FLAG-based Affinity Purification and LC-MS/MS Analysis of FTSH4-Interacting Partners in Arabidopsis thaliana Mitochondria

ABSTRACT: FTSH4 is a mitochondrial metalloprotease in Arabidopsis thaliana that plays an important role in protein quality control, exhibiting both proteolytic and chaperone-like activities. It increases plant tolerance to long-term moderate heat stress by preventing the accumulation of insoluble protein aggregates in mitochondria. Although FTSH4 is known to form high-molecular complexes anchored in the inner mitochondrial membrane, the precise composition of these complexes remains unclear. This dataset includes raw LC-MS/MS data from FLAG-based affinity purification experiments designed to identify proteins interacting with FTSH4 in Arabidopsis plants grown at two different temperatures: optimal temperature (22 degrees Celsius) and moderate heat stress (30 degrees Celsius). Mitochondria were isolated from four independent biological replicates of FTSH4H486Y (proteolytically inactive FTSH4 with FLAG tag) and ftsh4-1 mutant lines. Solubilized mitochondrial fractions were subjected to affinity purification using anti-FLAG resin, with the ftsh4-1 mutant serving as a negative control. Eluted proteins were analyzed using a Q Exactive Orbitrap mass spectrometer (Thermo Fisher Scientific) coupled to a nanoHPLC system. Data acquisition was performed in data-dependent acquisition (DDA) mode. The LC-MS/MS data were processed using Proteome Discoverer v1.4, and database searches were conducted via an in-house MASCOT server v2.5.1 against the SwissTrEMBL Arabidopsis thaliana protein database (release April 2022, 39,329 sequences), supplemented with the sequence of the studied mutant. The dataset enables the identification of components of the FTSH4 complexes and provides information on temperature-dependent changes in the FTSH4 interactome. This work was supported by the National Science Centre, Poland (grant 2017/27/B/NZ2/00558).

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (ncbitaxon:3702)

SUBMITTER: Hanna Janska  

PROVIDER: MSV000099719 | MassIVE | Sun Nov 02 10:03:00 GMT 2025

REPOSITORIES: MassIVE