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e-workflow for recording of glycomic mass spectrometric data in compliance with reporting guidelines

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, Fredrik Levander, Daniel Kolarich, Pauline M. Rudd, Manfred Wuhrer, Carsten Kettner, Nicolle H. Packer, Kiyoko F. Aoki-Kinoshita, Frédérique Lisacek, Niclas G. Karlsson
doi: https://doi.org/10.1101/401141
Miguel A. Rojas-Macias
1Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Julien Mariethoz
2Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
3Computer Science Department, University of Geneva, Geneva, Switzerland
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Peter Andersson
1Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Chunsheng Jin
1Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Vignesh Venkatakrishnan
1Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Nobuyuki P. Aoki
4Soka University, Hachioji, Tokyo, Japan
5SparqLite.com, Hachioji, Tokyo, Japan
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Daisuke Shinmachi
4Soka University, Hachioji, Tokyo, Japan
5SparqLite.com, Hachioji, Tokyo, Japan
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Christopher Ashwood
6Department of Molecular Sciences, Macquarie University, Sydney, Australia
7Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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Katarina Madunic
8Leiden University Medical Center, Leiden, Netherlands
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Tao Zhang
8Leiden University Medical Center, Leiden, Netherlands
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Rebecca L. Miller
9Department of Oncology, University of Oxford, Oxford, United Kingdom
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Oliver Horlacher
2Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
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Weston B. Struwe
10Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
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Fredrik Levander
11National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Immunotechnology, Lund University, Sweden
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Daniel Kolarich
12Institute for Glycomics, Gold Coast Campus, Griffith University, Gold Coast, QLD, Australia
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Pauline M. Rudd
13University College Dublin, Belfield, Dublin, Ireland
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Manfred Wuhrer
8Leiden University Medical Center, Leiden, Netherlands
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Carsten Kettner
14Beilstein-Institut, Frankfurt am Main, Germany
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Nicolle H. Packer
12Institute for Glycomics, Gold Coast Campus, Griffith University, Gold Coast, QLD, Australia
16Macquarie University, Sydney, Australia
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Kiyoko F. Aoki-Kinoshita
4Soka University, Hachioji, Tokyo, Japan
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Frédérique Lisacek
2Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
3Computer Science Department, University of Geneva, Geneva, Switzerland
15Section of Biology, University of Geneva, Geneva, Switzerland
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Niclas G. Karlsson
1Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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  • For correspondence: niclas.karlsson@medchem.gu.se
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ABSTRACT

Glycomics targets released glycans from proteins, lipids and proteoglycans. High throughput glycomics is based on mass spectrometry (MS) that increasingly depends on exchange of data with databases and the use of software. This requires an agreed format for accurately recording of experiments, developing consistent storage modules and granting public access to glycomic MS data. The introduction of the MIRAGE (Mimimum Requirement for A Glycomics Experiment) reporting standards for glycomics was the first step towards automating glycomic data recording. This report describes a glycomic e-infrastructure utilizing a well established glycomics recording format (GlycoWorkbench), and a dedicated web tool for submitting MIRAGE-compatible MS information into a public experimental repository, UniCarb-DR. The submission of data to UniCarb-DR should be a part of the submission process for publications with glycomics MSn that conform to the MIRAGE guidelines. The structure of this pipeline allows submission of most MS workflows used in glycomics.

Author contributions: M.A.R.-M. designed and lead the development of the database; J.M. O.H, and P.A. contributed to the UniCarb-DR implementation and designed the database and web interface; C.J. and N.G.K. contributed to the design of the upload forms, C.J., V.V., K.M., C.A., R.L.M, T.Z. contributed with data for beta-testing of the data submission tool and feedback; N.P.A, D.S. and K.F.A.-K. contributed to the setting up the communication with GlyTouCan; F.Le. contributed with design of Proteios for glyco MS data; W.B.S, D.K., P.M.R., M.W, C.K., N.H.P, K.F.A.-K, F. Li. and N.G.K. formed the advisory core that contributed with feedback on repository design, advised in implementation of glycomic MS/reporting guidelines and design of databases and coding; K.F.A.-K and N.G.K jointly received the funds for UniCarb-DR and GlyTouCan communication; F.Li. and N.G.K. jointly received funds for development of the UniCarb-DR infrastructure and structured the manuscript; N.G.K. proposed the UniCarb-DR concept and managed the project. M.A.R.-M. F.Li and N.G.K. jointly wrote the manuscript with input from the other authors. All authors signed of on the final version.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted August 27, 2018.
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e-workflow for recording of glycomic mass spectrometric data in compliance with reporting guidelines
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, Fredrik Levander, Daniel Kolarich, Pauline M. Rudd, Manfred Wuhrer, Carsten Kettner, Nicolle H. Packer, Kiyoko F. Aoki-Kinoshita, Frédérique Lisacek, Niclas G. Karlsson
bioRxiv 401141; doi: https://doi.org/10.1101/401141
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e-workflow for recording of glycomic mass spectrometric data in compliance with reporting guidelines
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, Fredrik Levander, Daniel Kolarich, Pauline M. Rudd, Manfred Wuhrer, Carsten Kettner, Nicolle H. Packer, Kiyoko F. Aoki-Kinoshita, Frédérique Lisacek, Niclas G. Karlsson
bioRxiv 401141; doi: https://doi.org/10.1101/401141

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