What We Haven't Heard About PIK-3

120025). Raw mass spectrometry data were processed using the MaxQuant software (Cox and Mann, 2008) version 1.2.3.3, using the default settings with minor changes (see Supplemental Experimental Procedures). Database searching was performed using the Andromeda search engine integrated into the MaxQuant environment (Cox et?al., 2011) against the mouse international protein index (IPI) database v3.68, concatenated with known contaminants as well as the reversed sequences of all entries. Protein, peptide, and site FDRs PIK-3 were controlled at a maximum of 1%. Data analyses were performed using Microsoft Office Excel, the R software environment, and the bioinformatics platform Perseus (Max Planck Institute of Biochemistry, Munich). Gene ontology (GO) annotation enrichment analysis was performed in Perseus, and significance was assessed using Fisher��s exact test. The whole quantified phosphoprotein data set was used as a background Ion Channel Ligand Library data set, and the Benjamini-Hochberg FDR method was used for multiple hypotheses testing (FDR?VEGFR inhibitor and Bing Su and Estela Jacinto for shared reagents. This work was supported by an NHMRC program grant (D.E.J.). D.E.J. is an NHMRC Senior Principal Research Fellow. D.J.F. is a Sir Henry Wellcome Postdoctoral Fellow. S.J.H. and D.E.J. designed and conceived the studies and wrote the manuscript. S.J.H. performed the MS studies, data analyses, functional assays, and immunoblotting. G.Y. performed fluorescence-activated cell sorting (FACS), immunoblotting, and functional assays. P.Y. performed computational analysis and developed analytical tools. D.J.F. assisted with MS studies and functional assays. J.S.