Literature DB >> 28337402

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

Pei-Lun Tsai1, Sung-Fang Chen2.   

Abstract

The purpose of this review is to provide updated information regarding bioinformatic software for the use in the characterization of glycosylated structures since 2013. A comprehensive review by Woodin et al.Analyst 138: 2793-2803, 2013 (ref. 1) described two main approaches that are introduced for starting researchers in this area; analysis of released glycans and the identification 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. Specifically, it also provides information regarding automated tools that can be used for glycan profiling using mass spectrometry.

Entities:  

Keywords:  glycan; glycopeptide; glycoproteomics; glycosylation; mass spectrometry

Year:  2017        PMID： 28337402      PMCID： PMC5358406          DOI： 10.5702/massspectrometry.S0064

Source DB:  PubMed          Journal:  Mass Spectrom (Tokyo)        ISSN： 2186-5116


  42 in total

1.  STAT: a saccharide topology analysis tool used in combination with tandem mass spectrometry.

Authors:  S P Gaucher; J Morrow; J A Leary
Journal:  Anal Chem       Date:  2000-06-01       Impact factor: 6.986

2.  Mass spectrometric analysis, automated identification and complete annotation of O-linked glycopeptides.

Authors:  Zsuzsa Darula; Robert J Chalkley; Peter Baker; Alma L Burlingame; Katalin F Medzihradszky
Journal:  Eur J Mass Spectrom (Chichester)       Date:  2010       Impact factor: 1.067

3.  Software platform for high-throughput glycomics.

Authors:  S Y Vakhrushev; D Dadimov; J Peter-Katalinić
Journal:  Anal Chem       Date:  2009-05-01       Impact factor: 6.986

4.  Automatic determination of O-glycan structure from fragmentation spectra.

Authors:  David Goldberg; Marshall Bern; Bensheng Li; Carlito B Lebrilla
Journal:  J Proteome Res       Date:  2006-06       Impact factor: 4.466

5.  A new computer program (GlycoX) to determine simultaneously the glycosylation sites and oligosaccharide heterogeneity of glycoproteins.

Authors:  Hyun Joo An; John S Tillinghast; David L Woodruff; David M Rocke; Carlito B Lebrilla
Journal:  J Proteome Res       Date:  2006-10       Impact factor: 4.466

6.  GPQuest: A Spectral Library Matching Algorithm for Site-Specific Assignment of Tandem Mass Spectra to Intact N-glycopeptides.

Authors:  Shadi Toghi Eshghi; Punit Shah; Weiming Yang; Xingde Li; Hui Zhang
Journal:  Anal Chem       Date:  2015-05-06       Impact factor: 6.986

7.  Automated annotation and quantitation of glycans by liquid chromatography/electrospray ionization mass spectrometric analysis using the MultiGlycan-ESI computational tool.

Authors:  Yunli Hu; Shiyue Zhou; Chuan-Yih Yu; Haixu Tang; Yehia Mechref
Journal:  Rapid Commun Mass Spectrom       Date:  2015-01-15       Impact factor: 2.419

8.  "Glyco-peakfinder"--de novo composition analysis of glycoconjugates.

Authors:  Kai Maass; René Ranzinger; Hildegard Geyer; Claus-Wilhelm von der Lieth; Rudolf Geyer
Journal:  Proteomics       Date:  2007-12       Impact factor: 3.984

9.  GlycoSpectrumScan: fishing glycopeptides from MS spectra of protease digests of human colostrum sIgA.

Authors:  Nandan Deshpande; Pia H Jensen; Nicolle H Packer; Daniel Kolarich
Journal:  J Proteome Res       Date:  2010-02-05       Impact factor: 4.466

10.  GlycomeDB - integration of open-access carbohydrate structure databases.

Authors:  René Ranzinger; Stephan Herget; Thomas Wetter; Claus-Wilhelm von der Lieth
Journal:  BMC Bioinformatics       Date:  2008-09-19       Impact factor: 3.169
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  14 in total

Review 1.  Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure-function relationships.

Authors:  John F Cipollo; Lisa M Parsons
Journal:  Mass Spectrom Rev       Date:  2020-04-29       Impact factor: 10.946

2.  Recent advances in mass spectrometry (MS)-based glycoproteomics in complex biological samples.

Authors:  Zhengwei Chen; Junfeng Huang; Lingjun Li
Journal:  Trends Analyt Chem       Date:  2018-10-15       Impact factor: 12.296

Review 3.  Mass spectrometry for the identification and analysis of highly complex glycosylation of therapeutic or pathogenic proteins.

Authors:  Yukako Ohyama; Kazuki Nakajima; Matthew B Renfrow; Jan Novak; Kazuo Takahashi
Journal:  Expert Rev Proteomics       Date:  2020-05-28       Impact factor: 3.940

Review 4.  Recent advances in mass spectrometry analysis of neuropeptides.

Authors:  Ashley Phetsanthad; Nhu Q Vu; Qing Yu; Amanda R Buchberger; Zhengwei Chen; Caitlin Keller; Lingjun Li
Journal:  Mass Spectrom Rev       Date:  2021-09-24       Impact factor: 9.011

Review 5.  The Glycoscience of Immunity.

Authors:  Julie Y Zhou; Douglas M Oswald; Kelsey D Oliva; Lori S C Kreisman; Brian A Cobb
Journal:  Trends Immunol       Date:  2018-05-11       Impact factor: 16.687

6.  Protein-Specific Analysis of Invertebrate Glycoproteins.

Authors:  Alba Hykollari; Daniel Malzl; Iain B H Wilson; Katharina Paschinger
Journal:  Methods Mol Biol       Date:  2019

7.  Differential Quantitative Determination of Site-Specific Intact N-Glycopeptides in Serum Haptoglobin between Hepatocellular Carcinoma and Cirrhosis Using LC-EThcD-MS/MS.

Authors:  Jianhui Zhu; Zhengwei Chen; Jie Zhang; Mingrui An; Jing Wu; Qing Yu; St John Skilton; Marshall Bern; K Ilker Sen; Lingjun Li; David M Lubman
Journal:  J Proteome Res       Date:  2018-10-29       Impact factor: 4.466

Review 8.  Advances in mass spectrometry-based glycoproteomics.

Authors:  Aiying Yu; Jingfu Zhao; Wenjing Peng; Alireza Banazadeh; Seth D Williamson; Mona Goli; Yifan Huang; Yehia Mechref
Journal:  Electrophoresis       Date:  2018-10-09       Impact factor: 3.535

9.  Distinct urinary glycoprotein signatures in prostate cancer patients.

Authors:  Rebeca Kawahara; Fabio Ortega; Livia Rosa-Fernandes; Vanessa Guimarães; Daniel Quina; Willian Nahas; Veit Schwämmle; Miguel Srougi; Katia R M Leite; Morten Thaysen-Andersen; Martin R Larsen; Giuseppe Palmisano
Journal:  Oncotarget       Date:  2018-09-04

Review 10.  Emerging glycobiology tools: A renaissance in accessibility.

Authors:  Douglas M Oswald; Brian A Cobb
Journal:  Cell Immunol       Date:  2018-04-25       Impact factor: 4.178
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