A flexible end-to-end automated sample preparation workflow enables reproducible large-scale bottom-up proteomics - Part 4

ABSTRACT: Bottom-up proteomics holds significant promise for clinical applications due to its high sensitivity and precision, but is limited by labor-intensive, low-throughput sample preparation meth-ods. Advanced automation is essential to enhance throughput, reproducibility, and accuracy and to allow standardization, thus making bottom-up proteomics amenable for large-scale studies. We developed a fully integrated, automated sample preparation platform that covers the entire process from biological sample input to mass spectrometry-ready peptide output and can be applied on a multitude of biological samples. With this end-to-end solution, we achieved high intra- and interplate reproducibility, as well as longitudinal consistency, result-ing in precise and reproducible workflows. We showed that our automated workflow surpass-es established manual and semi-automated workflows, while improving time efficiency. Finally, we demonstrated the suitability of our automated sample preparation platform for drug development by performing a high-content compound characterization for targeted pro-tein degradation . For this, we coupled application-specific workflows to perform high-content compound characterization by proteome profiling and confirm target degra-dation by precise and reliable protein quantification. Thus, the automated sample preparation platform facilitates rapid adaptation to emerging developments in proteomics sample prepara-tion, combining standardization, flexibility, and high-throughput capabilities to drive significant advancements in clinical assays and proteomics research.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Sandra Schär  

LAB HEAD: Roland Bruderer

PROVIDER: PXD063831 | Pride | 2025-10-17

REPOSITORIES: Pride