DOSCHEDA: a web application for interactive chemoproteomics data analysis

PeerJ Computer Science

Ronald Tomlinson¹  M. Paola Castaldi¹  Eric Miele¹  Bruno Contrino²  Piero Ricchiuto² 

[1] Department of Chemical Biology, Discovery Biology, Discovery Sciences, AstraZeneca, Waltham, MA, United States of America;Department of Quantitative Biology, Discovery Sciences, AstraZeneca, Cambridge, United Kingdom;

关键词: Quantitative Chemoproteomics;    Statistical Models;    Web interface;    Shiny;    TMT;    iTRAQ;   

DOI  :  10.7717/peerj-cs.129

来源: DOAJ

【 摘 要 】

Background Mass Spectrometry (MS) based chemoproteomics has recently become a main tool to identify and quantify cellular target protein interactions with ligands/drugs in drug discovery. The complexity associated with these new types of data requires scientists with a limited computational background to perform systematic data quality controls as well as to visualize the results derived from the analysis to enable rapid decision making. To date, there are no readily accessible platforms specifically designed for chemoproteomics data analysis. Results We developed a Shiny-based web application named DOSCHEDA (Down Stream Chemoproteomics Data Analysis) to assess the quality of chemoproteomics experiments, to filter peptide intensities based on linear correlations between replicates, and to perform statistical analysis based on the experimental design. In order to increase its accessibility, DOSCHEDA is designed to be used with minimal user input and it does not require programming knowledge. Typical inputs can be protein fold changes or peptide intensities obtained from Proteome Discover, MaxQuant or other similar software. DOSCHEDA aggregates results from bioinformatics analyses performed on the input dataset into a dynamic interface, it encompasses interactive graphics and enables customized output reports. Conclusions DOSCHEDA is implemented entirely in R language. It can be launched by any system with R installed, including Windows, Mac OS and Linux distributions. DOSCHEDA is hosted on a shiny-server at https://doscheda.shinyapps.io/doscheda and is also available as a Bioconductor package (http://www.bioconductor.org/).

【 授权许可】

Unknown