Gene interactions and pathways from curated databases and text-mining
J Proteome Res 2007, PMID: 17203973

The proteomic reactor facilitates the analysis of affinity-purified proteins by mass spectrometry: application for identifying ubiquitinated proteins in human cells.

Vasilescu, Julian; Zweitzig, Daniel R; Denis, Nicholas J; Smith, Jeffrey C; Ethier, Martin; Haines, Dale S; Figeys, Daniel

Mass spectrometry (MS) coupled to affinity purification is a powerful approach for identifying protein-protein interactions and for mapping post-translational modifications. Prior to MS analysis, affinity-purified proteins are typically separated by gel electrophoresis, visualized with a protein stain, excised, and subjected to in-gel digestion. An inherent limitation of this series of steps is the loss of protein sample that occurs during gel processing. Although methods employing in-solution digestion have been reported, they generally suffer from poor reaction kinetics. In the present study, we demonstrate an application of a microfluidic processing device, termed the Proteomic Reactor, for enzymatic digestion of affinity-purified proteins for liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. Use of the Proteomic Reactor enabled the identification of numerous ubiquitinated proteins in a human cell line expressing reduced amounts of the ubiquitin-dependent chaperone, valosin-containing protein (VCP). The Proteomic Reactor is a novel technology that facilitates the analysis of affinity-purified proteins and has the potential to aid future biological studies.

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Text Mining Data

Dashed line = No text mining data

Manually curated Databases

  • IRef Biogrid Interaction: SLC25A5 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: PSMC2 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — FGFR4 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — HSP90AB1 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: PABPC1 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: TRAP1 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — UBE2T (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: RPL13 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — HSP90AA1 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — UBE2D3 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — PSMA1 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: PCM1 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — WDR61 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: PSMD5 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — SLC25A4 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: ACTBL2 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — NUDT6 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: HTR1A — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — PHB2 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: HUNK — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: CCDC138 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — ATRIP (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: GALNT5 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: ATAD1 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: PRRC2B — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — UBA52 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — SYNE1 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — KIF16B (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: ACTA1 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — KIF14 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: ACTG1 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: TRAF3IP3 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — TBP (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — KMT2A (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: TARS — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — ASH1L (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: CBFA2T3 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: RPS16 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: WRNIP1 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBE2D1 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: PHB — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: RPL6 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: GUF1 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: ACTB — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: RPL24 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — PSMD1 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: VCP — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — RPL7 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — RAC1 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — SQSTM1 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — BAG2 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: RNF25 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — PSMC1 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — PSMC4 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — IGF2BP1 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — PSMA4 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: RPS3 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: HUWE1 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — PSMD2 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: PSMA7 — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: KARS — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — BAG6 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — UBE2D2 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: FOS — UBC (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: UBC — PSMC5 (physical association, affinity chromatography technology)
  • IRef Biogrid Interaction: PSMC6 — UBC (physical association, affinity chromatography technology)
In total, 67 gene pairs are associated to this article in curated databases