In my opinion, the development of Skyline has transformed the way targeted proteomics experiments are performed within our laboratory. As a laboratory interested in discovery and verification of biomarkers, Skyline, a vendor neutral software, offers all the necessary capabilities to perform a MRM experiments from start to finish. The ability to create spectral libraries from existing tandem mass spectrometry data which can then be used to select the optimal proteotypic peptides and transitions allows for easy MRM method-building for a few or hundreds of proteins. The export features allow instrument methods to be generated for MS platforms for simple unscheduled methods, in addition to creating scheduled methods, allowing for increased MRM throughput. It doesn’t stop there! Skyline makes data processing and integration very easy allowing users to visual their data in various graphical forms. The ability to create custom-design report templates which can be shared offers the ability to standardize data reporting within or across laboratories. Skyline’s development and support team is absolutely amazing and always open for feedback on how to expand and improve the software’s current features to meet the demands of its users. Skyline is easy to use and the effective tutorials and videos created by the Skyline team will have you up and running MRM experiments in no time!

Lisa J. Zimmerman, Ph.D.
Research Associate Professor, Ayers Institute, Vanderbilt University