Automated interpretation of tandem mass spectra of N-linked oligosaccharides obtained from matrix-assisted laser desorption/ionization

Oligosaccharides associated with proteins are known to give these molecules specific conformations and functions. The analysis of proteins would thus not be complete without studying glycans. However, high-throughput techniques in proteomics will soon overwhelm the current capacity of methods if no automation is incorporated into glycomics. The StrOligo (for structure of oligosaccharides) algorithm developed for this purpose will be discussed here.; Simulated tandem mass spectra were used to define the limits of the algorithm. Experimental tandem mass spectra were then acquired to validate the algorithm using a hybrid quadrupole-time-of-flight (QqTOF) instrument with a matrix-assisted laser desorption ionization (MALDI) source. The samples were composed of N-linked oligosaccharides from monoclonal antibody IgG, recombinant beta interferon, bovine fetuin and human integrin. Glycans were detached by enzymatic deglycosylation and labelled at the reducing end.; The algorithm first builds a relationship tree, explaining each observed loss of monosaccharide moiety and relating corresponding peaks to one another. The algorithm then analyzes the tree and proposes possible compositions and structures from combinations of adduct and fragment ion types. A score, which reflects agreement with experimental results, is then given to each proposed structure. The program then shows the structures found and the score they obtained and labels relevant peaks in the experimental mass spectrum using a modified nomenclature for the structure with the highest score.; The usefulness of the algorithm has been demonstrated by assigning structures to glycan populations of several glycoproteins. The algorithm has also been used to assign glycan populations to a specific glycosylation site of integrin. Analyses were completed in less than two minutes for the most complex structures, which is a substantial improvement over manual interpretation, which can take a few hours. StrOligo is thus a good step in the direction of high-throughput glycomics.