Protein phosphorylation plays a key role in vasopressin signaling in the renal-collecting duct. Large-scale identification and quantification of phosphorylation events triggered by vasopressin is desirable to gain a comprehensive systems-level understanding of this process. We carried out phosphoproteomic analysis of rat inner medullary collecting duct cells by using a combination of phosphopeptide enrichment by immobilized metal affinity chromatography and phosphorylation site identification by liquid chromatography-mass spectrometry n neutral loss scanning. A total of 714 phosphorylation sites on 223 unique phosphoproteins were identified from inner medullary collecting duct samples treated shortterm with either calyculin A or vasopressin. A number of proteins involved in cytoskeletal reorganization, vesicle trafficking, and transcriptional regulation were identified. Previously unidentified phosphorylation sites were found for membrane proteins essential to collecting duct physiology, including eight sites among aquaporin-2 (AQP2), aquaporin-4, and urea transporter isoforms A1 and A3. Through label-free quantification of phosphopeptides, we identified a number of proteins that significantly changed phosphorylation state in response to short-term vasopressin treatment: AQP2, Bclaf1, LRRC47, Rgl3, and SAFB2. In the presence of vasopressin, AQP2 monophosphorylated at S256 and diphosphorylated AQP2 (pS256͞261) increased in abundance, whereas AQP2 monophosphorylated at S261 decreased, raising the possibility that both sites are involved in vasopressin-dependent AQP2 trafficking. This study reveals the practicality of liquid chromotography-mass spectrometry n neutral loss scanning for large-scale identification and quantification of protein phosphorylation in the analysis of cell signaling in a native mammalian system. LC-MS͞MS ͉ collecting duct ͉ kidney ͉ Collecting Duct Phosphoprotein Database (CDPD) ͉ neutral loss E lucidation of cellular signaling networks requires methodologies for large-scale quantitative phosphoproteomic analysis that can be used to reveal dynamic system-wide changes in protein phosphorylation. Recent studies have introduced two new innovations, namely, immobilized metal affinity chromatography (IMAC) (1-3) and liquid chromatography-mass spectrometry (LC-MS) 3 neutral loss scanning (1-4), to increase the efficiency of phosphopeptide identification. Quantification of phosphopeptides in this setting has been challenging and has been successful so far in cultured cells (5) and yeast (6) but not in native mammalian cells and tissues. Here, we introduce a hybrid approach using IMAC for phosphopeptide enrichment, LC-MS multisequential (LC-MS n ) neutral loss scanning to identify phosphorylated residues in the peptides, and label-free quantification using numerical integration of pseudochromatograms constructed from MS peak heights.The method is used here for analysis of protein phosphorylation in vasopressin-sensitive inner medullary collecting duct (IMCD) cells freshly isolated from rat kidneys. ...