Me-iPLEX workflow. Upon treatment with sodium bisulfite, cytosines will remain as cytosines if methylated (black lollipop) or will be converted to a uracil if unmethylated. A multiplexed capture PCR amplifies regions surrounding CpGs of interest (uracil is replaced by thymine in PCR). Primers are annealed immediately 5′ to CpGs of interest, followed by a single-base extension PCR using terminator nucleotides. Extension products differ in mass according to the extended base, consistent with the CpG methylation status in the original DNA sample. Relative abundance of extension products is measured by MALDI-TOF mass spectrometry. Multiple extension products with unique masses can be combined into the same multiplexed reaction.