Our laboratory has found Skyline to be an instrumental tool in developing targeted mass spectrometry methods. Specifically, Skyline has enabled us to identify SRM/MRM transitions to hundreds of target peptides in an efficient manner, refine and optimize those transitions empirically, and share the results with collaborators. The ability to work with multiple vendors' platforms is particularly attractive for our laboratory, and this makes possible a single streamlined workflow for our targeted proteomics experiments. Support for the software has been fantastic. Tutorial videos and slidedecks get new users up and running in a timely manner, and the development team has been openly engaged in discussing and implementing new features.
  
Jeff Whiteaker, Ph.D.
Director of Proteomics, Paulovich Laboratory, Fred Hutchinson Cancer Research Center