Hexapeptide library as a universal tool for sample preparation in protein glycosylation analysis.
ABSTRACT Recent analytical advancements allow for large-scale glycomics and glycan-biomarker research with N-glycans released from complex protein mixtures of e.g. plasma with a wide range of protein concentrations. Protein enrichment techniques to obtain samples with a better representation of low-abundance proteins are hardy applied. In this study, hexapeptide ligands previously described for enrichment of low-abundance proteins in proteomics are evaluated for glycan analysis. A repeatable on-bead glycan release strategy was developed, and glycans were analyzed using capillary sieving electrophoresis on a DNA analyzer. Binding of proteins to the hexapeptide library occurred via the protein backbone. At neutral pH no discrimination between protein glycoforms was observed. Interestingly, glycan profiles of plasma with and without hexapeptide library enrichment revealed very similar patterns, despite the vast changes in protein concentrations in the samples. The most significant differences in glycosylation profiles were ascribed to a reduction in immunoglobulin-derived glycans. These results suggest that specific and sensitive biomarkers will be hard to access on the full plasma level using protein enrichment in combination with glycan analysis. Instead, fractionation techniques or profiling strategies on the glycopeptide level after enrichment are proposed for in-depth glycoproteomics research.
- SourceAvailable from: Dong Xia[show abstract] [hide abstract]
ABSTRACT: Systems biology aims to integrate multiple biological data types such as genomics, transcriptomics and proteomics across different levels of structure and scale; it represents an emerging paradigm in the scientific process which challenges the reductionism that has dominated biomedical research for hundreds of years. Systems biology will nevertheless only be successful if the technologies on which it is based are able to deliver the required type and quality of data. In this review we discuss how well positioned is proteomics to deliver the data necessary to support meaningful systems modelling in parasite biology. We summarise the current state of identification proteomics in parasites, but argue that a new generation of quantitative proteomics data is now needed to underpin effective systems modelling. We discuss the challenges faced to acquire more complete knowledge of protein post-translational modifications, protein turnover and protein-protein interactions in parasites. Finally we highlight the central role of proteome-informatics in ensuring that proteomics data is readily accessible to the user-community and can be translated and integrated with other relevant data types.Parasitology 07/2012; 139(9):1103-18. · 2.36 Impact Factor