G2C::Synapse Proteomics Datasets

Introduction

Links are provided to the synapse proteomics datasets from Genes to Cognition (G2C) Programme publications in the G2Cdb database. These can be browsed, compared and downloaded online. For each dataset the original proteomics results are given mapped back to the relevant species gene identifiers, and to orthologous genes in another mammalian species.

If you wish to search for the presence of an individual gene or protein of interest in all the warehoused synapse proteomics lists, simply paste the protein or gene identifier into the top right-hand search box, and select the 'Gene lists' tab from the G2Cdb::Gene report (e.g. Grin1, PSD-95, Shank2).

 

Synapse proteomics reports

Comparative analysis of human and mouse postsynaptic proteomes identifies high compositional conservation and abundance differences for key synaptic proteins

Bayés À, Collins MO, Croning MDR, van de Lagemaat LN, Choudhary JS, Grant SGN. [23071613]

Description Protein count Original species proteomics Orthologous list
Cortex PSD full protein list 1556 Mus musculus (view) Homo sapiens (view)
Cortex PSD consensus proteins 984 Mus musculus (view) Homo sapiens (view)

(View - MICROSITE)

 

Characterisation of the proteome, diseases and evolution of the human postsynaptic density

Bayés À, van de Lagemaat LN, Collins MO, Croning MDR, Whittle IR, Choudhary JS, Grant SGN. [21170055]

Description Protein count Original species proteomics Orthologous list
Cortex PSD full protein list 1461 Homo sapiens (view) Mus musculus (view)
Cortex PSD consensus proteins 748 Homo sapiens (view) Mus musculus (view)

(View - MICROSITE)

 

Targeted TAP purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins

Fernandez E, Collins MO, Uren RT, Kopanitsa MV, Komiyama NH, Croning MDR, Zografos L, Armstrong JD, Choudhary JS, Grant SGN. [19455133]

Description Protein count Original species proteomics Orthologous list
TAP PSD-95 'core' protein list 120 Mus musculus (view) Homo sapiens (view)

(View MICROSITE)

 

Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome.

Collins MO, Husi H, Yu L, Brandon JM, Anderson CN, Blackstock WP, Choudhary JS and Grant SG. [16635246]

Description Protein count Original species proteomics Orthologous list
AMPA receptor complex 10 Mus musculus (view) Homo sapiens (view)
Clathrin-coated vesicle 150 Mus musculus (view) Homo sapiens (view)
mGluR5 receptor complex 64 Mus musculus (view) Homo sapiens (view)
Mitochondrial proteome 91 Mus musculus (view) Homo sapiens (view)
NRC/MASC complex 186 Mus musculus (view) Homo sapiens (view)
Postsynaptic proteome (PSP) 1121 Mus musculus (view) Homo sapiens (view)
PSD complex 1080 Mus musculus (view) Homo sapiens (view)
Synaptosome 152 Mus musculus (view) Homo sapiens (view)

 

References

  • Comparative study of human and mouse postsynaptic proteomes finds high compositional conservation and abundance differences for key synaptic proteins.

    Bayés A, Collins MO, Croning MD, van de Lagemaat LN, Choudhary JS and Grant SG

    Molecular Physiology of the Synapse Laboratory, Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, UAB, Barcelona, Catalonia, Spain. ABayesP@santpau.cat

    Direct comparison of protein components from human and mouse excitatory synapses is important for determining the suitability of mice as models of human brain disease and to understand the evolution of the mammalian brain. The postsynaptic density is a highly complex set of proteins organized into molecular networks that play a central role in behavior and disease. We report the first direct comparison of the proteome of triplicate isolates of mouse and human cortical postsynaptic densities. The mouse postsynaptic density comprised 1556 proteins and the human one 1461. A large compositional overlap was observed; more than 70% of human postsynaptic density proteins were also observed in the mouse postsynaptic density. Quantitative analysis of postsynaptic density components in both species indicates a broadly similar profile of abundance but also shows that there is higher abundance variation between species than within species. Well known components of this synaptic structure are generally more abundant in the mouse postsynaptic density. Significant inter-species abundance differences exist in some families of key postsynaptic density proteins including glutamatergic neurotransmitter receptors and adaptor proteins. Furthermore, we have identified a closely interacting set of molecules enriched in the human postsynaptic density that could be involved in dendrite and spine structural plasticity. Understanding synapse proteome diversity within and between species will be important to further our understanding of brain complexity and disease.

