Glycomics, probably even more than any other current “-omic” field of study, places a great burden of data upon the researcher, necessitating informatics solutions. The computational challenges and approaches being employed to address this by no means simple task are summarised in two excellent reviews [13
]. In essence, the ever increasing complexity and quantity of data that are routinely produced from the glycomic analysis of cells and tissues requires support, in the form of data repositories and software tools, to facilitate faster analysis and more meaningful interrogation of the combined glycomic system.
To this end, databases of complex glycan structural data were born from the ashes of CarbBank, the five most prominent publically available examples of which are the Consortium for Functional Glycomics’ (CFG) relational database (http://www.functionalglycomics.org/glycomics/common/jsp/firstpage.jsp
), the Kyoto Encyclopedia of Genes and Genomes glycome informatics resource (KEGG GLYCAN) (http://www.genome.jp/kegg/glycan/
), the Japan Consortium for Glycobiology and Glycotechnology DataBases (JCGGDB) (http://jcggdb.jp/index_en.html
), Glycosciences.de (http://www.dkfz.de/spec/glycosciences.de/sweetdb/index.php
) and EuroCarbDB (http://www.ebi.ac.uk/eurocarb/home.action
). Of course, whenever databases are developed independently of each other, the problem of format and language will present itself. Each of the initiatives has developed its own standards, tools and databases, so as these projects grew (and the commercial and private access versions along with them) the issue of inter-compatibility was confronted and directly addressed by the glycoinformatics community[15
]. In response to this lack of standardisation, the Complex Carbohydrate Research Center (CCRC) at the University of Georgia has developed the GLYDE-II XML representation which is being accepted as the standard format for the exchange of carbohydrate structural data (CCRC Glyde-II; URL:http://glycomics.ccrc.uga.edu/core4/informatics-glyde-ii.html
In order to better populate these databases, the development of software tools to aid the arduous process of data analysis and annotation is of great importance. The complexity of glycoconjugates and the variety of techniques employed in the elucidation of their structures present significant roadblocks to an integrated single-package solution for glycomic analysis. Nonetheless, there are an increasing number of algorithms and tools designed to support these experiments [13
]. Perhaps the most promising of the glycomic mass spectrometric interpretation approaches is Cartoonist
], which has been adopted by the CFG and is designed to mimic the approach of a human expert in the annotation of MS data. Like many of the structure analysis programs, the Cartoonist
algorithms are being continually refined to produce a more non-expert user-friendly experience, which will enable a greater proportion of the scientific community to utilise the data presented by the repositories in a meaningful way.
The closest to a complete glycomic MS analysis tool thus far developed is the GlycoWorkBench tool developed by the EuroCarbDB initiative [17
]. It provides support to the manual interpretation of MS glycomic data, incorporating an increasing number of user-friendly features designed to assist the researcher. These include a glycan structure editor, mass-based structure prediction, fragmentation prediction tools and the semi-automated assignment of MS/MS spectra. Due to its modular design, GlycoWorkBench even has the capacity to integrate related tools, such as Cartoonist
, into its interface.
Of course, as the analysis of glycomic data becomes more accessible and more efficient through use of these informatic tools, the public databases (assuming they obtain sustainable funding) will continue to be populated with structurally-derived information, all of which will be accessible via the GLYDE-II XML exchange format. This broad and, most importantly, freely accessible base of data will begin to allow mining of the information in more and more meaningful ways, such as the prediction of glycan structures or potential bio-markers. Current and potential avenues of research in this area are discussed at length in the aforementioned pair of reviews [13
], which also include useful reference information and links concerning the vast majority of the current initiatives.