ProteomeScout: a repository and analysis resource for post-translational modifications and proteins

Abstract

ProteomeScout (https://proteomescout.wustl.edu) is a resource for the study of proteins and their post-translational modifications (PTMs) consisting of a database of PTMs, a repository for experimental data, an analysis suite for PTM experiments, and a tool for visualizing the relationships between complex protein annotations. The PTM database is a compendium of public PTM data, coupled with user-uploaded experimental data. ProteomeScout provides analysis tools for experimental datasets, including summary views and subset selection, which can identify relationships within subsets of data by testing for statistically significant enrichment of protein annotations. Protein annotations are incorporated in the ProteomeScout database from external resources and include terms such as Gene Ontology annotations, domains, secondary structure and non-synonymous polymorphisms. These annotations are available in the database download, in the analysis tools and in the protein viewer. The protein viewer allows for the simultaneous visualization of annotations in an interactive web graphic, which can be exported in Scalable Vector Graphics (SVG) format. Finally, quantitative data measurements associated with public experiments are also easily viewable within protein records, allowing researchers to see how PTMs change across different contexts. ProteomeScout should prove useful for protein researchers and should benefit the proteomics community by providing a stable repository for PTM experiments.

Figure 1.

A map of ProteomeScout features and example user workflows. Gateway refers to the homepage menu items and Web Tool refers to actions that occur on subpages off of the main menu. (A) Methods for searching and interacting with proteins. (B) Tools for understanding features around specific protein residues. (C) Methods for loading and evaluating datasets of PTMs.

Figure 2.

Example of protein information available on ProteomeScout. All figures were exported directly from the ProteomeScout interface (using ‘SVG Export’). (A) The ProteomeScout view of the EGFR sequence, full track below with an inset, which is the expanded view of the kinase activation loop. PTM track: bars indicate where PTMs occur, the color indicates the type of residue and, when applicable, the bar height is proportional to the number of different documented modifications. Mutations track: size of circle is proportional to the number of documented non-synonymous polymorphisms. Scansite track: Size of circle is proportional to the number of Scansite predictions. Labels under annotations are suppressed when the annotation is small, relative to the label. Labels are available when hovered over by the cursor or when that area is expanded; for example, the annotations for the L858 mutation are shown (inset). (B) Quantitative data for measurements from (13) experiment measuring relative phosphorylation as a function of time following EGF stimulation of human mammary epithelial cells. (C) Quantitative data for measurements from (40) experiment measuring phosphopeptide counts across a number of lung cancer cell lines.