Abstract
The retention time provides critical information for glycan annotation and quantification from the Liquid Chromatography Mass Spectrometry (LC-MS) data. However, the variation of the precise retention time of glycans is highly dependent on the experimental conditions such as the specific separating columns, MS instruments and/or the buffer used. This variation hampers the exploitation of retention time for the glycan annotation from LC-MS data, especially when inter-laboratory data are compared. To incorporate the retention time of glycan across experiments, Glucose Unit Index (GUI) can be computed using the dextrin ladder as internal standard. The retention time of glycans are then calibrated with respect to glucose units derived from dextrin ladders. Despite the successful application of the GUI approach, the manual calibration process is quite tedious and often error prone. In this work, we present a standalone software tool GlycanGUI, with a graphic user interface to automatically carry out the GUI-based glycan annotation/quantification and subsequent data analysis. When tested on experimental data, GlycanGUI reported accurate GUI values compared with manual calibration, and thus is ready to be used for automated glycan annotation and quantification using GUI.
Highlights
Glycosylation is a post-translational modification that plays critical roles in important biological processes such as immune response, cellular differentiation/adhesion and host-pathogen interactions (Varki et al, 2009)
GlycanGUI provides a graphic user interface that takes mass spectra data containing dextran ladder as the internal standard. It determines Glucose Unit (GU) values by fitting to 3rd order polynomial or logarithmic function (Supplementary Figure S1), which allows for calibrating the retention time to the corresponding Glucose Unit Index (GUI)
To assign the peaks of the dextrin ladders in Liquid Chromatography coupled Mass Spectrometry (LC-MS) data, each peak in a full MS spectrum was first compared against the theoretical mass-to-charge-ratios of dextrin ladders with putative ion charges and abducts using a user-defined mass tolerance
Summary
Glycosylation is a post-translational modification that plays critical roles in important biological processes such as immune response, cellular differentiation/adhesion and host-pathogen interactions (Varki et al, 2009). The Liquid Chromatography coupled Mass Spectrometry (LC-MS) is one of the most widely used techniques for glycan analysis due to its high sensitivity and throughput (Pabst and Altmann, 2011). The retention time is often used to assess the separation of glycans and to assist glycan identification (Pabst and Altmann, 2011). The precise retention time of a specific glycan may vary widely depending on the experimental conditions such as the separating columns, MS instruments and/or the buffer used. This variation hampers the interpretation of LCMS/MS data, especially when inter-laboratory data are compared without any calibrations
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