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.
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
Proteogenomics GTN Tutorials: https://training.galaxyproject.org/training-material/search?query=proteogenomics
Metaproteomics GTN Tutorials: https://training.galaxyproject.org/training-material/search?query=metaproteomics
Cancer Research Article: https://doi.org/10.1158/0008-5472.CAN-17-0331
Other publications: z.umn.edu/galaxypreferences