Literature DB >> 27654115

The minimum information required for a glycomics experiment (MIRAGE) project: sample preparation guidelines for reliable reporting of glycomics datasets.

Weston B Struwe1, Sanjay Agravat2, Kiyoko F Aoki-Kinoshita3, Matthew P Campbell4, Catherine E Costello5, Anne Dell6, Stuart M Haslam6, Niclas G Karlsson7, Kay-Hooi Khoo8, Daniel Kolarich9, Yan Liu10, Ryan McBride11, Milos V Novotny12, Nicolle H Packer4, James C Paulson11, Erdmann Rapp13, Rene Ranzinger14, Pauline M Rudd15, David F Smith16, Michael Tiemeyer14, Lance Wells14, William S York14, Joseph Zaia5, Carsten Kettner17.   

Abstract

The minimum information required for a glycomics experiment (MIRAGE) project was established in 2011 to provide guidelines to aid in data reporting from all types of experiments in glycomics research including mass spectrometry (MS), liquid chromatography, glycan arrays, data handling and sample preparation. MIRAGE is a concerted effort of the wider glycomics community that considers the adaptation of reporting guidelines as an important step towards critical evaluation and dissemination of datasets as well as broadening of experimental techniques worldwide. The MIRAGE Commission published reporting guidelines for MS data and here we outline guidelines for sample preparation. The sample preparation guidelines include all aspects of sample generation, purification and modification from biological and/or synthetic carbohydrate material. The application of MIRAGE sample preparation guidelines will lead to improved recording of experimental protocols and reporting of understandable and reproducible glycomics datasets.
© The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Entities:  

Keywords:  MIRAGE; glycobiology; glycomics; sample preparation

Mesh:

Substances:

Year:  2016        PMID: 27654115      PMCID: PMC5045532          DOI: 10.1093/glycob/cww082

Source DB:  PubMed          Journal:  Glycobiology        ISSN: 0959-6658            Impact factor:   4.313


  7 in total

1.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

2.  Symbol Nomenclature for Graphical Representations of Glycans.

Authors:  Ajit Varki; Richard D Cummings; Markus Aebi; Nicole H Packer; Peter H Seeberger; Jeffrey D Esko; Pamela Stanley; Gerald Hart; Alan Darvill; Taroh Kinoshita; James J Prestegard; Ronald L Schnaar; Hudson H Freeze; Jamey D Marth; Carolyn R Bertozzi; Marilynn E Etzler; Martin Frank; Johannes Fg Vliegenthart; Thomas Lütteke; Serge Perez; Evan Bolton; Pauline Rudd; James Paulson; Minoru Kanehisa; Philip Toukach; Kiyoko F Aoki-Kinoshita; Anne Dell; Hisashi Narimatsu; William York; Naoyuki Taniguchi; Stuart Kornfeld
Journal:  Glycobiology       Date:  2015-12       Impact factor: 4.313

3.  The importance of uniformity in reporting protein-function data.

Authors:  Rolf Apweiler; Athel Cornish-Bowden; Jan-Hendrik S Hofmeyr; Carsten Kettner; Thomas S Leyh; Dietmar Schomburg; Keith Tipton
Journal:  Trends Biochem Sci       Date:  2005-01       Impact factor: 13.807

Review 4.  The minimum information about a proteomics experiment (MIAPE).

Authors:  Chris F Taylor; Norman W Paton; Kathryn S Lilley; Pierre-Alain Binz; Randall K Julian; Andrew R Jones; Weimin Zhu; Rolf Apweiler; Ruedi Aebersold; Eric W Deutsch; Michael J Dunn; Albert J R Heck; Alexander Leitner; Marcus Macht; Matthias Mann; Lennart Martens; Thomas A Neubert; Scott D Patterson; Peipei Ping; Sean L Seymour; Puneet Souda; Akira Tsugita; Joel Vandekerckhove; Thomas M Vondriska; Julian P Whitelegge; Marc R Wilkins; Ioannnis Xenarios; John R Yates; Henning Hermjakob
Journal:  Nat Biotechnol       Date:  2007-08       Impact factor: 54.908

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

Authors:  Daniel Kolarich; Erdmann Rapp; Weston B Struwe; Stuart M Haslam; Joseph Zaia; Ryan McBride; Sanjay Agravat; Matthew P Campbell; Masaki Kato; Rene Ranzinger; Carsten Kettner; William S York
Journal:  Mol Cell Proteomics       Date:  2013-02-01       Impact factor: 5.911

6.  Glycomics: building upon proteomics to advance glycosciences.

Authors:  Lance Wells; Gerald W Hart
Journal:  Mol Cell Proteomics       Date:  2013-02-01       Impact factor: 5.911

7.  MIRAGE: the minimum information required for a glycomics experiment.

Authors:  William S York; Sanjay Agravat; Kiyoko F Aoki-Kinoshita; Ryan McBride; Matthew P Campbell; Catherine E Costello; Anne Dell; Ten Feizi; Stuart M Haslam; Niclas Karlsson; Kay-Hooi Khoo; Daniel Kolarich; Yan Liu; Milos Novotny; Nicolle H Packer; James C Paulson; Erdmann Rapp; Rene Ranzinger; Pauline M Rudd; David F Smith; Weston B Struwe; Michael Tiemeyer; Lance Wells; Joseph Zaia; Carsten Kettner
Journal:  Glycobiology       Date:  2014-03-20       Impact factor: 4.313

  7 in total
  28 in total

Review 1.  Recent Advances in the Analysis of Complex Glycoproteins.

