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. 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-part1" dataset: http://dx.doi.org/10.17632/9zdbd6j4r9.1 Description of the samples could be found in the excel sheet attached with the part 1 of the dataset.