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

• DOI: 10.1021/acschembio.1c00317
• Publication Date: 2021-08-10T16:12:17Z
• Authors: Yingrong Xu; Graham M. West; Mario Abdelmessih; Matthew D. Troutman; Robert A. Everley
• Keywords: protein coverage; Proteomics; chemical-denaturation-based SPROX; OnePot 2 D format; Proteome; Physiology; analysis specificity; data analysis; drug target engagement studies; Biochemistry; higher-molecular-weight proteins; protein-level quantification; resource efficiency; 0303 health sciences; drug modifications; MS time; well-studied pan-kinase inhibitor s.; Unique SPROX hits; Biotechnology; Biological Sciences not elsewhere classified; Drug Target Identification; Chemical Sciences not elsewhere classified; affinity purification methods; representative techniques; protein targets; Biophysics; Stability Proteomics Methods; OnePot 2 D formats; Inorganic Chemistry; 03 medical and health sciences; protein domain-level information; peptide-level quantification; Genetics; Humans; Molecular Biology; K 562 lysate; Protein Kinase Inhibitors; Pharmacology; prioritization strategies; TPP hits; kinase hits; 540; Staurosporine; 2 D setup; drug dose dimensions; OnePot 2 D Format Stability proteom.; thermal-denaturation-based TPP; K562 Cells; Protein Kinases

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 ∼10× throughput, achieved ∼1.6× 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 ∼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 ∼3× 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.