PXD000437

PXD000437 is an original dataset announced via ProteomeXchange.

Title	Amyloid Beta A4 Precursor Protein-binding Family B Member 1 (FE65) Interactomics Revealed Synaptic Vesicle Glycoprotein 2A (SV2A) and Sarcoplasmic/Endoplasmic Reticulum Calcium ATPase 2 (SERCA2) as New Binding Proteins in the Human Brain
Description	FE65 is a cytosolic adapter protein and an important binding partner of the amyloid precursor protein (APP). Dependent on Thr668 phosphorylation in APP, which influences amyloidogenic APP processing, FE65 undergoes nuclear translocation, thereby transmitting a signal from the cell membrane to the nucleus. As this translocation may be relevant in Alzheimer disease (AD) and as FE65 consists of three protein-protein interaction domains able to bind and affect a variety of other proteins and down-stream signaling pathways, the identification of the FE65 interactome is of central interest in AD research. In this study, we identified 121 proteins as new potential FE65 interacting proteins in a pulldown/mass spectrometry approach using human post-mortem brain samples as protein pools for recombinantly expressed FE65. Co-immunoprecipitation assays further validated the interaction of FE65 with the candidates SV2A and SERCA2. In parallel, we investigated the whole cell proteome of primary hippocampal neurons from FE65/FE65L1 double knockout mice. Bioinformatics pipeline: MGF files were generated from RAW files with ProteomDiscoverer 1.3 and imported into ProteinScape 2.1 and analyzed using MASCOT version 2.3.0) with the following parameters: peptide mass tolerance of 10 ppm, fragment mass tolerance of 0.5 Da, enzyme: Trypsin with one missed cleavage site, variable modifications: carbamidomethylation (C), oxidation (M), phosphorylation of S, T and Y, used database: Uniprot/SwissProt (2011_06), taxonomy Homo sapiens + one shuffled decoy per entry (results in 40620 entries, including decoys). For further details please contact Thorsten Müller (thorsten.t.mueller@rub.de), Medizinisches Proteom-Center, Ruhr-Universität Bochum.
HostingRepository	PRIDE
AnnounceDate	2016-05-18
AnnouncementXML	Submission_2016-05-18_07:05:59.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000437
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Julian Uszkoreit
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	instrument model: LTQ Orbitrap; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-08-30 06:47:27	ID requested
⏵ 1	2016-05-18 07:06:03	announced

Nensa FM, Neumann MH, Schr, ö, tter A, Przyborski A, Mastalski T, Susdalzew S, Loo, β, e C, Helling S, El Magraoui F, Erdmann R, Meyer HE, Uszkoreit J, Eisenacher M, Suh J, Gu, é, nette SY, R, ö, hner N, K, ö, gel D, Theiss C, Marcus K, M, ü, ller T, Amyloid beta a4 precursor protein-binding family B member 1 (FE65) interactomics revealed synaptic vesicle glycoprotein 2A (SV2A) and sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2) as new binding proteins in the human brain. Mol Cell Proteomics, 13(2):475-88(2014) [pubmed]

curator keyword: Biomedical

submitter keyword: FE65, human, brain

Katrin Marcus
contact affiliation	Medizinisches Proteom-Center, Ruhr-Universität Bochum
contact email	katrin.marcus@rub.de
lab head
Julian Uszkoreit
contact affiliation	Ruhr-Universität Bochum, Medizinisches Proteom-Center, Medical Bioinformatics, Algorithmic Proteomics
contact email	julian.uszkoreit@rub.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000437
     1. Label: PRIDE project
     2. Name: Amyloid Beta A4 Precursor Protein-binding Family B Member 1 (FE65) Interactomics Revealed Synaptic Vesicle Glycoprotein 2A (SV2A) and Sarcoplasmic/Endoplasmic Reticulum Calcium ATPase 2 (SERCA2) as New Binding Proteins in the Human Brain