Drug resistance to targeted anticancer reagent is a major hurdle in cancer therapy. Tumors are composed of heterogeneous cells that respond to drugs differently and communications between heterogeneous cell populations in tumors are associated with drug resistance. In order to investigate mechanisms that underlie cell-cell communications contributing drug resistance, we analyzed differential secretome between parent EGFR mutant non-small cell lung cancer cell lines (PC9 and HCC827) and those cells with acquired resistance to EGFR tyrosine kinase inhibitor, erlotinib (PC9ER and HCC827ER). Tryptic peptides obtained from conditioned media were labeled with tandem mass tag (TMT) reagents, high pH fractionated using HPLC, then analyzed in LC-MS/MS. About 4200 and 3400 proteins were identified and quantified from a pair of PC9/PC9ER and HCC827/HCC827ER, respectively. Differentially expressed proteins were defined by data processing that involves normalization using the subtraction of median values based on columns after transformed as log2 values and two-sample test with below 0.05 p-value. Our analysis revealed 143 increased and 67 decreased proteins commonly in PC9ER and HCC827ER cells compared to parent cells. The pathway analysis revealed that extracellular matrix organization, cell-cell adhesion and regulation of cell adhesion pathways were enriched from proteins decreased in resistance cells, while heterocycle biosynthetic process, cellular amino acid metabolic process and small molecule biosynthetic process were enriched from increased proteins. In addition, we enriched glycopeptides using HILIC and then analyzed in LC-MS/MS. 226 of 530 and 192 glycoproteins of 490 glycoproteins from PC9/PC9ER and HCC827/HCC827ER sample respectively were commonly identified from both proteomics and glycoproteomics. Glycan type and complexity of glycopeptides were differently quantified control and resistance cells. Combined proteomics and glycoproteomics study is expected to provide novel and deep insights into mechanism by which tumor heterogeneity contributes drug resistance.