Proteogenomics Shared Resource

Proteogenomics offers a powerful approach for molecular studies of cancer. Driven by customized bioinformatic tools, proteogenomics leverages next-generation sequencing (NGS) of DNA/RNA and high-resolution mass spectrometry (MS)-based proteomics data. Metaproteomics is a specialized form of proteogenomics, integrating metagenomics and MS-based proteomics to predict and confirm expression of proteins of microorganisms found in cancer-relevant samples while simultaneously characterizing the proteome response of the host.

Proteogenomics Shared Resource
Foundational workflows for proteogenomics and metaproteomics.

 A number of variations of this integrated multi-omic analysis can be pursued, including:

Identification of translated non-normal protein sequences contributing to cancer.  In its traditional embodiment, NGS gene and/or transcript sequencing data predicts non-normal (variant) protein sequences encoded by DNA or RNA variants or from genomic locations previously thought to be non-coding. MS-based proteomics confirms expression of these novel protein sequences, offering critical clues to the functional consequences of cancer-associated genomic alterations, as well as providing promising biomarkers.

Identification of tumor neoantigens.  In another variation, proteogenomics can also identify cancer-specific neoantigen peptides with promise for developing cancer immunotherapies, by integrating customized NGS analysis tools and MS-based immuno-peptidomics data

Functional characterization of microbiomes and their contributions to cancer. Using a clinical metaproteomic workflow to study cancer samples (e.g. tumor tissues or fluids), MS-based metaproteomics offers a means to characterize both microbial and host proteins and their enriched functions and pathways, which offer insights into microbe-host interactions underlying carcinogenesis, therapy response, and promising diagnostic biomarkers.

Services offered by the Proteogenomics Shared Resource include:

  • Study design, planning and strategy
  • Design of pilot studies
  • Analysis of pilot study data
  • Testing and optimization of new software tools and workflows customized to user studies
  • Introduction to example workflows and training of laboratory members in the use of bioinformatics tools to advance their research
  • Assistance with publications and grant proposal preparation
  • Making software tools and data available as required for publication and funding agencies

Investigators interested in utilizing the Proteogenomics Shared Resource should contact the Co-Directors Dr. Tim Griffin and Dr. Pratik Jagtap via email.