If you found this site useful, please cite:

Croote, D., Quake, S.R. Food allergen detection by mass spectrometry: the role of systems biology. npj Syst Biol Appl. 2016 Sep 29; 2:16022.

Export Peptides to Skyline


Following the selection of peptide targets for allergen detection, the next step in targeted mass spectrometry is the development of an SRM assay, which requires transitions for each peptide. During method development, optimal transitions are selected according to a number of criteria, including consistent retention time, reproducible fragmentation profile, strong signal intensity. Skyline is an open source software tool with an extensive list of features that greatly facilitates this process, which is why we provide a simple export function for loading peptides into Skyline.


  1. Export the csv containing the peptides in your cart using the button on the right of the page.
  2. Open Skyline and on the start screen select "Import Peptide List"
  3. Verify Peptide and Transition settings and select Next
  4. Open the csv and copy the data (Control-c)
  5. Paste the data using Control-v. For this to work the entry box should be blue.
  6. Select insert

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Peptides can be added to the cart for exporting using the "Add Peptide to Cart" button on any peptide page.

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Save a peptide to cart before exporting

Export as a csv

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