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Quantification of proteins by mass spectrometry at the level of entire proteomes has become a central aspect in contemporary proteomics. Sequential Window Acquisition of all THeoretical fragment-ion spectra (SWATH) mass spectrometry is a label-free protein quantification method enabling parallel quantification of up to several thousand proteins, thereby granting a comprehensive overview of highly complex samples. We optimized several parameters of the mass spectrometrical detection to increase the size of the library, enhance the precision of protein quantifications and decrease systematic errors induced by fragment ion interference. By these means enhanced differential analyses facilitate the detection of more significantly regulated proteins with a dynamic range of over three orders of magnitude., (Copyright © 2016 Elsevier B.V. All rights reserved.)