This dataset consists of three mass spectrometry experiments where different isolation window sizes were explored in combination with gas phase fractionation, using a yeast lysate with selective oxidation of methionine. The resulting DIA data, as .raw files, include (1) one run covering the 400--1200 m/z mass range acquired using 20 m/z isolation windows; (2) two runs acquired using 10 m/z isolation windows to cover 400--800 and 800--1200 m/z mass ranges; (3) four runs acquired using 5 m/z isolation windows covering 400--600, 600--800, 800--1000, and 1000--1200 m/z ranges, respectively.