GlycoPep Grader: A Web-Based Utility for Assigning the Composition of<i>N</i>-Linked Glycopeptides

Woodin, Carrie L.; Hua, David; Maxon, Morgan; Rebecchi, Kathryn R.; Go, Eden P.; Desaire, Heather

doi:10.1021/ac300393t

Cited by 69 publications

(95 citation statements)

References 35 publications

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“…40) "Byonic" is a commercially available so ware package that can be used for identifying peptides and proteins by tandem mass spectrometry. Byonic provides some features: Top-down and bottom-up search, Modi cation Fine Control ™ , Wildcard Search ™ , glycopeptide search, sequence variant search and modi cation site localization.…”

Section: Glycopeptide Ms/ms Datamentioning

confidence: 99%

A Brief Review of Bioinformatics Tools for Glycosylation Analysis by Mass Spectrometry

Tsai

Chen

2017

Mass Spectrometry

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e purpose of this review is to provide updated information regarding bioinformatic so ware for the use in the characterization of glycosylated structures since 2013. A comprehensive review by Woodin et al. Analyst 138: 2793Analyst 138: -2803Analyst 138: , 2013 described two main approaches that are introduced for starting researchers in this area; analysis of released glycans and the identi cation of glycopeptide in enzymatic digests, respectively. Complementary to that report, this review focuses on mass spectrometry related bioinformatics tools for the characterization of N-linked and O-linked glycopeptides. Speci cally, it also provides information regarding automated tools that can be used for glycan pro ling using mass spectrometry.

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Section: Glycopeptide Ms/ms Datamentioning

confidence: 99%

A Brief Review of Bioinformatics Tools for Glycosylation Analysis by Mass Spectrometry

Tsai

Chen

2017

Mass Spectrometry

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“…By choosing the appropriate software program, glycopeptide assignment can be made in a high-throughput fashion, and the false discovery rate of the identifications can also be determined (107,108). A majority of the currently available bioinformatics tools utilize both MS and MS/MS data to decipher glycopeptide compositions, and CID data are investigated most (109)(110)(111)(112)(113). A program called GlycoPeptideSearch (GPS) that assigns N-linked glycopeptides on the basis of CID spectra was recently developed (77,111).…”

Section: Automated Glycoproteomicsmentioning

confidence: 99%

“…A different approach was taken by Woodin et al (112), who developed an online software tool called GlycoPep Grader (GPG) that assigns the best-matching glycopeptide composition to each CID spectrum. GPG works in conjunction with a separate program such as GlycoMod (114) that generates a list of possible glycopeptide candidates based on high-resolution MS data.…”

Section: Automated Glycoproteomicsmentioning

confidence: 99%

“…By calculating and searching for potential peaks that denote glycan dissociations of the precursor ion, GPG scores every glycopeptide candidate based on the CID data and determines the most likely glycopeptide composition for every spectrum. A low false discovery rate was achieved by GPG when it was utilized to analyze glycoproteomics data from different proteins (112).…”

Section: Automated Glycoproteomicsmentioning

confidence: 99%

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Carbohydrates on Proteins: Site-Specific Glycosylation Analysis by Mass Spectrometry

Zhu

Desaire²

2015

Annual Rev. Anal. Chem.

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Glycosylation on proteins adds complexity and versatility to these biologically vital macromolecules. To unveil the structure-function relationship of glycoproteins, glycopeptide-centric analysis using mass spectrometry (MS) has become a method of choice because the glycan is preserved on the glycosylation site and site-specific glycosylation profiles of proteins can be readily determined. However, glycopeptide analysis is still challenging given that glycopeptides are usually low in abundance and relatively difficult to detect and the resulting data require expertise to analyze. Viewing the urgent need to address these challenges, emerging methods and techniques are being developed with the goal of analyzing glycopeptides in a sensitive, comprehensive, and high-throughput manner. In this review, we discuss recent advances in glycoprotein and glycopeptide analysis, with topics covering sample preparation, analytical separation, MS and tandem MS techniques, as well as data interpretation and automation.

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“…At the commencement of this work most available software relied on pre-defined glycan databases (255,261,263,(271)(272)(273), in a manner analogous to proteomic software. Software that did not require prior knowledge of glycan databases [reviewed in (244) In this work, OxoExtract was often used several times to search a single mzML file.…”

Section: Discussionmentioning

confidence: 99%

Structural characterisation of glycosylation of paramyxovirus attachment and fusion proteins by mass spectrometry

Pegg¹

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The family Paramyxoviridae (paramyxovirus) contains several significant human and animal pathogens.Represented within this family are human respiratory syncytial virus (hRSV) and Newcastle disease virus (NDV). The former contributes significantly to severe respiratory tract disease in infants, children and immunocompromised individuals. At present, highly efficacious therapeutics or safe and effective vaccines are not available for hRSV. NDV is the causative agent of Newcastle disease, afflicting a wide range of avian species. The desire to study NDV is due not only to the significant economic impact it has on the poultry industry worldwide, but also its potential use as an oncolytic agent and vaccine vector in humans and animals. Additionally, findings on NDV may be translated to closely related viruses that cause disease in humans, such as parainfluenza viruses.As outlined in Chapter 1 of this thesis, the infectious processes of all members of this family are driven by two major membrane glycoproteins whose ectodomains project from the viral envelope: the fusion (F) and attachment glycoproteins. The F glycoprotein is responsible for viral entry by means of fusion with host cell membranes while the variable attachment glycoproteins, haemagglutinin, haemagglutininneuraminidase (HN) and major surface glycoprotein (G), are involved in viral attachment to host cells.Previous studies have shown that altering the glycosylation profile of these proteins can modulate the ability of the virus to infect host cells and stimulate the host immune system. As yet, site-specific glycan heterogeneity of hRSV and NDV surface glycoproteins has not been defined at a chemical level. As described in Chapter 2, reverse-phase liquid chromatography tandem mass spectrometry (MS) strategies were implemented to characterise intact glycopeptides from the attachment and F glycoproteins of hRSV and NDV. Site-occupancy and monosaccharide compositions at a given site were determined using collision-induced dissociation, higher-energy collision dissociation, electron-transfer dissociation and electron-transfer dissociation combined with collision dissociation. As described in Chapter 3, a spectral processing program was developed called OxoExtract to aid identification of intact glycopeptides that were fragmented with higher-energy collision dissociation.The F and HN proteins of NDV were derived from virions propagated in embryonic eggs. Analyses of HN in Chapter 4 revealed high mannose N-linked glycans and complex or hybrid N-linked glycans that were variably fucosylated, sialylated and sulfated or phosphorylated. In total 63, 58, and 37 glycans were identified at sites N341, N433 and N481, respectively. In addition, a previously undocumented Olinked glycosylation site was identified in the stalk domain of the protein. Observed glycans from NDV F described in Chapter 5 were mainly high mannose, containing variations of five to nine mannose ii residues across four sites, N85, N191, N366 and N471. There was also evidence of fucosylated c...

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GlycoPep Grader: A Web-Based Utility for Assigning the Composition ofN-Linked Glycopeptides

Cited by 69 publications

References 35 publications

A Brief Review of Bioinformatics Tools for Glycosylation Analysis by Mass Spectrometry

A Brief Review of Bioinformatics Tools for Glycosylation Analysis by Mass Spectrometry

Carbohydrates on Proteins: Site-Specific Glycosylation Analysis by Mass Spectrometry

Structural characterisation of glycosylation of paramyxovirus attachment and fusion proteins by mass spectrometry

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