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Bioinformatics DOI:10.1093/bioinformatics/btu148

A framework for installable external tools in Skyline.

Publication TypeJournal Article
Year of Publication2014
AuthorsBroudy, D, Killeen, T, Choi, M, Shulman, N, Mani, DR, Abbatiello, SE, Mani, D, Ahmad, R, Sahu, AK, Schilling, B, Tamura, K, Boss, Y, Sharma, V, Gibson, BW, Carr, SA, Vitek, O, MacCoss, MJ, MacLean, B
Date Published2014 Sep 01
KeywordsMass Spectrometry, Proteomics, Software

UNLABELLED: Skyline 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 This Web site also provides access to installable external tools and documentation.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Alternate JournalBioinformatics
PubMed ID24813211
PubMed Central IDPMC4147880
Grant ListR01 GM103551 / GM / NIGMS NIH HHS / United States
UL1 TR001108 / TR / NCATS NIH HHS / United States