Project PXD001195

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Biological Dataset Biomedical Dataset
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Dynamics of AMPAR proteome across brain regions and in postnatal development


Native AMPA receptors (AMPAR) in the mammalian brain are macromolecular complexes whose functional characteristics vary across brain regions and postnatal development and change in response to neuronal activity. Both, structural and functional properties of the AMPARs are determined by their proteome, the ensemble of their protein building blocks. Here we use high-resolution quantitative mass spectrometry to analyze the entire pool of AMPARs affinity-isolated from distinct brain regions, selected sets of synapses/neurons and from whole brains at distinct stages of postnatal development. These analyses show that the AMPAR proteome is largely dynamic in both space and time: AMPARs exhibited profound region-specificity in their architecture and the constituents building their core and periphery. Likewise, AMPARs (ex)change numerous of their building blocks during postnatal development. These results provide an as yet unique resource for analysis of the individual subunits of native AMPAR complexes and their role in excitatory neurotransmission.

Sample Processing Protocol

See detailed process description in reference PMID XXXXXXXX

Data Processing Protocol

LC-MS/MS data was extracted using "extract_msn.exe" (grouping tolerance 0.05; Thermo Scientific) for LTQ Orbitrap XL and "msconvert.exe" (part of ProteoWizard;, version 2.2.3214) for Orbitrap Elite. Using the Mascot search engine (version 2.4.0; Matrix Science), peak lists were searched against UniProtKB/Swiss-Prot releases 2013_11 and 2013_01, respectively, (only mouse, rat and human entries plus P00761|TRYP_PIG, P00766|CTRA_BOVIN and P02769|ALBU_BOVIN). For preliminary searches peptide mass tolerance was set to ± 15 or 25 ppm. After performing a linear shift mass recalibration using a custom script, tolerance was reduced to ± 5 ppm for final searches. Fragment mass tolerance was set to ± 0.8 Da. One missed trypsin cleavage and common variable modifications including S/T/Y phosphorylation were accepted for peptide identification. Significance threshold was set to p < 0.05. Proteins identified by only one specific MS/MS spectrum or representing exogenous contaminations such as keratins or immunoglobulins were eliminated. For further details, see reference PMID XXXXXXX.


Alexander Haupt, University of Freiburg, Germany
Bernd Fakler, Institute of Physiology II, University of Freiburg, Germany ( lab head )

Submission Date


Publication Date



    Schwenk J, Baehrens D, Haupt A, Bildl W, Boudkkazi S, Roeper J, Fakler B, Schulte U. Regional diversity and developmental dynamics of the AMPA-receptor proteome in the mammalian brain. Neuron. 2014 Oct 1;84(1):41-54 PubMed: 25242221


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# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 39060 no assay title provided (mzIdentML) 3452 38802 5949 40288 10235
2 39025 no assay title provided (mzIdentML) 3422 36518 6167 39094 9460
3 39061 no assay title provided (mzIdentML) 2729 25192 3614 27821 6306
4 39024 no assay title provided (mzIdentML) 2759 24803 4001 28839 6500
5 39062 no assay title provided (mzIdentML) 1046 8831 1118 21895 2500
6 39027 no assay title provided (mzIdentML) 2163 19844 2939 25962 5083
7 39063 no assay title provided (mzIdentML) 2178 23201 3722 29606 6207
8 39026 no assay title provided (mzIdentML) 3437 38017 6835 35133 10257
9 39040 no assay title provided (mzIdentML) 1141 11758 1437 23176 3031
10 39041 no assay title provided (mzIdentML) 2634 27550 4285 28856 6858