Scientific Publications

A framework for installable external tools in Skyline.

Publication TypeJournal Article
AuthorsBroudy, D., Killeen T., Choi M., Shulman N., Mani D. R., Abbatiello SE, Mani D., Ahmad R., Sahu AK, Schilling B., Tamura K., Boss Y., Sharma V., Gibson BW, Carr SA, Vitek O., Maccoss MJ, and Maclean B.
AbstractSkyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. The Skyline document model contains extensive mass spectrometry data from targeted proteomics experiments performed using selected reaction monitoring, parallel reaction monitoring and data-independent and data-dependent acquisition methods. Researchers have developed software tools that perform statistical analysis of the experimental data contained within Skyline documents. The new external tools framework allows researchers to integrate their tools into Skyline without modifying the Skyline codebase. Installed tools provide point-and-click access to downstream statistical analysis of data processed in Skyline. The framework also specifies a uniform interface to format tools for installation into Skyline. Tool developers can now easily share their tools with proteomics researchers using Skyline. Availability and implementation: Skyline is available as a single-click self-updating web installation at http://skyline.maccosslab.org. This Web site also provides access to installable external tools and documentation.
Year of Publication2014
JournalBioinformatics (Oxford, England)
Date Published (YYYY/MM/DD)2014/05/09
ISSN Number1367-4803
DOI10.1093/bioinformatics/btu148
PubMedhttp://www.ncbi.nlm.nih.gov/pubmed/24813211?dopt=Abstract