Direct aliquoting from a single heated well enables fully automated high-throughput thermal proteome profiling
- 1Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
Abstract
Thermal proteome profiling (TPP) measures drug target engagement across the proteome by detecting ligand-induced changes in protein thermal stability, but conventional workflows are laborious and costly, which has limited their use in compound screening. We present DASH-PISA, a single-well thermal fractionation approach in which a lysate is heated through a series of defined temperatures in one well and sampled at each step, and the aliquots are pooled into another well. Because sampling and pooling both take place in plate format, the thermal treatment runs on a standard liquid-handling robot with an integrated thermocycler and a 96-channel pipette. Combined with filter-based separation of soluble protein, data-independent acquisition (DIA), and a spike-in SILAC reference, DASH-PISA forms a fully automated, high-throughput TPP workflow. As a proof of concept, stepwise single-well fractionation reproduced the melting curves of traditional TPP, and the pooled DASH-PISA workflow detected known kinase targets of staurosporine; a spike-in SILAC reference further improved their recovery. By running on commercially available automation, this workflow makes proteome-wide target identification practical at the scale required for compound-library screening.
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BibTeX
@misc{paakkonen2026direct,
title = {{Direct aliquoting from a single heated well enables fully automated high-throughput thermal proteome profiling}},
author = {M. Pääkkönen and I. Purma and J. Merilahti and O. Kauko},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.15.751689},
url = {https://www.biorxiv.org/content/10.64898/2026.09.15.751689v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Direct aliquoting from a single heated well enables fully automated high-throughput thermal proteome profiling
AU - M. Pääkkönen
AU - I. Purma
AU - J. Merilahti
AU - O. Kauko
PY - 2026
DA - 2026/09/15
PB - bioRxiv
DO - 10.64898/2026.09.15.751689
UR - https://www.biorxiv.org/content/10.64898/2026.09.15.751689v1
AB - Thermal proteome profiling (TPP) measures drug target engagement across the proteome by detecting ligand-induced changes in protein thermal stability, but conventional workflows are laborious and costly, which has limited their use in compound screening. We present DASH-PISA, a single-well thermal fractionation approach in which a lysate is heated through a series of defined temperatures in one well and sampled at each step, and the aliquots are pooled into another well. Because sampling and pooling both take place in plate format, the thermal treatment runs on a standard liquid-handling robot with an integrated thermocycler and a 96-channel pipette. Combined with filter-based separation of soluble protein, data-independent acquisition (DIA), and a spike-in SILAC reference, DASH-PISA forms a fully automated, high-throughput TPP workflow. As a proof of concept, stepwise single-well fractionation reproduced the melting curves of traditional TPP, and the pooled DASH-PISA workflow detected known kinase targets of staurosporine; a spike-in SILAC reference further improved their recovery. By running on commercially available automation, this workflow makes proteome-wide target identification practical at the scale required for compound-library screening.
ER -