Skyline: full support for easy MRM assay development and implementation Birgit Schilling  2010-12-08
What I like about Skyline is that it is a fine open source software program that has become instrumental in integrating mass spectrometric discovery and verification workflows. I particularly appreciate that I can very easily incorporate spectral libraries obtained from our own MS/MS discovery experiments into Skyline to then very quickly and efficiently design targeted verification MRM assays. It is particularly nice that Skyline supports any type of stable isotope labeling as well as posttranslational modifications (i.e. phospho peptides, acetylated peptides, deglycosylated peptides, etc.) as we often target posttranslationally modified peptides in our MRM assays. I also like the fact that all acquired LC-MRM assays and data sets can be fully processed and integrated in Skyline, which becomes particularly important if one performs a large study as Skyline also helps to keep imported data files organized. We are using Skyline documents to send MRM assay templates and MRM data back and forth between collaborators. Last but not least, software support from Skyline designers is exceptional.

Birgit Schilling, Ph.D.
Gibson Laboratory, Buck Institute for Age Research, Novato, CA