Improving SWATH by Overlapped Windows

This application note investigates the use of overlapping SWATH windows to improve the cycle time and reduce the SWATH window size. The ability to acquire all possible MS/MS fragments during each cycle of data acquisition has radically changed peptide quantitation capabilities. Since no prior information is required, data acquisition is greatly simplified. During data processing, the particulars of which peptides and proteins are studied can be changed at any time, without the need for reacquiring any data. This investigation demonstrated that overlapping windows enabled deconvolution to narrower windows without loss in duty cycle and that narrower windows improved MS/MS quality and quantitative properties.