Automated sample preparation for reproducible clinical proteomics

Mass spectrometry (MS)-based proteomic technologies are increasingly applied in a clinical context for disease classification and diagnostics, however their standardized use is still prevented by several bottlenecks in sample handling. Here, I will present how we integrated AFA-based ultrasonication in an automated proteomic workflow to enable routine, robust and comprehensive proteome analysis with minimal hands-on time. This can be applied to cells, fresh tissue and FFPE tissue, thus spanning the full range of clinical sample types and indicating universal utility. Moreover, 96 samples can be processed simultaneously, ensuring throughput under standardized conditions. Sensitivity of the approach will be shown from low-input experiments starting from 100-1000 cells. Data will be shown of the implementation of this pipeline to a cohort of 96 ependymoma tumor samples, where we integrated the obtained proteomic data with other omics layers allowing individualized molecular profiling and disease sub-classification.

 

Benefits of Adaptive Focused Acoustics for Proteomics Lab

 

Proteomics requires strategies capable of processing hundreds of samples in a robust and reproducible manner, independently of the origin of the material of interest. In this webinar I will show how the Proteomics Facility of the Biomedical Center at the University of Munich takes advantage of AFA-based ultrasonication to establish universal workflows that can be applied to the proteomic studies of diverse samples including FFPE, thrombi or low number of cells. The standardization, reproducibility and throughput of these workflows facilitated the analysis of large cohorts and provided our collaboration partners with proteomics data ready for clinical or biological interpretation and integration with other omics information.