British Society for Proteome Research (BSPR) Interact 2021 – Virtual

Opening Session Sponsored by Covaris and Presentation given by Jeroen Krijgsveld, German Cancer Research Center & University Heidelberg

Date: July 6th, 2021

Time: 10:30 am to 10:50 am BST

Automated sample preparation for reproducible proteomics in biology and the clinic

Proteome analysis is typically performed by direct integration of chromatography and mass spectrometry, allowing unattended and standardized analysis of multiple samples. In contrast, sample preparation prior to LC-MS is still largely a manual process, constituting a major source of variability in sample handling and, ultimately, in proteomic data. Here, we present how we established a generic, automated workflow for proteomic sample preparation by combining AFA-based ultrasonication and single-pot solid-phase-enhanced sample preparation (SP3), enabling routine and standardized proteome analysis with minimal hands-on time. Sonication is used for protein extraction from virtually any sample type, including cells, fresh tissue and FFPE tissues in a 96-well format, followed by protein clean-up and digestion by SP3 performed on a Bravo liquid handling platform. Sensitivity and reproducibility of the approach will be shown from low-input experiments starting from 100-1000 cells, from fresh tissues of various organs, and from FFPE tissue sections of cancer specimens. Furthermore, we used this pipeline to analyze a cohort of 96 ependymoma brain tumor samples, and integrated the obtained proteomic data with other omics layers for disease sub-classification. In conclusion, AFA-based ultrasonication combined with autoSP3 is a robust platform for standardized and parallel processing of a variety of tissue types for low-input proteomics, serving a wide range of clinical and non-clinical proteomic applications.

The annual British Society for Proteome Research (BSPR) flagship event for 2021 will be held virtually on the mornings of the 6th, 7th, and 8th July. The conference will feature prominent and upcoming scientists from the UK and across the globe, presenting the latest research and methodology in the field of proteomics as well as participating in round table discussions.