Skyline directly addresses a critical gap in our biomarker proteomics pipeline – the translation from biomarker discovery (‘omic LC/MS/MS) to biomarker verification (targeted LC/MS/MS).
Skyline has proven to be a fast, multiplexed, and reliable tool for the creation of complex MRM methods. We utilize spectral libraries and Skyline to quickly generate preliminary methods for our Xevo TQ, which target tens to hundreds of peptides with many transitions for each peptide. The data generated from a single Skyline-directed MRM analysis then allows us to maximize sensitivity and duty cycle by identifying the 2 to 3 best transitions and the proper retention time window for scheduled monitoring of each peptide. With the recent improvements in peak smoothing and integration algorithms along with the customizable reports, we are now using Skyline to also confidently analyze our targeted proteomics data. Finally, the deftness with which the Skyline development team takes user recommendations and includes them in new revisions of the software package is truly impressive.

J. Will Thompson, Ph.D. and M. Arthur Moseley, Ph.D
Duke Proteomics Core Facility
Duke Institute for Genome Sciences and Policy