Chondroitin Sulfate Proteoglycan 4 participates in the internalization of arginine-rich dipeptide repeat proteins

Label-free data-independent acquisition proteomics of samples generated by µMap photocatalytic proximity labeling, applied to the internalization of arginine-rich dipeptide repeat proteins. Biotinylated proteins were enriched and analysed on a Bruker timsTOF Pro 2 coupled to a nanoElute LC in dia-PASEF mode (m/z 100–1,700). Raw .d files were processed in DIA-NN 1.8.1 against in-silico spectral libraries predicted from UniProt reference proteomes (human UP000005640), with trypsin/P, up to 3 missed cleavages, 1% precursor FDR, match-between-runs and heuristic protein inference enabled. Protein-group matrices were log2-transformed, imputed, median-normalised and compared by two-sided Student’s t-test in Perseus v2.0.7.0.