Get hands-on experience using Skyline to work with empirically measured optimal collision energy (CE) values. In this tutorial, you will create scheduled CE optimization transitions lists for a document with 30 peptide precursors. Using supplied RAW files from a Thermo TSQ Vantage, you will recalculate the linear equation used to calculate CE for that instrument. You will also export a transition list with CE values optimized separately for each transition. (12 pages)

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* - written on Skyline v0.6, updated for v1.4

Also, see our paper in Analytical Chemistry (please cite)
Effect of Collision Energy Optimization on the Measurement of Peptides by Selected Reaction Monitoring (SRM) Mass Spectrometry
[abstract]