Skyline tutorials provide step-by-step, hands-on instruction designed to help you become proficient with Skyline using real experimental data. Whether you are new to Skyline or an experienced user seeking to explore advanced workflows, these tutorials offer structured guidance across a broad range of applications—from introductory concepts and full-scan acquisition strategies to small-molecule analysis and advanced data processing techniques. Each tutorial includes both explanatory material and practice datasets to ensure you can apply what you learn directly to your own research.
These tutorials introduce the Skyline environment, guiding you through basic concepts such as targeted method editing, refinement, and analyzing grouped study data. They are designed for first-time users to quickly gain familiarity with Skyline’s interface and workflow, while also providing a solid foundation for more advanced applications.
This section provides a first look at working with full-scan mass spectrometer data in Skyline. The tutorials introduce how Skyline can process all of the chromatography based quantitative methods from PRM to DIA to MS1 filtering from DDA data. They are ideal for users who are beginning to integrate full-scan data into their workflows and want to understand the underlying principles.
These tutorials expand upon the basics by exploring advanced full-scan methods such DIA and diaPASEF with iRT and mProphet peak scoring. You can also learn more about PRM, MS1 filtering of any DDA search, and library-free peptide search tools built into Skyline. Together, they provide a comprehensive foundation for designing and interpreting complex full-scan experiments.
This section focuses on the Skyline small-molecule capabilities. Tutorials guide you through targeted small-molecule analysis, method development, collision energy optimization, calibrated quantification, and the use of multidimensional spectral libraries that include ion mobility spectrometry (IMS). These workflows demonstrate how Skyline can support metabolomics, lipidomics, glycomics, and other small-molecule research with the same rigor applied in proteomics.
Skyline reports give you powerful ways to explore, customize, and share the results of your analyses. These tutorials demonstrate how to create and adapt Live Reports and export their tabular data for use in tools such as Excel, R, or Matlab. You will also learn how to annotate results, apply filters, pivot data, and generate visualizations, making it easier to communicate findings and integrate Skyline with downstream statistical workflows.
These tutorials cover advanced features and specialized workflows in Skyline. They are intended for users who have already gained experience with the introductory and intermediate tutorials and want to broaden their understanding of Skyline’s full capabilities. The topics provide deeper instruction on areas not fully addressed in the introductory sections, helping you make the most of Skyline in complex or specialized scenarios.
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