Open Close
General Information
Name
DPiM-2
Species
D. melanogaster
Result type
FlyBase ID
FBlc0000492
Project
Data Provider
DPiM
Title
10,969 high-confidence DPiM co-complex membership interactions (0.05% FDR) involving 2,297 proteins.
Status
Current
Accessions
    Biosample Source
    Overview
    Strain
    Stage
    Sex
    Tissue isolated
    Other tissues studied
    Cell component
    Key genes
    Sample preparation
    Each purified bait clone (DPiM_cDNA_bait_cDNA) was used to transiently transfect S2R+ cells in a 54ml culture. The individual S2R+ cultures were induced to produce FLAG-HA fusion protein by treatment with media containing 0.35 mM Cu2SO4 for 20 hours. Cells were lysed in buffer containing protease inhibitor and passed through a 0.45um durapore filter.
    Biosamples analyzed by this result (1)
    Biosample
    Type
    Title
    D. melanogaster, S2R+ cell line, transiently transfected with bait protein, source for DPiM affinity purifications.
    Data Analyzed
    Assay methods
    Key genes
    Protocol
    Each clarified lysate was bound overnight to crosslinked HA immunoaffinity resin. Unbound proteins were washed off with lysis buffer followed by PBS and then bound protein complexes were competitively eluted using synthetic HA peptide YPYDVPDYA (250 μg/ml) in PBS.
    Mode of Assay
    Copurified proteins were precipitated using trichloroacetic acid, washed with acetone, dried, digested overnight with trypsin, and analyzed by LC-MS/MS. LC-MS/MS spectral data were searched with SEQUEST (Eng et al., 2008) against a database of D. melanogaster proteins derived from FlyBase version 5.23. The LC-MS/MS identifications were filtered to, on average, a 0.3% peptide FDR.
    Raw Data Analyzed (1)
    Assay / Reagent collection
    Type
    Title
    Coaffinity purification of interacting proteins and identification by mass spectrometry, S2R+ cells, DPiM.
    Processed Data Analyzed (0)
    Result
    Type
    Title
    Analysis
    Methods
    Reference Genome
    Reference Annotation
    Data analysis
    The spectral data were searched with SEQUEST (Eng et al., 2008) against a database of D. melanogaster proteins derived from FlyBase version 5.23. The LC-MS/MS identifications were filtered to, on average, a 1.2% protein FDR and 0.3% peptide FDR. The compiled data set was filtered to a combined 0.8% FDR, and further post-processing was used to correct for column carryover issues. Both bait-prey and prey-prey protein interactions from coAP-MS data were analyzed and scored using HGSCore - a hypergeometric distribution error model, incorporating TSCs to improve the accuracy of co-occurrence prediction. A randomized data set of similar size was created to estimate FDR. Protein interactions were clustered using MCL (Enright et al., 2002).
    Comments
    The refined DPiM-2 dataset supercedes the original unfiltered protein interaction dataset, DPiM-1.
    Associated Data
    Size
    Associated interactions
    10,942 Interactions
    Files
    Additional Information
    Synonyms and Secondary IDs (4)
    Reported As
    Symbol Synonym
    DPiM-2
    Drosophila protein interaction map
    Name Synonyms
    10,969 high-confidence DPiM co-complex membership interactions (0.05% FDR) involving 2,297 proteins.
    Secondary FlyBase IDs
      References (4)