Scalable, Reliable, and Robust Workflows with Adaptive Focused Acoustics® (AFA®) compatible with other purification techniques for Protein Analysis in FFPE Tissue

High-throughput, robust, reliable and easy workflows play an extremely important role in complex areas such as, clinical proteomics, which requires analyses of complex large molecules in complicated matrices. The workflows are expected to standardize processing of samples from a variety of sources – ranging from fresh frozen tissues, blood and also from Formalin fixed paraffin embedded (FFPE) tissues. FFPE tissues provide a robust matrix to preserve tissue architecture. However, efficient removal of paraffin is an essential step to achieving high quality LC-MS data. Xylol, despite all its efficacy presents some severe health risks, and repeated steps of xylol removal compromises assay reproducibility. This study not only focuses on efficient, robust handling of FFPE tissues, but also demonstrates implementation of a one plate sample preparation (including digestion) on a liquid handling robot for automated processing of tissue lysates in a 96-well format. The process of AFA-enhanced Protein Aggregation Capture enables unbiased protein purification and digestion resulting in delivering peptides that can be directly analyzed by LC-MS, while significantly reducing time to results, variability in protein quantitation, and ultimately providing increased confidence in the data. This study shows data also applied this approach in the domain of clinical FFPE pulmonary adenocarcinoma (ADC) samples for identification and classification of samples according to histological growth patterns. This work efficiently showcases an optimal integration of AFA technology for automated end-to-end sample preparation and LC-MS analysis of 96 intact tissue samples.