[Project Page, Support] Skyline is a freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), DIA/SWATH and targeted DDA quantitative methods and analyzing the resulting mass spectrometer data. Its flexible configuration supports All Molecules. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale quantitative mass spectrometry studies in life sciences.

Build Targeted Methods

Use prior knowledge of your proteins and peptides of interest to improve your measurement selectivity and precision.

See Quantitative Results

Learn more about your quantitative measurements through the rich and interactive Skyline graphical data displays.

Store and Share Experiments

Panorama stores the entire Skyline data model, where you and your collaborators can explore it with a web browser.

Build Chromatogram Libraries

Use Panorama to build fully validated chromatogram assay libraries you can use in Skyline for new experiments.

[Project Page, Support] Panorama is a freely-available, open-source targeted proteomics website knowledgebase for sharing experiments and validated assays that integrates into a Skyline proteomics workflow.  It can be installed on a local server, or you can request a project on the PanoramaWeb.org server, hosted by the MacCoss Lab at the University of Washington. Access privileges within a project may be customized, allowing you to control fully who has access to data you publish to Panorama.

[Project Page] EncyclopeDIA is an open-source library search engine for DIA data analysis. It searches for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. Walnut, an implementation of PECAN, generates chromatogram libraries from FASTA databases when spectrum libraries are unavailable.

[Project Page] BiblioSpec 2.0 is the open-source spectral library build engine used by Skyline. It supports 18 different peptide search pipelines, and can be run separately from Skyline on Windows and Linux computers. It also supports using spectral libraries for peptide identification of MS/MS scans from DDA data.