Skyline is an essential tool for all mass spectrometry labs Chris Wu  2011-01-10 13:57
I would recommend Skyline to anyone interested in quantitative mass spectrometry measurements, particularly for multiplexed SRM analyses. One of the first things that I assign to new members of my lab, students I am mentoring, or collaborators wanting to be involved in the experimental pipeline, are the Skyline tutorials. The tutorials are comprehensive and easy to understand. This is extremely effective as an educational tool, particularly for those who have minimal or no background in quantitative mass spectrometry. For the members of my lab who are actively performing SRM-MS analyses, Skyline has TRANSFORMED the entire analytical pipeline (including the painful process of setting up methods for scheduled multiplexed experiments) to something that is routine and turnkey. Before Skyline was available, the most difficult parts of the experiment were 1) building the method and 2) data analysis. Now, the most difficult parts of the experiment are sample preparation and peptide separations, as it should be. Finally, and most importantly, the support for this software suite is phenomenal. Response times are typically within a few hours, and new features are continuously being added, frequently in direct response to user suggestions. I have never experienced this type of support for commercial proteomics software, on which I have unfortunately spent thousands of dollars. This is an open source tool developed in an academic lab, and I really don’t know how they maintain this type of service. It really feels like a community effort. Members of my lab have frequently commented they really feel involved in the software design process. This type of interactive support is truly unique and enabling and yet, disappointingly under-appreciated.

Christine Wu, Ph.D.
Associate Professor of Cell Biology
University of Pittsburgh School of Medicine