A Comparison of Two Stability Proteomics Methods for Drug Target Identification in OnePot 2D Format

Stability proteomics techniques that do not require drug modifications have emerged as an attractive alternative to affinity purification methods in drug target engagement studies. Two representative techniques include the chemical-denaturation-based SPROX (Stability of Proteins from Rates of Oxidation), which utilizes peptide-level quantification and thermal-denaturation-based TPP (Thermal Proteome Profiling), which utilizes protein-level quantification. Recently, the OnePot strategy was adapted for both SPROX and TPP to increase the throughput. When combined with the 2D setup which measures both the denaturation and the drug dose dimensions, the OnePot 2D format offers improved analysis specificity with higher resource efficiency. However, a systematic evaluation of the OnePot 2D format and a comparison between SPROX and TPP are still lacking. Here, we performed SPROX and TPP to identify protein targets of a well-studied pan-kinase inhibitor staurosporine with K562 lysate, in curve-fitting and OnePot 2D formats. We found that the OnePot 2D format provided similar to 10x throughput, achieved similar to 1.6x protein coverage and involves more straightforward data analysis. We also compared SPROX with the current gold-standard stability proteomics technique TPP in the OnePot 2D format. The protein coverage of TPP is similar to 1.5 fold of SPROX; however, SPROX offers protein domain-level information, identifies comparable numbers of kinase hits, has higher signal (R value), and requires similar to 3x less MS time. Unique SPROX hits encompass higher-molecular-weight proteins, compared to the unique TPP hits, and include atypical kinases. We also discuss hit stratification and prioritization strategies to promote the efficiency of hit followup.

Automated summary

Stability proteomics techniques have emerged as an attractive alternative in drug target engagement studies, with SPROX and TPP being representative methods. The adoption of the OnePot strategy has increased throughput and efficiency, with the OnePot 2D format offering improved analysis specificity. However, there is still a lack of systematic evaluation of the OnePot 2D format and a comparison between SPROX and TPP.