Sweet Substitute: A software tool for in silico fragmentation of peptide‐linked N‐glycans

A software tool, Sweet Substitute, is described, which assists tandem mass spectrometry (MS/MS)‐based glycosylation characterization from within a tryptic digest. The algorithm creates a virtual nanoelectrospray‐quadrupole time‐of‐flight style‐MS/MS spectrum of any user‐defined N ‐linked glycan structure. An empirical peak height modeling routine is implemented in the program. By comparing the theoretical MS/MS data with the deconvoluted and deisotoped experimental MS/MS data, the user is able to quickly assess whether a proposed candidate oligosaccharide structure is a plausible one.