Skyline: An open source software that supports your SRM workflow from the start to the end

Skyline: An open source software that supports your SRM workflow from the start to the end Christina Ludwig  2010-12-18
Skyline is my favorite software for SRM analysis, because I can use it throughout the whole SRM workflow: 1. starting with the design of SRM assays for all peptides/proteins of interest based on spectral libraries or on systematical filtering; 2. optimization and validation of these assays in a representative sample of interest; 3. analysis of the final SRM assay collection in high throughput; 4. quick quality control and comparison of all measurements; 5. and finally the in-depth quantitative manual analysis of the experiment. For my own work the most outstanding features of Skyline, compared to any other available SRM software, are the easy and straightforward import of spectral libraries from any source, the use of a background proteome, which provides a lot of important protein information and enables the choice of genetically unique peptides, and finally the support of any type of posttranslational modifications (in particular phosphorylation and neutral-loss transitions). In our institute triple quadrupole instruments from various different manufacturers are used on a regular basis, therefore I also very much appreciate the fact that Skyline can be applied to any data type and that methods, libraries, reports and results can very easily be shared.
The fast and competent support by the Skyline team is outstanding and I personally experienced the genuine implementation of my own suggestions and requests into Skyline. Hence I highly recommend the use of Skyline to everyone interested in doing SRM measurements!

Christina Ludwig, Ph.D.
Research scientist, group of Ruedi Aebersold
Institute of Molecular Systems Biology, ETH, Z├╝rich