Fragile X syndrome (FXS) is a common inherited form of mental retardation that is caused, in the vast majority of cases, by the transcriptional silencing of a single gene, fmr1. The encoded protein, FMRP, regulates mRNA translation in neuronal dendrites, and it is thought that changes in translation-dependent forms of synaptic plasticity lead to many symptoms of FXS. However, little is known about the potentially extensive changes in synaptic protein content that accompany loss of FMRP. Here, we describe the development of a high-throughput quantitative proteomic method to identify differences in synaptic protein expression between wild-type and fmr1؊/؊ mouse cortical neurons. The method is based on stable isotope labeling by amino acids in cell culture (SILAC), which has been used to characterize differentially expressed proteins in dividing cells, but not in terminally differentiated cells because of reduced labeling efficiency. To address the issue of incomplete labeling, we developed a mathematical method to normalize protein ratios relative to a reference based on the labeling efficiency. Using this approach, in conjunction with multidimensional protein identification technology (MudPIT), we identified >100 proteins that are up-or down-regulated. These proteins fall into a variety of functional categories, including those regulating synaptic structure, neurotransmission, dendritic mRNA transport, and several proteins implicated in epilepsy and autism, two endophenotypes of FXS. These studies provide insights into the potential origins of synaptic abnormalities in FXS and a demonstration of a methodology that can be used to explore neuronal protein changes in neurological disorders. stable isotope labeling ͉ proteomics ͉ mass spectrometry ͉ fragile X syndrome F ragile X syndrome (FXS) is the most common inherited form of mental retardation. It is characterized by low IQ (1) and a broad set of symptoms other than retardation that compound the level of impairment. These include autistic spectrum behaviors, attention deficit and hyperactivity, childhood seizures, and several physical manifestations (2, 3). The most profound neuroanatomical abnormality seen in the brains of FXS patients is a preponderance of long, thin, and ''tortuous'' dendritic spines in cortex (4). This cortical phenotype is recapitulated in the fmr1 knockout (KO) mouse model, which also exhibits abnormal spine morphologies in the hippocampus and cerebellum (5, 6).In the vast majority of cases, FXS is caused by expansion of a trinucleotide repeat (CGG) within the 5Ј-untranslated region of the X-linked gene fmr1, resulting in its transcriptional silencing. The encoded protein, FMRP, can act as a translational suppressor of mRNAs in dendrites, controlling the localized, activity-dependent expression of a potentially large subset of synaptic proteins (7). Knocking out fmr1 in mouse results in a perturbation of various forms of translation-dependent synaptic plasticity, including some forms of long-term potentiation (LTP) and group I metabotropic...