Affinity Capture-MS

An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.

Publication

A foundational atlas of autism protein interactions reveals molecular convergence

Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser M, Zhou Y, Guiley KZ, Chan U, Kaye JA, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Morris M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Rolland T, Bourgeron T, Finkbeiner S, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Huttenhain R, State MW, Willsey AJ, Krogan NJ

Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed in the human brain and enriched for ASD but not schizophrenia genetic risk, converged on protein complexes involved in neurogenesis, tubulin biology, ... [more]

Status: Preliminary Report

Quantitative Score

  • 0.992528521 [compPASS Score]

Throughput

  • High Throughput

Additional Notes

  • APMS data generated in HEK293T by overexpression of Strep-tagged patient derived ASD variant. Intensity of the interaction between the WT protein and the hit protein was compared to the intensity of the interaction between the patient derived variant and hit protein. Significant interaction intensity changes were defined as those with a log2(fold-change) >= 1 and p <= 0.05. Strengthened interactions were denoted as 'Up', weakened interactions were denoted as 'Down' and unchanged interactions were denoted as 'Not significant' based on these scores. ASD variant: Bait protein name: K228E - Interaction Strength: not significant, Log2fc: -0.135459966112576, p-value: 0.628822956299693
  • APMS data generated in HEK293T by overexpression of Strep-tagged patient derived ASD variant. Intensity of the interaction between the WT protein and the hit protein was compared to the intensity of the interaction between the patient derived variant and hit protein. Significant interaction intensity changes were defined as those with a log2(fold-change) >= 1 and p <= 0.05. Strengthened interactions were denoted as 'Up', weakened interactions were denoted as 'Down' and unchanged interactions were denoted as 'Not significant' based on these scores. ASD variant: Bait protein name: N374H - Interaction Strength: not significant, Log2fc: 0.0639931264305508, p-value: 0.817927032585308
  • Affinity purification-MS was used to capture high confidence wild-type protein interactors as defined by the thresholds: BFDR <= 0.05 and compPASS scores (rank_WD) >= 0.971. Baits are Strep-tagged proteins exogenously expressed in HEK 293T cells. ComPASS score: 0.992528521

Related interactions

InteractionExperimental Evidence CodeDatasetThroughputScoreCurated ByNotes
TBR1 CASK
Affinity Capture-Western
Affinity Capture-Western

An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner identified by Western blot with a specific polyclonal antibody or second epitope tag. This category is also used if an interacting protein is visualized directly by dye stain or radioactivity. Note that this differs from any co-purification experiment involving affinity capture in that the co-purification experiment involves at least one extra purification step to get rid of potential contaminating proteins.

Low-BioGRID
-
CASK TBR1
Affinity Capture-Western
Affinity Capture-Western

An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner identified by Western blot with a specific polyclonal antibody or second epitope tag. This category is also used if an interacting protein is visualized directly by dye stain or radioactivity. Note that this differs from any co-purification experiment involving affinity capture in that the co-purification experiment involves at least one extra purification step to get rid of potential contaminating proteins.

Low-BioGRID
-
TBR1 CASK
Affinity Capture-Western
Affinity Capture-Western

An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner identified by Western blot with a specific polyclonal antibody or second epitope tag. This category is also used if an interacting protein is visualized directly by dye stain or radioactivity. Note that this differs from any co-purification experiment involving affinity capture in that the co-purification experiment involves at least one extra purification step to get rid of potential contaminating proteins.

Low-BioGRID
-
TBR1 CASK
Two-hybrid
Two-hybrid

Bait protein expressed as a DNA binding domain (DBD) fusion and prey expressed as a transcriptional activation domain (TAD) fusion and interaction measured by reporter gene activation.

Low-BioGRID
-

Curated By

  • BioGRID