Reproducibility of SWATH™ MS Analysis and Implications for System Biology Studies

In system biology studies, collecting complete quantitative data is crucial for the construction and validation of the network models. Thus it is essential for the techniques applied to consistently, accurately and sensitively quantify a wide range of different species, especially the interactors that are located at the interfaces of the networks. This application note presents the analysis of a complex mixture with SWATH™-MS methods and evaluate the reproducibility of identification and quantification of a large number of peptides and proteins.