GlycoExtractor: a web-based interface for high throughput processing of HPLC-glycan data.
Recently, an automated high-throughput HPLC platform has been developed that can be used to fully sequence and quantify low concentrations of N-linked sugars released from glycoproteins, supported by an experimental database (GlycoBase) and analytical tools (autoGU). However, commercial packages that support the operation of HPLC instruments and data storage lack platforms for the extraction of large volumes of data. The lack of resources and agreed formats in glycomics is now a major limiting factor that restricts the development of bioinformatic tools and automated workflows for high-throughput HPLC data analysis. GlycoExtractor is a web-based tool that interfaces with a commercial HPLC database/software solution to facilitate the extraction of large volumes of processed glycan profile data (peak number, peak areas, and glucose unit values). The tool allows the user to export a series of sample sets to a set of file formats (XML, JSON, and CSV) rather than a collection of disconnected files. This approach not only reduces the amount of manual refinement required to export data into a suitable format for data analysis but also opens the field to new approaches for high-throughput data interpretation and storage, including biomarker discovery and validation and monitoring of online bioprocessing conditions for next generation biotherapeutics.
Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Dublin 4, Ireland. natalia.artemenko@nibrt.ie
Natalia V
NV
Artemenko
Matthew P
MP
Campbell
Pauline M
PM
Rudd
D015415:Biomarkers / Q000737:chemistry; D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D020407:Internet; D011134:Polysaccharides / Q000737:chemistry*; D012984:Software; D014584:User-Computer Interface
D015415:Biomarkers; D011134:Polysaccharides