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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