Informatics Tools for Glycomics: Assisted Interpretation and Annotation of Mass Spectra

Abstract

Recent years have seen an increase in both the development and use of informatics tools and databases in glycobiology-based research. Mass spectrometric methods, which are capable of detecting oligosaccharides in the low picoto femtomole range, are fundamental technologies used in glycan analysis. The availability of robust and reliable algorithms to automatically interpret MS spectra is critical to many glycomic projects. Unfortunately, the current state-ofthe-art in glycoinformatics is characterized by the existence of disconnected and incompatible islands of experimental data, resources, and proprietary applications. The development of tools for the robust automatic assignment of glycans on the basis of MS measurements is often hampered by the paucity of available MS data. Here, we review the methodologies for semi-automatic interpretation of MS spectra of glycans, based upon current technology. Three promising approaches are highlighted: (a) combinatorial approaches to the automatic assignment of possible monosaccharide superclass composition—Glyco-Peakfinder, (b) the scoring of a set of identified structures with theoretically calculated fragments–GlycoWorkbench and (c) the correlation of experimental masses to a database of theoretical fragment masses, in a technique known as Glycofragment Mass Fingerprinting.