Phosophoproteomic analysis was used to profile cell lines in the MCF-10A lineage of human mammary epithelial cells to determine how human breast cells can be reprogrammed during tumorigenic progression. Data were collected using a LTQ-XL mass spectrometer (Thermo). Phosphopeptides were enriched from cell extracts from 3 independent biological replicates, and each replicate was analyzed as 3 technical replicates for a total of 9 LC/MS/MS runs per cell line.