title: A framework for installable external tools in Skyline.
abstract: 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.
  
  
  METHODS
  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.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Broudy
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Trevor
authors.initials: T
authors.lastname: Killeen
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Meena
authors.initials: M
authors.lastname: Choi
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Shulman
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Deepak R
authors.initials: DR
authors.lastname: Mani
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Susan E
authors.initials: SE
authors.lastname: Abbatiello
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Deepak
authors.initials: D
authors.lastname: Mani
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Rushdy
authors.initials: R
authors.lastname: Ahmad
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Alexandria K
authors.initials: AK
authors.lastname: Sahu
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Birgit
authors.initials: B
authors.lastname: Schilling
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Kaipo
authors.initials: K
authors.lastname: Tamura
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Yuval
authors.initials: Y
authors.lastname: Boss
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Vagisha
authors.initials: V
authors.lastname: Sharma
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Bradford W
authors.initials: BW
authors.lastname: Gibson
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Carr
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Olga
authors.initials: O
authors.lastname: Vitek
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: MacCoss
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA.
authors.forename: Brendan
authors.initials: B
authors.lastname: MacLean
mesh_terms: D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D012984:Software