A framework for installable external tools in Skyline.

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.

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.

Unlabelled: MSstats is an R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. Version 2.0 of MSstats supports label-free and label-based experimental workflows and data-dependent, targeted and data-independent spectral acquisition.