improved by SRM or multiple‐reaction monitoring (MRM) using a triple quadrupole mass spectrometer .…”

Section: Rplc Separation Of Glycans Using Msmentioning

confidence: 99%

Characterization of isomeric glycan structures by LC‐MS/MS

et al. 2017

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The characterization of glycosylation is critical for obtaining a comprehensive view of the regulation and functions of glycoproteins of interest. Due to the complex nature of oligosaccharides, due to variable compositions and linkages, and ion suppression effects, the chromatographic separation of glycans, including isomeric structures, is necessary for exhaustive characterization by mass spectrometry (MS). This review introduces the fundamental principles underlying the techniques in liquid chromatography (LC) utilized by modern day glycomics researchers. Recent advances in porous graphitized carbon, reverse phase, ion exchange and HILIC LC utilized in conjunction with MS, for the characterization of protein glycosylation, are described with an emphasis on methods capable of resolving isomeric glycan structures.

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Quantitative Glycomics

Cited by 13 publications

References 210 publications

Sweet and Sour Ehrlichia: Glycoproteomics and Phosphoproteomics Reveal New Players in Ehrlichia ruminantium Physiology and Pathogenesis

Sweet and Sour Ehrlichia: Glycoproteomics and Phosphoproteomics Reveal New Players in Ehrlichia ruminantium Physiology and Pathogenesis

Towards a standardized bioinformatics infrastructure for N- and O-glycomics

Characterization of isomeric glycan structures by LC‐MS/MS

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