In this study, by using two classical macrophage cell models, RAW264.7 cell line from mouse and THP-1 cell line from human, combined with the applications of two classical stimulation methods for inducing classical activated (M1) and alternatively activated macrophages (M2) from the monocytes of both cell lines, we comprehensively identified and quantified proteins in different types of macrophages from both cell lines through high-throughput proteomics.