Targeted mass spectrometry comprises a set of methods able to quantify protein analytes in complex mixtures with high accuracy and sensitivity. These methods, e.g., Selected Reaction Monitoring (SRM) and SWATH MS, use specific mass spectrometric coordinates (assays) for reproducible detection and quantification of proteins. In this protocol, we describe how to analyze, in a targeted manner, data from a SWATH MS experiment aimed at monitoring thousands of proteins reproducibly over many samples. We present a standard SWATH MS analysis workflow, including manual data analysis for quality control (based on Skyline) as well as automated data analysis with appropriate control of error rates (based on the OpenSWATH workflow). We also discuss considerations to ensure maximal coverage, reproducibility, and quantitative accuracy.