Towards a Hierarchical Strategy to Explore Multi-Scale IP/MS Data for Protein Complexes

• DOI: 10.1371/journal.pone.0139704
• Publication Date: 2015-10-08T18:12:11Z
• Authors: Joachim Kutzera; Age K. Smilde; Tom F. Wilderjans; Huub C. J. Hoefsloot
• Keywords: 0301 basic medicine; Internet; Science; Q; R; Proteins; Mass Spectrometry; 004; User-Computer Interface; 03 medical and health sciences; Medicine; Immunoprecipitation; Protein Interaction Maps; Research Article

Protein interaction in cells can be described at different levels. At a low level, proteins function together small, stable complexes and higher sets of interacting complexes. All levels are crucial for the living organism, one challenges proteomics is to measure their One common method such measurements immunoprecipitation followed by mass spectrometry (IP/MS), which has potential probe protein forms. However, IP/MS data complex because proteins, diverse forms, manifest themselves ways data. Numerous bioinformatic tools finding currently available, but most do not provide information about level discovered complexes, no tool geared specifically unraveling visualizing these We present new explore datasets show its performance on several real-life datasets. Our creates clusters that represent unlike previous methods, it arranges them tree-shaped structure, reporting why specific predicted build where divided into smaller In every analysis method, parameters have chosen. suggest values comes with adapted visualization display effect result. The fast graphical feedback allow user interact changing examining also exploring organizational given dataset. available as GNU-R source code includes examples www.bdagroup.nl.