    Funded by: Medical Research Council: G0802238; Wellcome Trust

    PloS one 2012;7;10;e46683

  • Characterization of the proteome, diseases and evolution of the human postsynaptic density.

    Bayés A, van de Lagemaat LN, Collins MO, Croning MD, Whittle IR, Choudhary JS and Grant SG

    Genes to Cognition Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK.

    We isolated the postsynaptic density from human neocortex (hPSD) and identified 1,461 proteins. hPSD mutations cause 133 neurological and psychiatric diseases and were enriched in cognitive, affective and motor phenotypes underpinned by sets of genes. Strong protein sequence conservation in mammalian lineages, particularly in hub proteins, indicates conserved function and organization in primate and rodent models. The hPSD is an important structure for nervous system disease and behavior.

    Funded by: Chief Scientist Office: CZB/4/486; Medical Research Council: G0802238, G0802238(89569); Wellcome Trust: 066717, 077155

    Nature neuroscience 2011;14;1;19-21

  • Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins.

    Fernández E, Collins MO, Uren RT, Kopanitsa MV, Komiyama NH, Croning MD, Zografos L, Armstrong JD, Choudhary JS and Grant SG

    Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Cambridge, UK.

    The molecular complexity of mammalian proteomes demands new methods for mapping the organization of multiprotein complexes. Here, we combine mouse genetics and proteomics to characterize synapse protein complexes and interaction networks. New tandem affinity purification (TAP) tags were fused to the carboxyl terminus of PSD-95 using gene targeting in mice. Homozygous mice showed no detectable abnormalities in PSD-95 expression, subcellular localization or synaptic electrophysiological function. Analysis of multiprotein complexes purified under native conditions by mass spectrometry defined known and new interactors: 118 proteins comprising crucial functional components of synapses, including glutamate receptors, K+ channels, scaffolding and signaling proteins, were recovered. Network clustering of protein interactions generated five connected clusters, with two clusters containing all the major ionotropic glutamate receptors and one cluster with voltage-dependent K+ channels. Annotation of clusters with human disease associations revealed that multiple disorders map to the network, with a significant correlation of schizophrenia within the glutamate receptor clusters. This targeted TAP tagging strategy is generally applicable to mammalian proteomics and systems biology approaches to disease.

    Funded by: Wellcome Trust

    Molecular systems biology 2009;5;269

  • Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome.

    Collins MO, Husi H, Yu L, Brandon JM, Anderson CN, Blackstock WP, Choudhary JS and Grant SG

    Genes to Cognition, The Wellcome Trust Sanger Institute, Hinxton, UK.

    Characterization of the composition of the postsynaptic proteome (PSP) provides a framework for understanding the overall organization and function of the synapse in normal and pathological conditions. We have identified 698 proteins from the postsynaptic terminal of mouse CNS synapses using a series of purification strategies and analysis by liquid chromatography tandem mass spectrometry and large-scale immunoblotting. Some 620 proteins were found in purified postsynaptic densities (PSDs), nine in AMPA-receptor immuno-purifications, 100 in isolates using an antibody against the NMDA receptor subunit NR1, and 170 by peptide-affinity purification of complexes with the C-terminus of NR2B. Together, the NR1 and NR2B complexes contain 186 proteins, collectively referred to as membrane-associated guanylate kinase-associated signalling complexes. We extracted data from six other synapse proteome experiments and combined these with our data to provide a consensus on the composition of the PSP. In total, 1124 proteins are present in the PSP, of which 466 were validated by their detection in two or more studies, forming what we have designated the Consensus PSD. These synapse proteome data sets offer a basis for future research in synaptic biology and will provide useful information in brain disease and mental disorder studies.

    Funded by: Wellcome Trust

    Journal of neurochemistry 2006;97 Suppl 1;16-23

© G2C 2014. The Genes to Cognition Programme received funding from The Wellcome Trust and the EU FP7 Framework Programmes:
EUROSPIN (FP7-HEALTH-241498), SynSys (FP7-HEALTH-242167) and GENCODYS (FP7-HEALTH-241995).

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