Reliable identification of protein-protein interactions by crosslinking mass spectrometry_Protein coelution

Quantitative proteomics dataset on soluble, SEC-fractionated high-molecular weight proteome of E. coli for protein coelution analysis. This data was used to identify proteins for a subsequent crosslinking mass spectrometry search (DB creation) and to correlate protein elution behaviour to validate/falsify potential PPIs from the CLMS-based approach. Cleared E. coli lysate was fractionated in the range of 3 MDa to 150 kDa (44 fractions). The proteins in each fraction were precipitated, derivatized and proteolysed in-solution. Then, each fraction was acquired via LC-MS on Q Exactive HF and the raw data searched with MaxQuant with iBAQ quantitation enabled.