GlycoMod - A software tool for determining glycosylation compositions from mass spectrometric data

Abstract

GlycoMod (http://www.expasy.ch/tools/glycomod/) is a software tool designed to find all possible compositions of a glycan structure from its experimentally determined mass. The program can be used to predict the composition of any glycoprotein-derived oligosaccharide comprised of either underivatised, methylated or acetylated monosaccharides, or with a derivatised reducing terminus. The composition of a glycan attached to a peptide can be computed if the sequence or mass of the peptide is known. In addition, if the protein is known and is contained in the SWISS-PROT or TrEMBL databases, the program will match the experimentally determined masses against all the predicted protease-produced peptides (including any post-translational modifications annotated in these databases) which have the potential to be glycosylated with either N- or O-linked oligosaccharides. Since many possible glycan compositions can be generated from the same mass, the program can apply compositional constraints to the output if the user supplies either known or suspected monosaccharide constituents. Furthermore, known oligosaccharide structural constraints on monosaccharide composition are also incorporated into the program to limit the output.

Mass spectrometry-based N-linked glycomic profiling as a means for tracking pancreatic cancer metastasis

“…Our results show the presence of various 41 N-glycan structures, including that of high-mannose type glycans and complex bi-, tri-, and tetra-antennary glycans with sialic acid and/or fucose residues. The composition of the N-glycans are predicted from experimental mass values using GlycoMod tool (ExPASy: SIB bioinformatics resource portal), 6 and further corroborated for detailed structure via tandem mass spectrometric analysis.…”

N-glycome profiling of Bothrops jararaca newborn and adult venoms

“…Collision parameters were left at default values with normalized collision energy set to 35% or to a value leaving a minimal precursor peak. Activation Q was set at 0.25 and activation time at 30 ms. Sodiated adduct masses were used to perform the searches for putative glycan composition using GlycoMod tool (http:// ca.expasy.org/tools/glycomod/) [24]. For assigning glycan composition, all masses were monoisotopic, mass tolerance was set to 2 Da and permethylation derivatives of monosaccharide residues were selected.…”

FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification

“…Several tools exist to identify potential co-and post-translational modifications (PTMs) by comparing observed and predicted masses, e.g. FindMod (http://www.expasy.org/tools/findmod/) [5] and GlycoMod (http://www.expasy.org/tools/glycomod/) [6].…”