Brendan MacLean   Brendan MacLean worked at Microsoft for 8 years in the 1990s where he was a lead developer and development manager for the Visual C++/Developer Studio Project.  Since leaving Microsoft, Brendan has been the Vice President of Engineering for Westside Corporation, Director of Engineering for BEA Systems, Inc., Sr. Software Engineer at the Fred Hutchinson Cancer Research Center, and a founding partner of LabKey Software.  In this last position he was one of the key programmers responsible for the Computational Proteomics Analysis System (CPAS), made significant contributions to the development of X!Tandem and the Trans Proteomic Pipeline, and created the LabKey Enterprise Pipeline.  For the last 4 and a half years he has worked as a Sr. Software Engineer within the MacCoss lab and been responsible for all aspects of design, development and support in creating the Skyline Targeted Proteomics Environment and its growing worldwide user community.

Status of the Skyline open-source software project 5 years after its inception

The Skyline project started just after ASMS 2008 as a 2-year effort to bring better SRM/MRM software tools to the NCI-CPTAC Verification Working Group that could support the variety of mass spectrometers in use in participating laboratories. Nearly 5 years later, the Skyline project is a thriving proteomics community open-source collaboration with solid support for another 3 years, hundreds of users and thousands of instances started each week. In this presentation, the Skyline lead software engineer will present recent developments and a roadmap for the project's future. Topics covered will include:
  • Advances in chromatogram extraction from full-scan acquisition data
  • Expanding support for new instrument vendors and new instruments
  • New peak picking algorithm based on mProphet, with probability based confidence metrics
  • Improved support for interaction with external tools like QuaSAR and MSstats
  • Experimental meta data and statistics in Skyline

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