A new computer program (GlycoX) to determine simultaneously the glycosylation sites and oligosaccharide heterogeneity of glycoproteins.

A new computer program, GlycoX, was developed to aid in the determination of the glycosylation sites and oligosaccharide heterogeneity in glycoproteins. After digestion with the nonspecific protease, each glycan at a specific glycosylation site contains a small peptide tag that identifies the location of the glycan. GlycoX was developed in MATLAB requiring the entry of the exact masses of the glycopeptide and the glycan spectra in the form of a mass-intensity table and taking advantage of the accurate mass capability of the mass analyzer, in this case a Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer. This program computes not only the glycosylation site but also the composition of the glycans at each site. Several glycoproteins were used to determine the efficacy of GlycoX. These glycoproteins range from the simple, with one site of glycosylation, to the more complex, with multiple (three) sites of glycosylation. The results obtained using the computer program were the same as those determined manually. Model glycoproteins yielded the correct results, and new glycoproteins with unknown glycosylation were examined with the site of glycosylation and the corresponding glycans determined. Furthermore, other functions in GlycoX, including an auto-isotope filter to identify monoisotopic peaks and an oligosaccharide calculator to obtain the oligosaccharide composition, are demonstrated.