In typical data independent acquisition (DIA) methods on Q-TOF instruments, the quadrupole mass filter or ion trap either operates in wide pass mode or in stepped mode with typical transmission windows in the range of 1-20Da. Here we describe a mode of DIA operation whereby a resolving quadrupole is scanned repetitively over alternating low and elevated energy scans.The m/z range of the quadrupole was continuously and repetitively scanned with data acquired using a ToF acquisition system capable of delivering 2000 ToF spectra / s. Alternate scans contain low energy data for precursor and high energy data for fragment ions. The resulting 2D data format can be processed using both commercial and open source software for identification / quantitative results.The effect of the scanning quadrupole transmission window has been investigated to assess qualitative performance. Tryptic digest standards were injected onto a LC system and separated using a 90 minute gradient. It was found that quadrupole transmission windows of 20-30 Da provided optimum protein identifications. Over 1,000 proteins were identified from a cytosolic E.coli digest standard (4% FDR). Additional evaluations of this methodology for qualitative and quantitative proteomic analyses will be made via the analyses of two disparate sample cohorts - characterization of synaptic proteomes as part of a study of developmental brain disorders, and differential analyses of protein:protein complexes of calcineurin (Aspergillus fumigatus) as a function of mechanism-of-action of several antifungal drugs.