Optimization of Acquisition and Data-Processing Parameters . - NCBIJ Proteome Res. 2017 Feb 3;16(2):738-747. doi: 10.1021/acs.jproteome.6b00767. Epub 2017 Jan 3. Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry. Li S(1), Cao Q(2), Xiao W(3), Guo.optimization parameters improved,Optimization of Acquisition and Data-Processing Parameters for .Dec 20, 2016 . Fine tuning these interdependent parameters can further improve the throughput and accuracy of SWATH quantification compared to the original setting adopted in most SWATH proteomic studies. Furthermore, we compared the effectiveness of two widely used peak extraction software PeakView and.