EUROCarbDB(CCRC): a EUROCarbDB node for storing glycomics standard data

Abstract

Motivation: In the field of glycomics research, several different techniques are used for structure elucidation. Although multiple techniques are often used to increase confidence in structure assignments, most glycomics databases allow storing of only a single type of experimental data. In addition, the methods used to prepare a sample for analysis is seldom recorded making it harder to reproduce the analytical data and results.

Results: We have extended the freely available EUROCarbDB framework to allow the submission of experimental data and the reporting of several orthogonal experimental datasets. The features aim to increase the understandability and reproducibility of the reported data.

Availability and implementation: The installation with the glycan standards is available at http://glycomics.ccrc.uga.edu/eurocarb/. The source code of the project is available at https://code.google.com/p/ucdb/.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Three N-glycan and eight O-glycan compounds have been provided by the CFG as analytical standards. Each is displayed using the CFG cartoon representation together with the name used to identify each structure

Fig. 2.

Design of the O-glycan analysis experiment. Each glycan sample was divided into aliquots and analyzed by NMR without further treatment and tandem MSⁿ. Additional aliquots were analyzed by MSⁿ after being subjected to reductive β-elimination to release O-glycans as oligoglycosyl alditols, and again after permethylation and selection of ions formed by complexation with Li⁺ and Na⁺

Fig. 3.

Design of the N-glycan experiment. Each native glycan sample was divided into two aliquots: one was analyzed by NMR without modification, and the other was permethylated and analyzed as the Na⁺ adduct by tandem MS

Fig. 4.

The design of an experiment is a multistep process. It starts by defining protocols, which are general but detailed descriptions of laboratory tasks, including lists of any parameters that may vary. Protocol variants are then instantiated in the context of an experiment template, which specifies a linear or branched sequence of protocol variants. In the Figure, arrows leading from protocol variants to protocols represent instantiation. These steps involve the explicit specification of protocol parameter values. An experiment template thus defined can then be instantiated as an actual experiment (arrows from experiment to experiment template represent instantiation). Each experiment encapsulates all of the MS, HPLC and/or NMR data acquired during a discrete analysis of a specific sample along with the metadata describing how these data were obtained

Fig. 5.

Screenshot of an experiment overview containing (1) experiment name; (2) description; (3) description URI; (4) glycan structure identified in this experiment; (5) evidence types provided to identify the glycan structure; (6) protocol names; (7) evidence/data files (mzXML); (8) annotation (Glyco Workbench File); (9) NMR protocol/data

Fig. 6.

Screenshot of a protocol summary. For each protocol that is part of an experiment a similar summary is available. Each summary includes the name of the protocol (e.g. Aliquoting), its description, a link to the Web page describing the protocol and a list of variable parameters, each documented with a name, description, unit of measurements and value