Abstract Next-generation sequencing (NGS) is routinely used for detection and determination of genetic mutations. While formalin fixed paraffin embedded (FFPE) samples have been a blessing for ensuring tumor tissue integrity, library construction for NGS using FFPE samples has been extremely challenging. Need for extraction of high quality and amplifiable DNA and RNA can make the workflow significantly more complex and challenging. The recent years have been witnessing a growing interest in precision medicine, and in monitoring biological systems via a multiomics approach. While such approaches can offer a holistic perspective of a system, they can be challenging owing to their inherent complexities, sample limitations, and lack of appropriate sample preparation methods. In addition to genomic data, proteomic data from FFPE samples are also gaining importance as more biomarkers are being discovered and optimized for detection and monitoring of diseases and their progression under specific therapy. Discovery and characterization to monitoring and quantification of proteins from FFPE samples can be complex – when it comes to ensuring extraction, purification, and digestion of proteins in high quality and quantity. Adaptive Focused Acoustics® (AFA®) Technology is an advanced acoustic technology that employs highly controlled bursts of focused high-frequency acoustic energy to efficiently and reproducibly proess samples in a temperature-controlled and non-contact environment This study presents an optimal use of AFA based workflows along with kits and methods for extraction, isolation, purification of TNA (DNA and RNA) from one 10 μm FFPE scroll. In addition, proteins can be extracted, purified (using a protein aggregation capture protocol), and digested in an expedited process in the same plate, also from one 10 μm FFPE scroll. The results not only show high yield, purity, and amplifiability for TNA but also reproducible and high yield of proteins and peptides – thereby offering every researcher achieve high quality, reliable, and reproducible data. Citation Format: Debadeep Bhattacharyya. Total Nucleic Acid to Proteins from FFPE: Confident Data with Comprehensive Sample Prep Workflows abstract. In: Proceedings of Frontiers in Cancer Science 2024; 2024 Nov 13-15; Singapore. Philadelphia (PA): AACR; Cancer Res 2025;85 (15Suppl): Abstract nr P65.
Debadeep Bhattacharyya (Fri,) studied this question.