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Literature DB >> 23293784

Software for automated interpretation of mass spectrometry data from glycans and glycopeptides.

Carrie L Woodin¹, Morgan Maxon, Heather Desaire.

Abstract

The purpose of this review is to provide those interested in glycosylation analysis with the most updated information on the availability of automated tools for MS characterization of N-linked and O-linked glycosylation types. Specifically, this review describes software tools that facilitate elucidation of glycosylation from MS data on the basis of mass alone, as well as software designed to speed the interpretation of glycan and glycopeptide fragmentation from MS/MS data. This review focuses equally on software designed to interpret the composition of released glycans and on tools to characterize N-linked and O-linked glycopeptides. Several websites have been compiled and described that will be helpful to the reader who is interested in further exploring the described tools.

Entities: Chemical Disease Gene Species

Mesh：

Substances：

Year: 2013 PMID： 23293784 PMCID： PMC3633625 DOI： 10.1039/c2an36042j

Source DB: PubMed Journal: Analyst ISSN： 0003-2654 Impact factor: 4.616

75 in total

Review 1. New technologies for glycomic analysis: toward a systematic understanding of the glycome.

Authors: John F Rakus; Lara K Mahal
Journal: Annu Rev Anal Chem (Palo Alto Calif) Date: 2011 Impact factor: 10.745

2. Semi-automated identification of N-Glycopeptides by hydrophilic interaction chromatography, nano-reverse-phase LC-MS/MS, and glycan database search.

Authors: Petr Pompach; Kevin B Chandler; Renny Lan; Nathan Edwards; Radoslav Goldman
Journal: J Proteome Res Date: 2012-02-06 Impact factor: 4.466

3. Improving confidence in detection and characterization of protein N-glycosylation sites and microheterogeneity.

Authors: Anoop M Mayampurath; Yin Wu; Zaneer M Segu; Yehia Mechref; Haixu Tang
Journal: Rapid Commun Mass Spectrom Date: 2011-07-30 Impact factor: 2.419

4. Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks.

Authors: R Gupta; E Jung; A A Gooley; K L Williams; S Brunak; J Hansen
Journal: Glycobiology Date: 1999-10 Impact factor: 4.313

5. GlycoPep grader: a web-based utility for assigning the composition of N-linked glycopeptides.

Authors: Carrie L Woodin; David Hua; Morgan Maxon; Kathryn R Rebecchi; Eden P Go; Heather Desaire
Journal: Anal Chem Date: 2012-05-21 Impact factor: 6.986

Review 6. Protein glycosylation in development and disease.

Authors: J W Dennis; M Granovsky; C E Warren
Journal: Bioessays Date: 1999-05 Impact factor: 4.345

7. O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.

Authors: R Gupta; H Birch; K Rapacki; S Brunak; J E Hansen
Journal: Nucleic Acids Res Date: 1999-01-01 Impact factor: 16.971

Review 8. Concepts and principles of O-linked glycosylation.

Authors: P Van den Steen; P M Rudd; R A Dwek; G Opdenakker
Journal: Crit Rev Biochem Mol Biol Date: 1998 Impact factor: 8.250

Review 9. Integrating bioinformatics tools to handle glycosylation.

Authors: Yuliet Mazola; Glay Chinea; Alexis Musacchio
Journal: PLoS Comput Biol Date: 2011-12-29 Impact factor: 4.475

10. Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB.

Authors: Thomas Lütteke; Martin Frank; Claus-W von der Lieth
Journal: Nucleic Acids Res Date: 2005-01-01 Impact factor: 16.971

24 in total

1. Structural analysis of N-/O-glycans assembled on proteins in yeasts.

Authors: Eun Jung Thak; Jungho Kim; Dong-Jik Lee; Jeong Yoon Kim; Hyun Ah Kang
Journal: J Microbiol Date: 2018-01-04 Impact factor: 3.422

2. Sialic acid linkage-specific permethylation for improved profiling of protein glycosylation by MALDI-TOF MS.

Authors: Kuan Jiang; He Zhu; Lei Li; Yuxi Guo; Ebtesam Gashash; Cheng Ma; Xiaolin Sun; Jing Li; Lianwen Zhang; Peng George Wang
Journal: Anal Chim Acta Date: 2017-06-13 Impact factor: 6.558

3. Two New Tools for Glycopeptide Analysis Researchers: A Glycopeptide Decoy Generator and a Large Data Set of Assigned CID Spectra of Glycopeptides.

Authors: Jude C Lakbub; Xiaomeng Su; Zhikai Zhu; Milani W Patabandige; David Hua; Eden P Go; Heather Desaire
Journal: J Proteome Res Date: 2017-07-25 Impact factor: 4.466

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

Authors: Pei-Lun Tsai; Sung-Fang Chen
Journal: Mass Spectrom (Tokyo) Date: 2017-02-24

Review 5. Glycosylation profiling to evaluate glycoprotein immunogens against HIV-1.

Authors: Anna-Janina Behrens; Weston B Struwe; Max Crispin
Journal: Expert Rev Proteomics Date: 2017-09-14 Impact factor: 3.940

Review 6. Algorithms and design strategies towards automated glycoproteomics analysis.

Authors: Han Hu; Kshitij Khatri; Joseph Zaia
Journal: Mass Spectrom Rev Date: 2016-01-04 Impact factor: 10.946

Review 7. Glycomics and glycoproteomics of membrane proteins and cell-surface receptors: Present trends and future opportunities.

Authors: Kevin Brown Chandler; Catherine E Costello
Journal: Electrophoresis Date: 2016-03-29 Impact factor: 3.535