Updated publication reference for PubMed record(s): 26757066. This dataset includes twelve DIA methods with various mass-isolation windows that analyze precursor ranges from 400-1250 m/z as well as shotgun acquired data with the same instrument and LC gradient. The mass-isolation windows analyzed included 3, 6, and 26 m/z widths. Each 3 m/z window method analyzed a 140 precursor m/z range, 6 m/z windows analyzed either a 200 or 280 precursor m/z range, and the 26 m/z isolation window method analyzed an 800 precursor m/z range from 400-1200 m/z. All data were collected with a 5600+ Sciex QTOF with a 70 minute reverse phase gradient. Shotgun analyses were collected with the sample samples, instrument, and gradient.