Sample preparation guidelines
The guidelines in version 1.0 as approved by 18 February, 2016, are available in PDF format. doi:10.3762/mirage.1
Registered with FAIRsharing
Published in: Glycobiology, 2016, 26(9):907-910. doi:10.1093/glycob/cww082
Guidelines
Overview
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Guideline |
Version |
Published |
|---|---|---|
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1.0; 18 Feb., 2016 |
Glycobiology, 2016, 26(9):907-910 |
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1.0; 24 Apr., 2013 |
Mol. Cell. Proteomics, 2013, 12:991-995 |
|
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1.0; 22 June, 2016 |
Glycobiology, 2017, 27(4):280-284 |
|
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1.0; 1 Mar., 2018 |
Glycobiology, 2019, 29(5):349-354 |
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1.0; 21 Sept., 2020 |
Manuscript in preparation |
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1.0, 21 Sept., 2020 |
Manuscript in preparation |
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1.0, 9 July, 2021 |
Glycobiology, 2022, 32(7):580-587 |
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1.0, 10 April, 2023 |
Manuscript in preparation |
Authors of this document
Weston B. Struwe, Erdmann Rapp, Daniel Kolarich, Matthew P. Campbell, Stuart M. Haslam, Joseph Zaia, Ryan McBride, Yan Liu, Sanjay Agravat, William S. York, Rene Ranzinger and Carsten Kettner
General Comments
The sample preparation guidelines are designed to include all aspects of sample generation, purification and modification from biological and/or synthetic material. Fundamentally, the application of MIRAGE sample preparation guidelines will lead to improved recording of experimental protocols and reporting of understandable and reproducible glycomics datasets.
In addition, these guidelines are considered as a common basis for any further MIRAGE reporting guidelines in order to keep the requirements for data analysis short and consistent.
Following aspects are covered
- Sample Origin: General information, Biologically derived material, Chemically derived material, Description of starting material
- Sample processing: (1) isolation: enzymatic and/or chemical treatment; (2) modification: Enzymatic and/or chemical modifications; (3) purification: steps
- Defined sample: sample name
MS guidelines
The guidelines in version 1.0 as approved by April 24, 2013, are available in PDF format.
doi:10.3762/mirage.2
Registered with FAIRsharing
Published in: Mol.Cell. Proteomics, 2013, 12:991-995. doi:10.1074/mcp.O112.026492
To assist authors:
- Exemplar publications reporting data in compliance with the guidelines.
Authors of this document
Matthew Campbell, Stuart Haslam, Carsten Kettner, Daniel Kolarich, René Ranzinger, Erdmann Rapp, Weston Struwe, Will York, Joe Zaia
Statement
Based on the MIAPE guidelines template, MIAPE-MS version 2.24.
General Comments
We believe that a basic description on the sample preparation workflow is required. In contrast to proteomics, different types of glycoconjugates require partially different release approaches, which in turn can have direct influence on the conditions/parameters mentioned below. Parameters that should be included could be:
- released glycans or still attached to protein/lipid/…
- type of glycan (N-glycan, O-glycan,proteoglycan fragment,…)
- sample pre-treatment prior MS-Analyses (non, reduced, permethylated, endo/exoglycosidase digested, fluorescent label, online/offline LC-separation, …
Glycan microarray guidelines
The guidelines in the version 1.0 as approved by
22 June 2016 are available in PDF format.
doi:10.3762/mirage.3
Registered with FAIRsharing
Published in: Glycobiology, 2017, 27(4):280-284 doi:10.1093/glycob/cww118
To assist authors:
- Exemplar publications reporting data in compliance with the guidelines.
- Template with data example.
Authors of this document
Yan Liu, Ten Feizi, David Smith, James Paulson, Ryan McBride, Carsten Kettner, Daniel Kolarich, René Ranzinger, Will York
General Comments
These guidelines were drafted to be intentionally minimal and apply only to information required for generating interpretable data from a glycan array experiment. We have identified 8 areas, numbered in the workflow shown below, that are required for generating an unambiguous glycan array in the first instance and obtaining binding data. For each numbered component of the workflow area we provide guidelines for the minimal information that should be provided in reporting results.
- Sample: Glycan binding sample and assay conditions
- Glycan library
- Printing surface
- Array Printer
- Glycan microarray with "map"
- Detector and data processing
- Glycan microarray data presentation
- Interpretation and conclusion from microarray data
Liquid Chromatography guidelines
The guidelines in the version 1.0 as approved by
1 March 2018 are available in PDF format. doi:10.3762/mirage.4
Registered with FAIRsharing
Published in Glycobiology 2019, 29(5):349-354, doi:10.1093/glycob/cwz009.
Authors of this document
Matthew P. Campbell, Daniel Kolarich, Erdmann Rapp, Weston B. Struwe, Pauline M. Rudd, Catherine E. Costello, Milos Novotny, René Ranzinger, William S. York, Carsten Kettner
General Comments
These guidelines are intended to improve the reporting of liquid chromatography (LC) glycan data. The MIRAGE-LC module covers all aspects of instrument setup and modality of data handling and manipulation cross-linked with other MIRAGE recommentations.
