Skyline is the ideal all-in-one solution for our targeted analysis of cell surface proteins Thomas Bock  2011-01-31
In our laboratory we increasingly move towards the targeted analysis of cell surface proteins. With the integration of Skyline into our SRM workflows, I think we found an ideal all-in-one solution that combines a user friendly interface with the necessary flexibility that is needed in our research environment.
One of my preferred features is the easy generation and handling of large N glycopeptide spectral libraries that I further use for the selection and quality control of peptide transitions. The possibility to introduce a background proteome is great for additional protein information and to filter for proteotypic peptide sequences.
Skyline’s powerful data analysis capabilities are fantastic and its features for peak picking and integration are routinely used in our laboratory.
In addition, I highly profited from the excellent software support and the nice video tutorials helped me to being productive in a very short time after installation of the software. To me, Skyline is the optimal solution for anybody planning to do SRM measurements.

Thomas Bock, Diplombiologe
PhD-student, group of Dr. Bernd Wollscheid,
NCCR Neuro Center for Proteomics,
Institute of Molecular Systems Biology, ETH Zürich, Switzerland