The study of N-linked glycosylation has long been complicated by a lack of bioinformatics tools. Especially, there is still a lack of fast and robust data processing tools for targeted (relative) quantitation. We have developed a modular, high-throughput data processing software, MassyTools, that is capable of calibrating spectra, extracting data and performing quality control calculations based on a user defined list of glycan or glycopeptide compositions. Typical examples of output include relative areas after background subtraction, isotopic pattern-based quality scores, spectral quality scores and signal-to-noise ratios. We demonstrated the performance on MALDI-TOF-MS glycan and glycopeptide data from different samples. MassyTools yielded better calibration than the commercial software flexAnalysis generally showing two-fold better ppm errors after internal calibration. Relative quantitation using MassyTools and flexAnalysis gave similar results, yielding a relative standard deviation (RSD) of the