GlycReSoft: A Software Package for Automated Recognition of Glycans from LC/MS Data

Abstract

Glycosylation modifies the physicochemical properties and protein binding functions of glycoconjugates. These modifications are biosynthesized in the endoplasmic reticulum and Golgi apparatus by a series of enzymatic transformations that are under complex control. As a result, mature glycans on a given site are heterogeneous mixtures of glycoforms. This gives rise to a spectrum of adhesive properties that strongly influences interactions with binding partners and resultant biological effects. In order to understand the roles glycosylation plays in normal and disease processes, efficient structural analysis tools are necessary. In the field of glycomics, liquid chromatography/mass spectrometry (LC/MS) is used to profile the glycans present in a given sample. This technology enables comparison of glycan compositions and abundances among different biological samples, i.e. normal versus disease, normal versus mutant, etc. Manual analysis of the glycan profiling LC/MS data is extremely time-consuming and efficient software tools are needed to eliminate this bottleneck. In this work, we have developed a tool to computationally model LC/MS data to enable efficient profiling of glycans. Using LC/MS data deconvoluted by Decon2LS/DeconTools, we built a list of unique neutral masses corresponding to candidate glycan compositions summarized over their various charge states, adducts and range of elution times. Our work aims to provide confident identification of true compounds in complex data sets that are not amenable to manual interpretation. This capability is an essential part of glycomics work flows. We demonstrate this tool, GlycReSoft, using an LC/MS dataset on tissue derived heparan sulfate oligosaccharides. The software, code and a test data set are publically archived under an open source license.

A Liquid Chromatography-Mass Spectrometry-based Approach to Characterize the Substrate Specificity of Mammalian Heparanase

“…The LC-MS raw files from Thermo Fisher LTQ-Orbitrap were converted to mzXML format using MSConvert from ProteoWizard (28) before deconvolution by DeconTools. The composition profiles were generated using GlycReSoft, developed in our laboratory (29), with the output data from DeconTools. HS oligosaccharide compositions are given as [⌬HexA,HexA,GlcN,Ac,SO 3 ], with a number for each denoting the number of the corresponding residues.…”

Specific Glycosylation of Membrane Proteins in Epithelial Ovarian Cancer Cell Lines: Glycan Structures Reflect Gene Expression and DNA Methylation Status

“…Furthermore, the development of glyco-bioinformatics databases and tools such as UniCarb KB (17), GlycoMod (18), GlycoWorkBench (19), GlycReSoft (20), and Multiglycan (21) have accelerated the pace of glycan characterization. In ovarian cancer, the majority of studies investigating N-glycans have been performed using serum (22)(23)(24)(25), in which significant cancer-associated changes such as increased levels of branching of the N-glycans attached to glycoproteins (24) and increased sialylation of N-glycopeptides (25) have been found.…”

Bioinformatics for Glycan Structure Determination by Mass Spectrometry

“…The bioinformatics approaches related to glycan MS analysis introduced in this minireview are, of course, only a fraction of recent progress and many of them were not covered here (45)(46)(47)(48)(49)(50)(51)(52)(53)(54).…”