Aims

The MIRAGE project focuses on the following aims: The development of publication guidelines for interaction and structural glycomics data as well as the development of data exchange formats.

1. Publication standards for interaction analysis data

Interaction analysis includes experiments which seek to identify and define the recognition of glycan receptors by binding partner proteins. These interactions may be as limited as the interaction of an individual proteins with a single glycan or as broad as the evaluation of whole binding of cells to populations of glycans.

Initial efforts focus on the interactions that can be evaluated on a glycan microarray. Future expansion would include all types of interaction experiments, including, but not limited to: SPR (surface plasmon resonance), flow cytometry, ELISA, STD-NMR and ITC (isothermal calorimetry).

The aims for this task are:

  • define and provide for interaction experiments, e.g.,
  1. sample reporting guidelines
  2. experimental guidelines
  3. platform guidelines
  4. results guidelines
  • provide templates for reporting within the above guidelines
  • suggest guidelines for data reporting (normalization standards)
  • conventions for glycan nomenclature in order to facilitate cross platform comparisons of different glycan arrays
  • interact with the MIRAGE working group “Bioinformatics” to establish basic structure for data reporting
  • recruit users/experts in other platforms to review/critique guidelines for use in those experiments

Status

In 2010 a subgroup of the WGGDS (Working Group for Glycomics Data(base) Standards) started a initiative to create a standard exchange format for glycan array data. The initative started with a data collection of information that have to be stored to consistently describe an glycan array experiment.

Reporting Guidelines for Glycan Microarray Data have been developed, approved by both the MIRAGE Commission and the community and published in 2017. These guidelines were drafted to be intentionally minimal and apply only to information required for generating interpretable data from a glycan array experiment. Bearing in mind the authors' hestiance to follow guidelines, here, the Commission provides a number of exemplar publications reporting glycan microarray data and a template completed with a data example.

Reporting Guidelines for Sample Preparations are designed to include all aspects of sample generation, purification and modification from biological and/or synthetic material. 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. After their approval the guidelines were published 2016.

Currently, the group is developing reporting guidelines for glycan binding protein specificity data and carbohydrate-binding protein array data.

(July 2020)

 

2. Publication Standards for structural analysis Data

With the rising interest in global glycoconjugate characterization (glycomics/glycoproteomics) a growing number of labs are implementing a range of technologies to achieve this goal. This increasing interest presents an important step towards glycomic systems biology, especially with concomitant development of suitable data repositories that allow access to the large amount of data acquired at different institutions.

Nevertheless, sample preparation plays a crucial role in glycoconjugate analysis. It can influence the occurrence of artefacts, which, in turn, can result in misinterpretations. In this context it is of utmost importance that critical sample handling and data analysis parameters are reported in an organised fashion to enable critical review of recorded data at a later stage. The lack of adequate and generally applicable software tools as utilised in proteomic research adds an additional challenge for glycoconjugate structural determination.

Thus, the goals of this task are:

  • identify and define crucial sample preparation and analysis parameters
  • provide templates for reporting
  • suggest guidelines for data reporting / data deposition
  • interact with the MIRAGE working group “Bioinformatics” to establish basic structure for data reporting
  • seek input from the wider glycobiology research community.

Status

The guidelines for mass spectrometry data were completed and send to the wider scientific community for discussion and feedback. The suggestions were considered and the guidelines were in Molecular and Cellular Proteomics in 2013. In order to assist authors in how to apply the MIRAGE MS guidelines, exemplar publications reporting MS experimental data in compliance with the guidelines are provided.

Members of the MIRAGE Commission have developed reporting guidelines for liquid chromatography (LC). 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. These guidelines have been approved by both the Commission and the community and were published in Glycobiology in 2018.

The Commission is working now on reporting guidelines for NMR data and glycopeptide analysis data.

(July 2020)

3. Development of Data exchange formats

The Comission is collaborating with interested members from the community to cover the informatics aspects of the MIRAGE project.

The aims are:

  • definition of data exchange file formats based on the guidelines provided by the other working groups
  • definition of a guideline for the development of glycomics databases
  • working with the two other working groups to integrate guidelines for data processing into the general guidelines

Status

Definition of the Biological source data collection at the Second GlycoInformatics Workshop in Potsdam, 2011.

A prototype of the software-based decision tree has been developed for the mass spectrometry guidelines and discussed with the members of all the three working groups. This tool provides the user a framework to navigate through the comprehensive mass spectrometry guideline by retrieving the required information about the experiment performed and presenting the user only those parts of the guideline which apply to this match. The work on this tool is still in progress.

First steps have been made towards a data exchange format for mass-spectrometry data on the basis of mzML but this projects has been stopped due to some reasons. With regards to glycopeptide analysis data, members of the MIRAGE Commission are now collaborating with HUPO-PSI on an eventual extension of mzIdentML to include glycan information in this data exchange format. First results are to be expected soon.

(July 2020)