BACKGROUND/AIM: Pul-down assay is a popular in vitro method for identification of physical interactors of selected proteins. Here, for the first time, we compared three conventional variants of pull-down assay with the streptavidin-modified surface plasmon resonance (SPR) chips for the detection of PDZ and LIM domain protein 2 (PDLIM2) interaction partners. MATERIALS AND METHODS: PDLIM2 protein-protein interactions were analysed by three variants of pull-down assay on streptavidin beads using LC-MS/MS in "Sequential Window Acquisition of all Theoretical fragment ion spectra (SWATH)" mode and compared with LC-SWATH-MS/MS data from SPR chips. RESULTS: The results showed that (i) the use of SPR chip led to comparable data compared to on-column streptavidin beads, (ii) gravity flow and microflow in wash and elution steps provided better results than centrifugation, and (iii) type and concentration of detergent did not significantly affect the interactome data of cancer-associated PDLIM2. CONCLUSION: Our study supports further application of SPR-based affinity purification with SWATH mass spectrometry for reproducible and controlled characterization of cancer-associated interactomes.

• Klíčová slova
• LC-SWATH-MS/MS, PDLIM2, SPR, protein-protein interactions, pull-down assay,
• MeSH
• chromatografie kapalinová MeSH
• interakční proteinové domény a motivy genetika   MeSH
• lidé MeSH
• mikrofilamentové proteiny genetika   izolace a purifikace   MeSH
• nádory genetika   patologie   MeSH
• povrchová plasmonová rezonance * MeSH
• proteiny s doménou LIM genetika   izolace a purifikace   MeSH
• streptavidin chemie   MeSH
• tandemová hmotnostní spektrometrie MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• mikrofilamentové proteiny MeSH
• PDLIM2 protein, human MeSH Prohlížeč
• proteiny s doménou LIM MeSH
• streptavidin MeSH