This study aimed to investigate the link between DNA methylation and protein expression on a genome wide level, using a combination of MBD-sequencing and shotgun and positional proteomics on two human colon cancer cell lines: a wild type HCT116 cell line and a double knock out HCT116 cell line (DNMT1 -/- and DNMT3b -/-). The protein content of the HCT116 WT and DKO cell lines was not only analyzed using a standard shotgun proteomics approach, but also with the N-terminal COFRADIC technique (Staes et al., 2011), in order to determine the (alternative) translation start site of the expressed proteins.