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.
Highlights
ProteomeScout is a database of protein post-translational modifications, protein annotations and a web resource for analysis of posttranslational modifications (PTMs) and proteins
We have developed a number of methods, and utilized them in our own work, which led to novel insights from PTM experiments, including prediction of novel protein interactions from dynamic phosphorylation data (17), the identification of upregulated motifs downstream of the the EGFRvIII receptor (18), prediction of PTMs acting in specific pathways (19) and dissection of poorly understood signaling networks (20)
This button is associated with graphics generated on ProteomeScout and indicates that graphic can be downloaded in Scalable Vector Graphics (SVG) format
Summary
ProteomeScout is a database of protein post-translational modifications, protein annotations and a web resource for analysis of PTMs and proteins. ProteomeScout is unique in the world of post-translational modification (PTM). The purposeful design of these features was inspired by the historical progression of resources for other types of molecules, including: the UCSC Genome Browser (1) and the Gene Expression Omnibus (GEO) (2). A sampling of PTMspecific databases includes Phosida (4), PhosphoSitePlus (5), phospho.ELM (6), PTMScout (7), dbPTM (8), PTMSD (9), PTMCode (10) and O-GLYCBASE (11). The names of these databases reflect the progression of PTM research, and despite initially being focused on phosphorylation, many of them encompass multiple modification types
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