Proteogenomics

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.

Variations of Integrated Multi-Omic Analysis

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.

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.

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Services

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.

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Information

Tutorials

Publications

Use Cases

Galaxy-P Presentations

Access and Acknowledgment

Required Acknowledgment for Shared Resource Use
Research supported by the MCC Cancer Center Support Grant, including work using MCC Shared Resources, must cite the MCC and each Shared Resource used.

“This work was supported in part by NIH P30 CA77598 utilizing the following Masonic Cancer Center, University of Minnesota shared resource(s)..."

Public Access Compliance
Investigators must follow the NIH Public Access Policy by submitting the final peer‑reviewed manuscript to PubMed Central and including the PMCID in all applicable publications.

Variations of Integrated Multi-Omic Analysis

+ Services

+ Information

+ Tutorials

+ Publications

+ Use Cases

Services

Information

Tutorials

Publications

Use Cases