We are a research organization with a deep interest in pattern recognition within a biological context. We are invested in the integration of the fields of proteomics and genomics in the burgeoning field of proteogenomics. The work of our members with both the ENCODE consortium and the Clinical Proteomic Tumor Analysis Consortium has led to several exciting advances in technology and methods as well as uncovering many unique biological insights.
Proteogenomics,where mass spectrometric data is mapped against theoretical peptides from genomic or protein databases, is a powerful method for the discovery of novel or abnormal proteins. Knowledge of disease-specific protein forms can be exploited to discover biomarkers that can lead to early-detection disease screens.
To fully explore the power of proteogenomics, we are actively seeking collaborations and bring the following to the table:
Proteogenomic analysis: Proteogenomic search results contain copious data wherein the information supporting novel protein expression is dwarfed by known or false findings. If we enter into a collaboration with you, we will perform proteogenomic analyses of your data on several databases (e.g. contaminant, reference protein, reference genome, etc.), cross-compare the results of those analyses to highlight the novel peptides, and create an easy-to-navigate report. This is accomplished using our latest version of Peppy.
Peppy: Integrated proteogenomic search software. Peppy provides a unified pipeline for the creation of a peptide database from a 6-frame translation and in silico digestion of a genome. False discovery rates are automatically derived for every search via target-decoy strategy.