PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies.

Molecular & Cellular Proteomics : MCP
Kristen M NaegleForest M White

Abstract

The rate of discovery of post-translational modification (PTM) sites is increasing rapidly and is significantly outpacing our biological understanding of the function and regulation of those modifications. To help meet this challenge, we have created PTMScout, a web-based interface for viewing, manipulating, and analyzing high throughput experimental measurements of PTMs in an effort to facilitate biological understanding of protein modifications in signaling networks. PTMScout is constructed around a custom database of PTM experiments and contains information from external protein and post-translational resources, including gene ontology annotations, Pfam domains, and Scansite predictions of kinase and phosphopeptide binding domain interactions. PTMScout functionality comprises data set comparison tools, data set summary views, and tools for protein assignments of peptides identified by mass spectrometry. Analysis tools in PTMScout focus on informed subset selection via common criteria and on automated hypothesis generation through subset labeling derived from identification of statistically significant enrichment of other annotations in the experiment. Subset selection can be applied through the PTMScout flexible query interf...Continue Reading

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Citations

Sep 12, 2012·Molecular & Cellular Proteomics : MCP·Hannah JohnsonForest M White
Oct 16, 2012·Briefings in Bioinformatics·Roman SloutskyKristen M Naegle
Apr 19, 2012·Science Signaling·Boris KholodenkoWalter Kolch
Jul 6, 2014·Clinical Proteomics·Emily S Boja, Henry Rodriguez
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Jun 4, 2013·Free Radical Biology & Medicine·Traci MarinJohn Y-J Shyy
Apr 26, 2015·Database : the Journal of Biological Databases and Curation·Payman NickchiShiva Kalantari
Nov 12, 2013·Cell·Yongcheol ChoValeria Cavalli
Nov 22, 2014·Nucleic Acids Research·Matthew K MatlockKristen M Naegle
Dec 2, 2017·PloS One·Güliz VanliChristian Widmann
May 21, 2013·Integrative Biology : Quantitative Biosciences From Nano to Macro·Emily R MiraldiForest M White
Sep 14, 2017·Current Protocols in Bioinformatics·Arshag D MooradianKristen M Naegle
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Feb 18, 2011·Science Signaling·Forest M White

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