Thyroglobulin (Tg) is secreted by thyroid epithelial cells. It is essential for thyroid hormonogenesis and iodine storage. Although studied for many years, only indirect and partial surveys of its post-translational modifications were reported. Here, we present a direct proteomic approach, used to study the degree of iodination of mouse Tg without any preliminary purification. A comprehensive coverage of Tg was obtained using a combination of different proteases, MS/MS fragmentation procedures with inclusion lists and a hybrid mass highresolution LTQ-Orbitrap XL mass spectrometer. Although only 16 iodinated sites are currently known for human Tg, we uncovered 37 iodinated tyrosine residues, most of them being mono-or diiodinated. We report the specific isotopic pattern of thyroxine modification, not recognized as a normal peptide pattern. Four hormonogenic sites were detected. Two donor sites were identified through the detection of a pyruvic acid residue in place of the initial tyrosine. Evidence for polypeptide cleavages sites due to the action of cathepsins and dipeptidyl proteases in the thyroid were also detected. This work shows that semi-quantitation of Tg iodination states is feasible for human biopsies and should be of significant medical interest for further characterization of human thyroid pathologies.Thyroglobulin (Tg) 3 is one of the most abundant proteins produced by the thyroid gland and comprises two identical subunits of ϳ330 kDa. This prohormonal glycoprotein is secreted by thyroid epithelial cells. It is stored in the lumen of thyroid follicles in a highly condensed and covalently crosslinked form with numerous disulfide bridges. There, Tg is used as a scaffold for thyroid hormonogenesis and as an iodine reservoir. Many post-translational modifications are known to occur on this protein such as glycosylation, sulfation, and iodination (1). A signal peptide is processed during its export to the lumen. The most specific Tg post-translational modification is certainly its iodination and 3,5,3Ј-triiodothyronine (T3) and thyroxine (T4) thyroid hormone synthesis. Indeed, through the combined action of NADPH oxidase and thyroperoxidase on the outer surface of the thyrocyte apical membrane, iodide ions that are also transported to the follicular lumen are covalently linked to some Tg tyrosyl residues to form mono-or diiodotyrosines (MIT or DIT, respectively). Coupling of two of these DIT residues then leads to the formation of T4 at an acceptor site, whereas coupling one MIT and one DIT moiety essentially forms T3 (2). In this reaction, the release of an iodotyrosyl moiety at the donor site leaves an "empty" side chain and the fate of this unusual residue is controversial. Some authors claim that a dehydroalanine is left instead of the tyrosine, whereas others observed pyruvic acid associated with cleavage of the polypeptide chain (3-7). Finally, the protein is proteolytically processed in the lumen, followed by endocytosis in lysosomes, to release the hormones. The principal proteases involved inclu...