per. High-throughput identification of IMCD proteins using LC-MS/ MS. Physiol Genomics 25: 263-276, 2006. First published January 31, 2006 doi:10.1152/physiolgenomics.00214.2005.-The inner medullary collecting duct (IMCD) is an important site of vasopressinregulated water and urea transport. Here we have used protein mass spectrometry to investigate the proteome of the IMCD cell and how it is altered in response to long-term vasopressin administration in rats. IMCDs were isolated from inner medullas of rats, and IMCD proteins were identified by liquid chromatography/tandem mass spectrometry (LC-MS/MS). We present a WWW-based "IMCD Proteome Database" containing all IMCD proteins identified in this study (n ϭ 704) and prior MS-based identification studies (n ϭ 301). We used the isotope-coded affinity tag (ICAT) technique to identify IMCD proteins that change in abundance in response to vasopressin. Vasopressin analog (dDAVP) or vehicle was infused subcutaneously in Brattleboro rats for 3 days, and IMCDs were isolated for proteomic analysis. dDAVP and control samples were labeled with different cleavable ICAT reagents (mass difference 9 amu) and mixed. This was followed by one-dimensional SDS-PAGE separation, in-gel trypsin digestion, biotin-avidin affinity purification, and LC-MS/MS identification and quantification. Responses to vasopressin for a total of 165 proteins were quantified. Quantification, based on semiquantitative immunoblotting of 16 proteins for which antibodies were available, showed a high degree of correlation with ICAT results. In addition to aquaporin-2 and ␥-epithelial Na channel (␥-ENaC), five of the immunoblotted proteins were substantially altered in abundance in response to dDAVP, viz., syntaxin-7, Rap1, GAPDH, heat shock protein (HSP)70, and cathepsin D. A 28-protein vasopressin signaling network was constructed using literature-based network analysis software focusing on the newly identified proteins, providing several new hypotheses for future studies.inner medullary collecting duct; systems biology; mass spectrometry; liquid chromatography; aquaporin-2; epithelial Na channel; vasopressin VASOPRESSIN CONTROLS RENAL WATER excretion in part by regulating the permeability of collecting duct cells to water. The main protein target for this process is the water channel aquaporin-2 (AQP2). Vasopressin regulates AQP2 in two ways to increase collecting duct water permeability (28). 1) Over a period of minutes, vasopressin stimulates trafficking of AQP2-containing vesicles to the apical region of the collecting duct cells where they fuse with the plasma membrane to increase water permeability. 2) Over a period of hours to days, vasopressin increases AQP2 protein abundance in the collecting duct cells, in part due to increased transcription of the AQP2 gene. The signaling pathways involved in these responses remain incompletely understood.In recent years, large-scale identification of proteins by mass spectrometry has become practical, and such techniques are finding increasing use in the discov...