Skyline is a very user-friendly, intuitive software tool that significantly speeds up my MRM-MS analysis. I particularly appreciate its compatibility with various MS platforms from different vendors and ease-of-use which make performing MRM assays using Skyline a smooth experience. Video tutorials and exceptional tech support are yet another great thing about this software. The usefulness of Skyline for performing MRM experiments is without question. Additionally, I found Skyline to be a fast and robust tool for calculating m/z of tryptic peptides and their modified forms. I use this functionality on a regular basis when I work on projects which aim to look for PTMs using LC-MS/MS and MALDI-MS and, in my opinion, the flexibility of Skyline as a m/z calculator makes it a great replacement of some popular software tools already available which are much less flexible.
Pawel Sadowski, Ph.D.
Postdoc fellow and satisfied Skyline user, NYU Protein Analysis Facility