Phosphorylation can dramatically change a protein's biological location or activity. The profound influence of protein phosphorylation on mammalian brain development has strong genetic support. This is exemplified by the important brain phenotypes observed in mice with loss of function mutations in genes encoding kinases such as p35/cyclin-dependent kinase 5 (Cdk5) 1 (1, 2), loss of tyrosine phosphorylation sites in signaling molecules such as the Reelin-stimulated adaptor protein Disabled-1 (3), or loss of genes encoding proteins that interact with phosphorylated protein motifs such as 14-3-3⑀ (4).Historically, the analysis of protein phosphorylation sites has been restricted to studies at the single-protein level. Recently, larger-scale MS-based analyses have emerged. However, such studies have been challenging due to a) the immaturity of methods to enrich for low-abundance phosphoproteins or phosphopeptides and b) the reduction in quality of informative tandem mass spectra obtained from phosphopeptides subjected to CID (5). The latter challenge is due primarily to the propensity for precursor ions containing phosphoserine or phosphothreonine to undergo -elimination of phosphoric acid with an accompanied reduction of structurally informative ions from peptide backbone fragmentation. Recent advances in metal ion affinity chromatography have permitted large-scale phosphorylation analysis (200 -400 sites identified) in yeast (6) and plants (7). Here, using strong cation exchange (SCX) chromatography at low pH to enrich for tryptic phosphopeptides (8), we show the first large-scale proteomic profiling of phosphorylation sites from primary animal tissue. These methods promise to greatly enrich our global view of the dynamic changes of phosphoproteins during brain development and may be applied to a variety of primary tissues or comparative states in cultured cells.
EXPERIMENTAL PROCEDURESMice and Tissue Preparation-A timed pregnant Swiss Webster mouse was obtained from Taconic (Germantown, New York). Developing forebrains and midbrains were dissected from embryos at day 16.5 (E16.5). The tissue from four brains (10 mg) was dounce homogenized in 25 mM Tris pH 7.2, 137 mM NaCl, 10% glycerol, 1% Nonidet P-40, 25 mM NaF, 10 mM Na 2 P 2 O 7 , 1 mM Na 3 VO 4 , 1 mM DTT, 1 mM PMSF, 10 g/ml leupeptin, and 1% aprotinin.Gel Electrophoresis and In-gel Digests-Cleared extracts were boiled in bromphenol blue sample buffer (150 mM Tris pH 6.8, 2% SDS, 5% -mercaptoethanol, 7.8% glycerol), and 6 mg of extract was loaded onto a hand-poured, 7.5-20% gradient SDS-polyacrylamide (37.5:1 acrylamide:bis-acrylamide) preparative gel (see Fig. 2A). The Coomassie blue-stained gel was cut into four regions and then diced into 1-mm cubes. The gel pieces were washed with water and further destained with 50% ACN, 50 mM NH 4 HCO 3 pH 8.5. Gel slices were dehydrated with ACN, dried, and subjected to in-gel digestion with sequencing-grade modified trypsin (12.5 ng/l; Promega, Madison, WI) in 50 mM NH 4 HCO 3 overnight at 37°C. Peptides were extr...