A universal peptide matrix interactomics approach to disclose motif dependent protein binding


  • E. Ramberger
  • L. Suarez-Artiles
  • D. Perez-Hernandez
  • M. Haji
  • O. Popp
  • U. Reimer
  • A. Leutz
  • G. Dittmar
  • P. Mertins


  • Molecular & Cellular Proteomics


  • Mol Cell Proteomics 20: 100135


  • Protein-protein interactions (PPIs) mediated by intrinsically disordered regions (IDRs) are often based on short linear motifs (SLiM). SLiMs are implicated in signal transduction and gene regulation, yet remain technically laborious and notoriously challenging to study. Here, we present an optimized method for a PRotein Interaction Screen on a peptide MAtrix (PRISMA) in combination with quantitative mass spectrometry. The protocol was benchmarked with previously described SLiM based PPIs using peptides derived from EGFR, SOS1, GLUT1 and CEBPB and extended to map binding partners of kinase activation loops. The detailed protocol provides practical considerations for setting up a PRISMA screen and subsequently implementing PRISMA on a liquid handling robotic platform as a cost effective high-throughput method. Optimized PRISMA can be universally applied to systematically study SLiM based interactions and associated post translational modifications (PTMs) or mutations to advance our understanding of the largely uncharacterized interactomes of intrinsically disordered protein regions.