The following parameters should be included in the report:
- equipment used, including the specification of
- column details & characteristics,
- mobile phase,
- properties of the chromatographic run,
- pre- and post run processes,
- column outputs - fractions,
- data annotation,
- exoglycosidase treatment
Guidelines for Reporting Nuclear Magnetic Resonance Data on Binding of Glycans to Receptors
The guidelines in the version 1.0 as approved by 21 September 2020 are available in PDF format. doi:10.3762/mirage.5
Registered with FAIRSharing: bsg-s001542.
Published: Manuscript in preparation.
To assist authors:
- Exemplar publications reporting data in compliance with these guidelines: coming soon.
Authors of this document
María Ángeles Canales Mayordomo, Jesús Jiménez-Barbero, James Paulson
Advisors
Koichi Kato (National Institute of National Sciences, IMS), Barbara Mulloy (Imperial College London), Göran Widmalm (Stockholm University)
Statement
Based on the MIRAGE Glycan microarray guidelines version 1.0 (doi:10.3762/mirage.3).
General Comments
These guidelines are proposed to comprehensively describe the NMR experiments and data obtained to characterize glycan recognition by various receptors. The receptor can be a glycan binding protein (such as lectins and antibodies), a glycan binding organism (such as cells) or can have a different nature including synthetic glycan binding molecules.
Guidelines for Reporting Nuclear Magnetic Resonance Data on Glycan Structures
The guidelines in the version 1.0 as approved by 21 September 2020 are available in PDF format. doi:10.3762/mirage.6.
Registered with FAIRSharing: bsg-s001543
Published: Manuscript in preparation.
To assist authors:
- Exemplar publications reporting data in compliance with these guidelines:coming soon.
Authors of this document
María Ángeles Canales Mayordomo, Jesús Jiménez-Barbero, James Paulson
Advisors
Koichi Kato (National Institute of National Sciences, IMS), Barbara Mulloy (Imperial College London), Göran Widmalm (Stockholm University)
Statement
Based on the MIRAGE Glycan microarray guidelines version 1.0 (doi:10.3762/mirage.3).
General Comments
These guidelines are proposed to comprehensively describe NMR experiments and data obtained for the characterization of glycan composition, glycan conformation and glycan dynamics both for natural and unnatural glycans.
Guidelines for Reporting Capillary Electrophoresis Analysis Data on Glycan Structures
The guidelines in the version 1.0 as approved by 9 July 2021 are available in PDF format.
doi:10.3762/mirage.7.
Registered with FAIRSharing: bsg-s001623bsg
Published in Glycobiology, 2022, 32(7):580-587, doi:10.1093/glycob/cwac021
To assist authors:
Data reporting examples
showing the application of the MIRAGE CE Guidelines for two different glycomics studies and one glycoproteomics study:
- Laser induced fluorescence detection (LIF)
- transient-isotachophoresis capillary zone electrophoresis-electrospray ionization - mass spec (t-ITP-CZE-ESI-MS)
- transient-isotachophoresis capillary zone electrophoresis-electrospray ionization - tandem mass spec (t-ITP-CZE-ESI-MS/MS)
Authors of this document
Guinevere Lageveen-Kammeijer, Erdmann Rapp, Deborah Chang, Pauline M Rudd, Carsten Kettner, Joseph Zaia
Statement
These guidelines interact with the following MIRAGE Guidelines
- MIRAGE Sample Preparation Guidelines (doi:10.3762/mirage.1)
- MIRAGE Mass Spectrometric Guidelines (doi:10.3762/mirage.2)
General Comments
This guideline for glyco/(proteo)mics analyzed by capillary electrophoresis aim for standardized and high quality reporting of experimental conditions in the scientific literature.
The guidelines cover all aspects of a glyco(proteo)mics CE experiment including sample preparation, CE operation mode (CZE, CGE, CEC, MEKC, cIEF, cITP), instrument configuration, capillary separation conditions, detection, data analysis, and experimental descriptors.
Guidelines for Reporting Lectin Microarray Analysis Data
The guidelines in the version 1.0 as approved by 10 April 2023 are available in PDF format.
doi:10.3762/mirage.8.
Registered with FAIRSharing: FAIRsharing.9a2f48
Manuscript in preparation.
Authors of this document
Hiroaki Tateno, Kiyoko Aoki-Kinoshita, Ten Feizi, Lara Mahal and James Paulson
Statement
These guidelines interact with the following MIRAGE Guidelines
- MIRAGE Sample Preparation Guidelines (doi:10.3762/mirage.1)
General Comments
This guideline for lectins analyzed by microarrays aim for standardized and high quality reporting of experimental conditions in the scientific literature.
The guidelines cover all aspects of a lectin microarray experiment including sample preparation, lectin libraries, description of the immobilization surface (e.g. the microarray slide) and its production, detection and data processing as well as data representation and storage.