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

Tsai, Pei-Lun; Chen, Sung Fang

doi:10.5702/massspectrometry.s0064

Cited by 35 publications

(29 citation statements)

References 46 publications

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“…Technical challenges are still preventing or at least discouraging more general Proteomics focused laboratories. Key steps in the glycoproteomics workflow including glycopeptide enrichment, liquid chromatography–mass spectrometry (LC-MS/MS) acquisition and computational data analysis are still common bottlenecks that limit the identification rate and the quantitative accuracy when investigating the extensive micro- and macro-heterogeneity inherently associated with the N- and O -glycoproteome [ 25 , 26 ].…”

Section: Introductionmentioning

confidence: 99%

Distinct urinary glycoprotein signatures in prostate cancer patients

et al. 2018

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Novel biomarkers are needed to complement prostate specific antigen (PSA) in prostate cancer (PCa) diagnostic screening programs. Glycoproteins represent a hitherto largely untapped resource with a great potential as specific and sensitive tumor biomarkers due to their abundance in bodily fluids and their dynamic and cancer-associated glycosylation. However, quantitative glycoproteomics strategies to detect potential glycoprotein cancer markers from complex biospecimen are only just emerging. Here, we describe a glycoproteomics strategy for deep quantitative mapping of N- and O-glycoproteins in urine with a view to investigate the diagnostic value of the glycoproteome to discriminate PCa from benign prostatic hyperplasia (BPH), two conditions that remain difficult to clinically stratify. Total protein extracts were obtained, concentrated and digested from urine of six PCa patients (Gleason score 7) and six BPH patients. The resulting peptide mixtures were TMT-labeled and mixed prior to a multi-faceted sample processing including hydrophilic interaction liquid chromatography (HILIC) and titanium dioxide SPE based enrichment, endo-/exoglycosidase treatment and HILIC-HPLC pre-fractionation. The isolated N- and O-glycopeptides were detected and quantified using high resolution mass spectrometry. We accurately quantified 729 N-glycoproteins spanning 1,310 unique N-glycosylation sites and observed 954 and 965 unique intact N- and O-glycopeptides, respectively, across the two disease conditions. Importantly, a panel of 56 intact N-glycopeptides perfectly discriminated PCa and BPH (ROC: AUC = 1). This study has generated a panel of intact glycopeptides that has a potential for PCa detection.

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Section: Introductionmentioning

confidence: 99%

Distinct urinary glycoprotein signatures in prostate cancer patients

et al. 2018

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“…Strategies for comparison of multiple injections may also be desired and a number of approaches have been employed. A range of software have been used in viral glycomics study and these have been covered in recent reviews which cover up to 2017 (Dallas et al, 2013; Tsai & Chen, 2017; Narimatsu et al, 2018). Here we cover more recent studies and their associated informatics.…”

Section: Glycoinformatics: Current Trends and Projectionsmentioning

confidence: 99%

Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure–function relationships

Cipollo

Parsons

2020

Mass Spectrometry Reviews

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The advancement of viral glycomics has paralleled that of the mass spectrometry glycomics toolbox. In some regard the glycoproteins studied have provided the impetus for this advancement. Viral proteins are often highly glycosylated, especially those targeted by the host immune system. Glycosylation tends to be dynamic over time as viruses propagate in host populations leading to increased number of and/or “movement” of glycosylation sites in response to the immune system and other pressures. This relationship can lead to highly glycosylated, difficult to analyze glycoproteins that challenge the capabilities of modern mass spectrometry. In this review, we briefly discuss five general areas where glycosylation is important in the viral niche and how mass spectrometry has been used to reveal key information regarding structure–function relationships between viral glycoproteins and host cells. We describe the recent past and current glycomics toolbox used in these analyses and give examples of how the requirement to analyze these complex glycoproteins has provided the incentive for some advances seen in glycomics mass spectrometry. A general overview of viral glycomics, special cases, mass spectrometry methods and work‐flows, informatics and complementary chemical techniques currently used are discussed. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev

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“…There are various bioinformatics tools for the automated glycopeptide and glycan identification and the following software can be applied for glycopeptide MS: “GlycoMod”, “GlycoX”, “GlycopepDB” “Massy tools” and “GlycoSpectrumScan” and MSMS “GlycoMiner”, “Protein Prospector”, “GlycopepID”, “GlycoMasterDB” and many more. (18) As these are generally applied to mammalian glycomes and glycoproteomes, caution is required when using search engines to annotate invertebrate glycans. For publication, consider the MIRAGE guidelines for presentation of glycomic data (19) as well as use of the diagrammatic Symbol Nomenclature for Glycans (20).…”

Section: Notesmentioning

confidence: 99%

Protein-Specific Analysis of Invertebrate Glycoproteins

Hykollari¹,

Malzl²,

Wilson³

et al. 2018

Functional Proteomics

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Summary N-glycans are post-translational modifications of proteins attached to the amide side chains of asparagine residues, with possible heterogeneity due to different structures being possible at the same glycosylation site. In contrast to the mammalian systems, invertebrate N-glycosylation presents a challenge in analysis as there exist unfamiliar epitopes and a high degree of structural and isomeric variation between different species. A simple analytical approach to analyse N-glycans on specific glycoproteins is presented, which involves a combination of tryptic peptide mass spectrometry and “off-line” RP-HPLC MALDI-TOF MS/MS complemented by blotting to recognize specific epitopes. An additional N-glycan enrichment and labelling step can facilitate the analysis of single structures and even provide isomeric separation of N-glycans from specific proteins.

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

Cited by 35 publications

References 46 publications

Distinct urinary glycoprotein signatures in prostate cancer patients

Distinct urinary glycoprotein signatures in prostate cancer patients

Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure–function relationships

Protein-Specific Analysis of Invertebrate Glycoproteins

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