Authors:  Stefan Gaunitz; Gabe Nagy; Nicola L B Pohl; Milos V Novotny
Journal:  Anal Chem       Date:  2016-11-23       Impact factor: 6.986

2.  GlyTouCan: an accessible glycan structure repository.

Authors:  Michael Tiemeyer; Kazuhiro Aoki; James Paulson; Richard D Cummings; William S York; Niclas G Karlsson; Frederique Lisacek; Nicolle H Packer; Matthew P Campbell; Nobuyuki P Aoki; Akihiro Fujita; Masaaki Matsubara; Daisuke Shinmachi; Shinichiro Tsuchiya; Issaku Yamada; Michael Pierce; René Ranzinger; Hisashi Narimatsu; Kiyoko F Aoki-Kinoshita
Journal:  Glycobiology       Date:  2017-10-01       Impact factor: 4.313

3.  Multi-isotype Glycoproteomic Characterization of Serum Antibody Heavy Chains Reveals Isotype- and Subclass-Specific N-Glycosylation Profiles.

Authors:  Kevin Brown Chandler; Nickita Mehta; Deborah R Leon; Todd J Suscovich; Galit Alter; Catherine E Costello
Journal:  Mol Cell Proteomics       Date:  2019-01-18       Impact factor: 5.911

4.  Collision Cross Sections and Ion Mobility Separation of Fragment Ions from Complex N-Glycans.

Authors:  David J Harvey; Yasunori Watanabe; Joel D Allen; Pauline Rudd; Kevin Pagel; Max Crispin; Weston B Struwe
Journal:  J Am Soc Mass Spectrom       Date:  2018-04-19       Impact factor: 3.109

5.  Balancing sufficiency and impact in reporting standards for mass spectrometry imaging experiments.

Authors:  Ove J R Gustafsson; Lyron J Winderbaum; Mark R Condina; Berin A Boughton; Brett R Hamilton; Eivind A B Undheim; Michael Becker; Peter Hoffmann
Journal:  Gigascience       Date:  2018-10-01       Impact factor: 6.524

6.  Profiling Anti-Neu5Gc IgG in Human Sera with a Sialoglycan Microarray Assay.

Authors:  Shani Leviatan Ben-Arye; Hai Yu; Xi Chen; Vered Padler-Karavani
Journal:  J Vis Exp       Date:  2017-07-13       Impact factor: 1.355

Review 7.  Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses.

Authors:  L Renee Ruhaak; Gege Xu; Qiongyu Li; Elisha Goonatilleke; Carlito B Lebrilla
Journal:  Chem Rev       Date:  2018-03-19       Impact factor: 60.622

8.  Decrease of core 2 O-glycans on synovial lubricin in osteoarthritis reduces galectin-3 mediated crosslinking.

Authors:  Sarah A Flowers; Kristina A Thomsson; Liaqat Ali; Shan Huang; Yolanda Mthembu; Suresh C Regmi; Jan Holgersson; Tannin A Schmidt; Ola Rolfson; Lena I Björkman; Martina Sundqvist; Anna Karlsson-Bengtsson; Gregory D Jay; Thomas Eisler; Roman Krawetz; Niclas G Karlsson
Journal:  J Biol Chem       Date:  2020-09-14       Impact factor: 5.157

9.  Reference glycan structure libraries of primary human cardiomyocytes and pluripotent stem cell-derived cardiomyocytes reveal cell-type and culture stage-specific glycan phenotypes.

Authors:  Christopher Ashwood; Matthew Waas; Ranjuna Weerasekera; Rebekah L Gundry
Journal:  J Mol Cell Cardiol       Date:  2020-01-21       Impact factor: 5.000

10.  β-Catenin/CBP inhibition alters epidermal growth factor receptor fucosylation status in oral squamous cell carcinoma.

Authors:  Kevin Brown Chandler; Khalid A Alamoud; Vanessa L Stahl; Bach-Cuc Nguyen; Vinay K Kartha; Manish V Bais; Kenichi Nomoto; Takashi Owa; Stefano Monti; Maria A Kukuruzinska; Catherine E Costello
Journal:  Mol Omics       Date:  2020-03-23
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