ASAP-Automated Sonication-Free Acid-Assisted Proteomes-from Cells and FFPE Tissues

Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable resource for retrospective studies, but protein extraction and subsequent sample processing steps have been shown to be challenging for mass spectrometry (MS) analysis. Streamlined high-throughput sample preparation workflows are essential for efficient peptide extraction from complex clinical specimens such as fresh frozen tissues or FFPE. Overall, proteome analysis has gained significant improvements in the instrumentation, acquisition methods, sample preparation workflows, and analysis pipelines, yet even the most recent FFPE workflows remain complex and are not readily scalable. Here, we present an optimized workflow for automated sonication-free acid-assisted proteome (ASAP) extraction from FFPE sections. ASAP enables efficient protein extraction from FFPE specimens, achieving similar proteome coverage as established methods using expensive sonicators, resulting in reduced sample processing time. The broad applicability of ASAP on archived pediatric tumor FFPE specimens resulted in high-quality data with increased proteome coverage and quantitative reproducibility. Our study demonstrates the practicality and superiority of the ASAP workflow as a streamlined, time- and cost-effective pipeline for high-throughput FFPE proteomics of clinical specimens.

Automated summary

Formalin-fixed, paraffin-embedded (FFPE) tissues are valuable for retrospective studies, but their protein extraction and processing for mass spectrometry (MS) analysis are challenging. To address this, an optimized workflow called ASAP was developed for efficient protein extraction from FFPE sections without using sonicators. ASAP demonstrated high-quality data with increased proteome coverage and reproducibility in analyzing archived pediatric tumor FFPE specimens. It offers a streamlined, time- and cost-effective pipeline for high-throughput FFPE proteomics in clinical specimens.