Abstract 4875: HIVE Proteomics: Integrated, cloud-based RNA-Seq and proteomics analysis of prostate adenocarcinoma samples

Abstract Automated bottom-up proteomics workflows implemented with modern mass-spectrometry instrumentation can readily generate millions of peptide fragmentation spectra from cell-lines and clinically derived samples. The tandem mass-spectra promise to reveal wild-type and somatic mutations, insertions, and deletions and alternatively spliced isoforms translated to functional protein isoforms in tumor samples. However, the available reference proteomes represent a poor analysis substrate for the observation of protein evidence of genomic and transcript variation. The advent of cheap and fast RNA sequencing (RNA-Seq) provides an elegant solution to the lack of sample-specific reference proteomes. We anticipate that the falling cost of RNA-Seq will prompt an increasing number of proteomics labs to use contract next-gen sequencing (NGS) services to obtain RNA-Seq data to derive sample-specific reference proteomes. In contrast to public repositories of genomic variation, sample-specific RNA-Seq data captures transcribed rare, individual, cell-type, and sample-specific genomic variation. RNA-Seq-based transcripts also provide sample-specific information on observable proteins. Furthermore, paired RNA-Seq and proteomics data links gene expression and protein abundance, enabling the study of gene regulation linked to protein abundance dynamics. However, the analysis of multi-gigabyte paired mass-spectra and RNA-Seq datasets pose significant scientific and logistical challenges. Few proteomics labs have the personnel, archival data storage, computational resources, or informatics pipelines needed. The cloud-based genomics analysis platform High-performance Integrated Virtual Environment (HIVE) will provide turn-key integrated proteomics and RNA-Seq analyses to the wider proteomics community in a secure, trackable, sharable, and scalable computing platform. We will then use this integrated proteomics_RNA-Seq analysis pipeline to identify high-value mutations in prostate adenocarcinoma samples, thereby demonstrating the utility of the platform while also generating key data for future investigations. Citation Format: Hayley Dingerdissen, Raja Mazumder. HIVE Proteomics: Integrated, cloud-based RNA-Seq and proteomics analysis of prostate adenocarcinoma samples. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4875. doi:10.1158/1538-7445.AM2015-4875