This dataset contains mzXML files obtained in an experiment designed to assess technical variation introduced by sample preparation procedure for the analysis of Fc-linked IgG N-glycosylation profiles of mouse immunoglobulin G with LC-MS of tryptic glycopeptides. To test the technical variation introduced by each step we used replicates of combined BALB/c and C3H mouse serum pool sample. The serum pool was aliquoted by 100 µl per sample onto protein G monolithic plate for IgG isolation. Since the starting serum sample was pooled, all the variation observed in the sample measurements is purely technical. There were 5 different conditions designated as A-E in the experiment, each condition included 18 or 19 replicates: A - each of the 19 replicates on from IgG isolation was treated separately, so each sample measurement contains the variation originating from all sample preparation steps; B - samples were pooled after step 1 of sample preparation and aliquoted before step 2, sample measurements contain technical variation resulting from steps 2-5; C - samples were pooled and aliquoted after steps 1 and 2, the measurements contain technical variation resulting from steps 3-5; D - samples were pooled after steps 1-3, measurements contain technical variation from steps 4-5; E - samples were pooled after steps 1-4, measurements contain technical variation resulting only from step 5 which includes MS analysis and subsequent data processing. Tryptic glycopeptides were 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 observed that the IgG isolation procedure introduces most of the variation. This folder contains only a part of the data. To download the complete dataset please also download "MIgGGly-TechnicalVariation-part2" dataset: http://dx.doi.org/10.17632/y3t2kkfx7v.1 Description of the samples could be found in the attached excel sheet.