The Skyline Software Ecosystem: Efforts to Achieve Transparency, Interoperability, and Robustness of Quantitative LC-MS Assays

Michael MacCoss
University of Washington

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Michael MacCoss (Presenter) University of Washington

Presenter Bio: Michael MacCoss became interested in biomedical applications of mass spectrometry while working in Dr. Patrick Griffin’s protein mass spectrometry lab at Merck Research Laboratories. He obtained a Ph.D. with Professor Dwight Matthews and pursued a postdoc with Professor John R. Yates III. In 2004 he started the MacCoss lab at the University of Washington and it became obvious that while mass spectrometry data could be collected quickly and robustly, the lack of computational tools for the visualization and analysis of these data was a stumbling block. In 2009 he recruited Brendan MacLean with the goal of developing professional quality software tools for quantitative proteomics. Mike has worked closely with the Skyline development team and our outstanding group of laboratory scientists and collaborators to ensure that our software uses analytical approaches that have been thoroughly vett

Relevant Financial Disclosures (within past 24 months) Grant/Research Support Skyline is supported by these instrument vendors Agilent Bruker Sciex Shimadzu ThermoFisher Waters. Committee/Board/Advisory Board Newomics Salary ThermoFisher Scientific Discussing Products? NO, presenter will NOT present educational content related to products/services of the ineligible company(ies) listed above. Conflict mitigation NOT REQUIRED.

Skyline is a freely-available and open source Windows client application for building quantitative LC-MS methods and the analysis of the resulting mass spectrometry data. We have applied state-of-the-art technologies for creating methods, iteratively refining assays, and the visualization of quantitative mass spectrometry experiments across all major instrument vendors. Originally Skyline was developed specifically for targeted proteomics but has expanded to support method development and data analysis for all molecular species. There have been over 90,000 new installations of Skyline since it was first publicly released at ASMS 2009, with 1000 installations on average each month over the past 6 months, and consistently >8000 software boot-ups per week for the last year. Additionally, Skyline supports an external tool framework with 13 tools available currently (some with >10,000 installations themselves). The server side project Panorama (http://panoramaweb.org), supports managing Skyline documents (both results and assay validation), sharing data within a group or to the entire community, and real-time collection and tracking of instrument system suitability data. Recent capability like quantitative signal calibration, assay figures of merit, and audit logging have been developed in close collaboration and with iterative feedback with members of the MSACL community. I will present a perspective on the history of the project, provide examples of how these tools have been used in assay development, and provide a vision for the future.