Skyline

Skyline enables creation of targeted mass spectrometry methods and quantitative analysis of proteomic and lipidomic data, including datasets from liquid chromatography–ion mobility spectrometry–collision-induced dissociation–mass spectrometry (LC-IMS-CID-MS).

Key Features:

• Method creation for targeted MS (SRM/MRM): Supports design and management of selected reaction monitoring (SRM) and multiple reaction monitoring (MRM) methods for targeted proteomics and lipidomics.
• MS/MS spectral library support: Allows use and generation of MS/MS spectral libraries from diverse sources for peptide and small-molecule identification.
• Native instrument file import: Imports native output files from triple quadrupole and related instruments, including Agilent, Applied Biosystems, Thermo Fisher Scientific, and Waters formats.
• Multidimensional data processing: Processes small-molecule and lipidomic datasets that include ion mobility dimensions and collision-induced dissociation data.
• Ion mobility filtering: Applies ion mobility–based filtering for analysis and annotation of lipid species with structural similarity.
• Data visualization and integrity inspection: Provides graphical displays for inspection of chromatograms, ion mobility traces, and data integrity during acquisition and analysis.
• Dynamic reporting and export: Produces tabular reports via a dynamic report designer for export and downstream statistical analysis.
• Lipidomics annotation protocol: Implements steps for importing lipidomic data, predicting retention times, validating annotations, and exporting annotation results.

Scientific Applications:

• Targeted proteomics: Development and execution of SRM/MRM assays for quantitative peptide and protein measurements.
• Lipidomics: Annotation and quantification of lipid species, including analyses that leverage ion mobility and MS/MS information to resolve structurally similar lipids.
• Multidimensional MS analyses: Quantitative analysis of datasets generated by LC-IMS-CID-MS and related multidimensional separation techniques.
• Method development and validation: Creation, validation, and export of targeted MS methods and associated quantitative results for downstream statistical interpretation.

Methodology:

Creation of SRM/MRM methods; generation and use of MS/MS spectral libraries; import of native instrument files (Agilent, Applied Biosystems, Thermo Fisher Scientific, Waters); processing of LC-IMS-CID-MS and ion mobility–containing datasets; ion mobility filtering; retention time prediction; annotation validation; export of tabular reports.