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

Miguel A. Rojas‐Macias; Julien A. Mariethoz; Peter Andersson; Chunsheng Jin; Vignesh Venkatakrishnan; Nobuyuki P. Aoki; Daisuke Shinmachi; Christopher Ashwood; Katarina Madunić; Tao Zhang; Rebecca Louise Miller; Oliver Horlacher; Weston B. Struwe; Fredrik Levander; Daniel Kolarich; Pauline Mary Rudd; Manfred Wuhrer; Carsten Kettner; Nicolle H. Packer; Kiyoko Flora Aoki-Kinoshita; Frédérique Lisacek; Niclas G. Karlsson

doi:10.1101/401141

BioinformaticsbioRxivAug 27, 2018

Preprint

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

Miguel A. Rojas‐Macias, Julien A. Mariethoz iD, Peter Andersson, Chunsheng Jin iD, Vignesh Venkatakrishnan iD, Nobuyuki P. Aoki iD, Daisuke Shinmachi iD, Christopher Ashwood iD, Katarina Madunić iD, Tao Zhang iD, Rebecca Louise Miller iD, Oliver Horlacher iD, Weston B. Struwe iD, Fredrik Levander iD, Daniel Kolarich iD, Pauline Mary Rudd iD, Manfred Wuhrer iD, Carsten Kettner iD, Nicolle H. Packer iD, Kiyoko Flora Aoki-Kinoshita iD, Frédérique Lisacek iD, Niclas G. Karlsson iD

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.

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