Releasing N-glycan from Peptide N-terminus by N-terminal Succinylation Assisted Enzymatic Deglycosylation

Weng, Yuhua; Sui, Zhigang; Jiang, Hao; Shan, Yichu; Chen, Lingfan; Zhang, Shen; Zhang, Lihua; Zhang, Yukui

doi:10.1038/srep09770

Cited by 20 publications

(16 citation statements)

References 27 publications

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“…To expand the database, we also collected human glycosite-containing peptides from all papers regarding to human glycosite-containing peptide analysis published since 2003. Using the same strategy as above, we eventually collected 22,618 glycosite-containing peptides that belong to 8818 unique glycosites from 70 papers published by other laboratories [7, 14, 15, 17, 18, 33, 41–104]. Altogether, the N -GlycositeAtlas contains 30,872 unique glycosite-containing peptides that match to 14,644 unique glycosites in 7204 glycoproteins (Fig.…”

Section: Resultsmentioning

confidence: 99%

N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping

Sun

et al. 2019

Clin Proteom

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Background N-linked glycoprotein is a highly interesting class of proteins for clinical and biological research. The large-scale characterization of N-linked glycoproteins accomplished by mass spectrometry-based glycoproteomics has provided valuable insights into the interdependence of glycoprotein structure and protein function. However, these studies focused mainly on the analysis of specific sample type, and lack the integration of glycoproteomic data from different tissues, body fluids or cell types. Methods In this study, we collected the human glycosite-containing peptides identified through their de-glycosylated forms by mass spectrometry from over 100 publications and unpublished datasets generated from our laboratory. A database resource termed N -GlycositeAtlas was created and further used for the distribution analyses of glycoproteins among different human cells, tissues and body fluids. Finally, a web interface of N -GlycositeAtlas was created to maximize the utility and value of the database. Results The N -GlycositeAtlas database contains more than 30,000 glycosite-containing peptides (representing > 14,000 N-glycosylation sites) from more than 7200 N -glycoproteins from different biological sources including human-derived tissues, body fluids and cell lines from over 100 studies. Conclusions The entire human N -glycoproteome database as well as 22 sub-databases associated with individual tissues or body fluids can be downloaded from the N -GlycositeAtlas website at http://nglycositeatlas.biomarkercenter.org .

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Section: Resultsmentioning

confidence: 99%

N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping

Sun

et al. 2019

Clin Proteom

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“…In addition, it is rarely possible to identify tryptic peptides with N-terminal glycosylated asparagine (Asn) residues, due to the poor deglycosylation capacity of Peptide-N-Glycosidase F (PNGase F) [40]. To improve the efficiency of N-glycosylation site identification, we tested several proteases for their applicability to the N-glycoproteomic study.…”

Section: Discussionmentioning

confidence: 99%

In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins

Pan

Wang

et al. 2016

Oncotarget

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N-glycosylation is one of the most prominent and abundant posttranslational modifications of proteins. It is estimated that over 50% of mammalian proteins undergo glycosylation. However, the analysis of N-glycoproteins has been limited by the available analytical technology. In this study, we comprehensively mapped the N-glycosylation sites in the mouse brain proteome by combining complementary methods, which included seven protease treatments, four enrichment techniques and two fractionation strategies. Altogether, 13492 N-glycopeptides containing 8386 N-glycosylation sites on 3982 proteins were identified. After evaluating the performance of the above methods, we proposed a simple and efficient workflow for large-scale N-glycosylation site mapping. The optimized workflow yielded 80% of the initially identified N-glycosylation sites with considerably less effort. Analysis of the identified N-glycoproteins revealed that many of the mouse brain proteins are N-glycosylated, including those proteins in critical pathways for nervous system development and neurological disease. Additionally, several important biomarkers of various diseases were found to be N-glycosylated. These data confirm that N-glycosylation is important in both physiological and pathological processes in the brain, and provide useful details about numerous N-glycosylation sites in brain proteins.

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“…272 To improve the deglycosylation efficiency of N-terminal Asn residues, Weng et al succinylated the N-terminus before PNGase F treatment. 273 …”

Section: Identification Of Sites Of Glycosylationmentioning

confidence: 99%

Chemical Glycoproteomics

Palaniappan

Bertozzi²

2016

Chem. Rev.

248

205

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Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.

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Releasing N-glycan from Peptide N-terminus by N-terminal Succinylation Assisted Enzymatic Deglycosylation

Cited by 20 publications

References 27 publications

N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping

N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping

In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins

Chemical Glycoproteomics

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