The mzXML files contain measurements obtained in an experiment designed to compare Fc-linked IgG N-glycosylation profiles of mouse immunoglobulin G with LC-MS of tryptic glycopeptides. IgG was affinity purified on protein G monolithic plates, digested with trypsin and analysed on a nanoACQUITY UPLC system (Waters, USA) coupled to a Compact MS (Bruker Daltonics, Bremen, Germany) in the gradient of 80% acetonitrile in 0.1% trifluoroacetic acid (for the detailed description of the LC-MS analysis see Pezer, M. et al. Effects of allergic diseases and age on the composition of serum IgG glycome in children. Sci. Rep. 6, 33198 (2016)) We have applied our method to a sample set of 3 inbred strains: BALB/c, C57BL6 and C3H. All animals were males of 15 weeks old. We observed differences in subclass-specific and strain-specific N-glycosylation of IgG, which suggests a significant genetic component in the regulation of Fc-linked IgG N-glycosylation. Description of the samples could be found in the attached excel sheet.