Literature DB >> 34236658

Glycan Compositions with GlyConnect Compozitor to Enhance Glycopeptide Identification.

Julien Mariethoz1,2, Catherine Hayes1,2, Frédérique Lisacek3,4.   

Abstract

Glycoproteomics is unquestionably on the rise and its current development benefits from past experience in proteomics, in particular when attending to bioinformatics needs. An extensive range of software solutions is available, but the reproducibility of mass spectrometry data processing remains challenging. One of the key issues in running automated glycopeptide identification software is the selection of a reference glycan composition file. The default choices are often too broad, and a fastidious literature search to properly target this selection can be avoided. This chapter suggests the use of GlyConnect Compozitor to collect relevant information on glycosylation in a given tissue or cell line and shape an appropriate glycan composition set that can be input in the majority of search engines accommodating user-defined compositions.

Entities:  

Keywords:  Database; Glycan; Glycopeptide identification; Glycosylation; Software

Mesh：

Substances：

Year:  2021        PMID： 34236658     DOI： 10.1007/978-1-0716-1641-3_7

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  46 in total

1.  The proteomics standards initiative.

Authors:  Sandra Orchard; Henning Hermjakob; Rolf Apweiler
Journal:  Proteomics       Date:  2003-07       Impact factor: 3.984

2.  GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical.

Authors:  Davide Alocci; Julien Mariethoz; Alessandra Gastaldello; Elisabeth Gasteiger; Niclas G Karlsson; Daniel Kolarich; Nicolle H Packer; Frédérique Lisacek
Journal:  J Proteome Res       Date:  2019-01-15       Impact factor: 4.466

3.  The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting mass-spectrometry-based glycoanalytic data.

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Journal:  Mol Cell Proteomics       Date:  2013-02-01       Impact factor: 5.911

Review 4.  Advances in LC-MS/MS-based glycoproteomics: getting closer to system-wide site-specific mapping of the N- and O-glycoproteome.

Authors:  Morten Thaysen-Andersen; Nicolle H Packer
Journal:  Biochim Biophys Acta       Date:  2014-05-12

5.  GlyGen: Computational and Informatics Resources for Glycoscience.

Authors:  William S York; Raja Mazumder; Rene Ranzinger; Nathan Edwards; Robel Kahsay; Kiyoko F Aoki-Kinoshita; Matthew P Campbell; Richard D Cummings; Ten Feizi; Maria Martin; Darren A Natale; Nicolle H Packer; Robert J Woods; Gaurav Agarwal; Sena Arpinar; Sanath Bhat; Judith Blake; Leyla Jael Garcia Castro; Brian Fochtman; Jeffrey Gildersleeve; Radoslav Goldman; Xavier Holmes; Vinamra Jain; Sujeet Kulkarni; Rupali Mahadik; Akul Mehta; Reza Mousavi; Sandeep Nakarakommula; Rahi Navelkar; Nagarajan Pattabiraman; Michael J Pierce; Karen Ross; Preethi Vasudev; Jeet Vora; Tatiana Williamson; Wenjin Zhang
Journal:  Glycobiology       Date:  2020-01-28       Impact factor: 4.313

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.  Advancing Solutions to the Carbohydrate Sequencing Challenge.

Authors:  Christopher J Gray; Lukasz G Migas; Perdita E Barran; Kevin Pagel; Peter H Seeberger; Claire E Eyers; Geert-Jan Boons; Nicola L B Pohl; Isabelle Compagnon; Göran Widmalm; Sabine L Flitsch
Journal:  J Am Chem Soc       Date:  2019-08-21       Impact factor: 16.383

Review 8.  Towards a standardized bioinformatics infrastructure for N- and O-glycomics.

Authors:  Miguel A Rojas-Macias; Julien Mariethoz; Peter Andersson; Chunsheng Jin; Vignesh Venkatakrishnan; Nobuyuki P Aoki; Daisuke Shinmachi; Christopher Ashwood; Katarina Madunic; Tao Zhang; Rebecca L Miller; Oliver Horlacher; Weston B Struwe; Yu Watanabe; Shujiro Okuda; Fredrik Levander; Daniel Kolarich; Pauline M Rudd; Manfred Wuhrer; Carsten Kettner; Nicolle H Packer; Kiyoko F Aoki-Kinoshita; Frédérique Lisacek; Niclas G Karlsson
Journal:  Nat Commun       Date:  2019-07-22       Impact factor: 14.919

9.  ProteomeXchange provides globally coordinated proteomics data submission and dissemination.

Authors:  Juan A Vizcaíno; Eric W Deutsch; Rui Wang; Attila Csordas; Florian Reisinger; Daniel Ríos; José A Dianes; Zhi Sun; Terry Farrah; Nuno Bandeira; Pierre-Alain Binz; Ioannis Xenarios; Martin Eisenacher; Gerhard Mayer; Laurent Gatto; Alex Campos; Robert J Chalkley; Hans-Joachim Kraus; Juan Pablo Albar; Salvador Martinez-Bartolomé; Rolf Apweiler; Gilbert S Omenn; Lennart Martens; Andrew R Jones; Henning Hermjakob
Journal:  Nat Biotechnol       Date:  2014-03       Impact factor: 54.908

10.  Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis.

Authors:  Weiqian Cao; Mingqi Liu; Siyuan Kong; Mengxi Wu; Yang Zhang; Pengyuan Yang
Journal:  Mol Cell Proteomics       Date:  2021-02-06       Impact factor: 5.911
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  1 in total

1.  In silico analysis of the human milk oligosaccharide glycome reveals key enzymes of their biosynthesis.

Authors:  Andrew G McDonald; Julien Mariethoz; Gavin P Davey; Frédérique Lisacek
Journal:  Sci Rep       Date:  2022-06-27       Impact factor: 4.996
  1 in total

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