We have developed a method for inducing pancreatic cancer stem cell-like cells (P-CSLC) and reported that calreticulin (CRT) is a novel marker for cancer stem cells. In this study, we applied this result and identified a new therapeutic target potential for pancreatic cancer stem cells through a comprehensive approach of proteomics and mRNA analysis using a next-generation sequencer. In particular, we identified several types of molecules highly expressed in CRT-positive P-CSLC by a comprehensive approach and activated metabolic pathways in the same cells, and showed their potential as therapeutic targets. Furthermore, we were able to analyze the surface antigens associated with P-CSLC and cancer associated fibroblasts (CAFs).