A systematic study of posttranslational modifications of the estrogen receptor isolated from the MCF-7 human breast cancer cell line is reported. Proteolysis with multiple enzymes, mass spectrometry, and tandem mass spectrometry achieved very high sequence coverage for the full-length 66-kDa endogenous protein from estradiol-treated cell cultures. Nine phosphorylated serine residues were identified, three of which were previously unreported and none of which were previously observed by mass spectrometry by any other laboratory. Two additional modified serine residues were identified in recombinant protein, one previously reported but not observed here in endogenous protein and the other previously unknown. Although major emphasis was placed on identifying new phosphorylation sites, N-terminal loss of methionine accompanied by amino acetylation and a lysine side chain acetylation (or possibly trimethylation) were also detected. The use of both HPLC-ESI and MALDI interfaced to different mass analyzers gave higher sequence coverage and identified more sites than could be achieved by either method alone. The estrogen receptor is critical in the development and progression of breast cancer. One previously unreported phosphorylation site identified here was shown to be strongly dependent on estradiol, confirming its potential significance to breast cancer. Greater knowledge of this array of posttranslational modifications of estrogen receptor, particularly phosphorylation, will increase our understanding of the processes that lead to estradiol-induced activation of this protein and may aid the development of therapeutic strategies for management of hormonedependent breast cancer. Molecular & Cellular Proteomics 8:467-480, 2009.The ␣-isoform of the estrogen receptor (ER␣) 1 is a 66-kDa nuclear transcription factor that mediates transcriptional regulation of genes involved in cell proliferation and differentiation and plays a pivotal role in the development and progression of breast cancer (1-3). Consequently the development of therapies for management of hormone-dependent breast cancer has targeted signaling pathways based on modulation of ER␣ activity (4 -6). Current knowledge and understanding of ER␣ activity is derived from over 30 years of accumulated scientific evidence that has sought to delineate ER-mediated mechanisms and signaling pathways under pathological conditions modeled in cultured breast cancer cell lines. Because the function or activity of a protein may depend strongly on the presence of posttranslational modifications (PTMs), significant research has focused on detection and quantitation of such modifications in ER␣. The constellation of PTMs on a protein constitutes a molecular code that may dictate protein conformation, localization, and function. Thus biological inference based on ER␣ structure requires a comprehensive study of all possible PTMs on the constituent amino acids.Modifications to ER␣ reported to date are listed in Table I. Two of the most common and important PTMs that modulate the...