Enhancing cognate target elution efficiency in gel-free chemical proteomics

•A new elution strategy for LCMS coupled to chemical proteomics is shown.•Method is beneficial for both drug immobilization protocols and biotinylated drugs.•We observed enhanced target recovery without enrichment of non-specific proteins.•This was not constrained neither to particular targets, nor to a single drug.

Gel-free liquid chromatography mass spectrometry coupled to chemical proteomics is a powerful approach for characterizing cellular target profiles of small molecules. We have previously described a fast and efficient elution protocol; however, altered target profiles were observed. We hypothesised that elution conditions critically impact the effectiveness of disrupting drug-protein interactions. Thus, a number of elution conditions were systematically assessed with the aim of improving the recovery of all classes of proteins whilst maintaining compatibility with immunoblotting procedures. A double elution with formic acid combined with urea emerged as the most efficient and generically applicable elution method for chemical proteomics

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