The ProteomeScoutAPI [publication] is a Python automatic programming interface for the ProteomeScout database downloads that allows for the easy interaction with post-translational modification information including proteins and their annotations. We used the database and API to test the hypothesis that mutations near sites of modifications are more likely to be involved in human disease (since they are more likely to affect the regulation and recognition of the modification). The results can be found in our iPythonNotebooks from the publication.
The motivation and features of the combined ProteomeScout and API are:
Enable the easy analysis of the PTMome
Allow for reproducible analyses
Allow for easy re-analysis in the future for the new PTMome
A foundation of our work is the ability to have proteome information at our fingertips. This includes the current knowledge of tyrosine phosphorylation, quantitative measurements measured on those sites, and related protein annotations. In enabling this research for our own lab, we also construct tools that can be used by the broader research community, with a focus on extendibility and reproducibility.
A major piece of ongoing work in the lab is to develop methods that will allow us to identify what phosphotyrosines will be recognized by a binding domain. Specifically, we hope to push this area of research into arenas that allow us to predict the relative competition between domains for phosphotyrosine sequences and phosphotyrosine sequences for domains. This information will enable us to begin to predict the consequence of context differences between cells in response to the same extracellular cue. We will feel we have succeeded when these predictions can be used to explain complex network phenomena.
A major barrier to the study of protein phosphorylation is the ability to create phosphorylated proteins for in vitro study. The Naegle lab has been developing a cheap and fast method for producing phosphorylated proteins that capitalizes on observations made of enzymatic specificity.