The molecular mechanisms for the self-renewal and pluripotency of human induced pluripotent stem cells (hiPSCs) remain unclear. Obtaining a deep proteome profile of hiPSCs will help clarify these mechanisms. Here we applied a long gradient time (8 hours) with meter-long column analysis to achieve rapid and deep profiling of the hiPSC proteome. The data accompanying this paper have been deposited to jPOST with the identifiers JPST000081, JPST000082, JPST000083, JPST000085, JPST000086, JPST000087, JPST000088, and JPST000089.