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Chromatogram libraries capture representative chromatograms for a given target in a given set of instrumentation. Users can upload additional documents and then curate which version of a chromatogram is considered the most representative and should be the one stored in the library. A completed library can be downloaded as a .clib file, which is a SQLite database. That can then be imported into Skyline to inform and score future assays that use the same small molecules, peptides, or proteins.

Choose the Chromatogram Library folder type to include the tools for creating libraries. The Rank peptides within proteins by peak area box should be checked when you have targeted results containing relative peptide peak areas for a given protein. Leave this box unchecked if you do not yet have quantitative data from proteolytically digested proteins, such as when you are working with synthetic peptides.


The Panorama Chromatogram Libraries Tutorial shows you how to build a chromatogram library for peptides. The same type of functionality is available for small molecules. In this tutorial you will:

  • Build a chromatogram library in Panorama
  • Use it in Skyline to select peptides and product ions to measure in a new experimental setting
  • Compare library chromatograms with new data to validate peptide indentifications.


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