As a test use case, we performed a large-scale survey of PIN alterations in breast cancer by using mCF/MS to compare the composition and levels of protein macromolecules in three established human cell lines (mammary-tumor derived triple-negative MDA-MB-231, estrogen receptor-positive MCF7, and non-transformed MCF10A breast epithelial cells). The gene discussed is ESR1; the disease is breast carcinoma.