Thermal proteome profiling (TPP) provides a powerful
approach to
studying proteome-wide interactions of small therapeutic molecules
and their target and off-target proteins, complementing phenotypic-based
drug screens. Detecting differences in thermal stability due to target
engagement requires high quantitative accuracy and consistent detection.
Isobaric tandem mass tags (TMTs) are used to multiplex samples and
increase quantification precision in TPP analysis by data-dependent
acquisition (DDA). However, advances in data-independent acquisition
(DIA) can provide higher sensitivity and protein coverage with reduced
costs and sample preparation steps. Herein, we explored the performance
of different DIA-based label-free quantification approaches compared
to TMT-DDA for thermal shift quantitation. Acute myeloid leukemia
cells were treated with losmapimod, a known inhibitor of MAPK14 (p38α).
Label-free DIA approaches, and particularly the library-free mode
in DIA-NN, were comparable of TMT-DDA in their ability to detect target
engagement of losmapimod with MAPK14 and one of its downstream targets,
MAPKAPK3. Using DIA for thermal shift quantitation is a cost-effective
alternative to labeled quantitation in the TPP pipeline.