Brendan MacLean Biography


MacLean2015In February, 2014, I was invited to participate in the 6th Annual Meeting of Proteomics Society, India and Indo-US Workshop, and I was encouraged to add a 2-day workshop on targeted proteomics to the other post-conference workshops.  It is gratifying to be asked to increase my participation even further next year and to see the proposed overall focus of a 2015 workshop include targeted quantitative proteomics so centrally, with a 6-day course following the seminars.  Since August 2008, I have been primarily focused on the creation and dissemination of the Skyline Targeted Proteomics Environment software, as a member of the MacCoss lab at the University of Washington, Department of Genome Sciences.  Skyline now has over 4000 registered users.  It has been installed over 30,000 times and, on average, 5-6000 instances are started each week.  Targeted proteomics was the Nature Methods 2012 Method of the Year, and Skyline was highlighted as playing an important role in the growth and promise of this new method.  Targeted proteomics is rapidly becoming a critical tool for testing quantitative hypotheses and validating proposed biomarker panels in proteomics.  Over the past two years, I have collaborated closely with the Aebersold lab at ETH, Zurich and members of several other labs in the US and Europe on a series of week-long courses and workshops to further disseminate targeted proteomics best practices and data processing and analysis with Skyline.  I am well connected with talented instructors of targeted quantitative proteomics worldwide, and already look forward to another week-long course in Barcelona and workshops in S. Korea, Japan and India in the final months of 2014.  In my experience, the week-long course format adds a lot in value for the students, beyond 1 and 2 day workshops. In Europe and the US such courses have been oversubscribed at a 30 student limit and have received universally favorable reviews from all participants.  Working with instructors from India to bring such in-depth instruction in targeted quantitative proteomics to Indian researchers has exciting potential to open new avenues of proteomics research in India and new collaborations between Indian and US researchers.

Brendan 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. Since August, 2008 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.

Key Publications:

  • MacLean B, et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics (2010) Feb 3, doi: 10.1093/bioinformatics/btq054
  • Carr, S. A. et al. Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach. Mol. Cell. Proteomics Mcp (2014). doi:10.1074/mcp.M113.036095
  • Sharma V, et al. Panorama: A Targeted Proteomics Knowledge Base. J Proteome Res. (2014) Aug 18. PMID: 25102069.
  • Broudy D, et al. A framework for installable external tools in Skyline. Bioinformatics. (2014) Sep 1;30(17):2521-3. doi: 10.1093/bioinformatics/btu148. Epub 2014 May 9.
  • Bereman, MS et al. Implementation of Statistical Process Control for Proteomic Experiments Via LC MS/MS. J. Am. Soc. Mass Spectrom. (2014). doi:10.1007/s13361-013-0824-5.
  • Chambers MC et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol. (2012) Oct;30(10):918-20. doi: 10.1038/nbt.2377.
  • Bereman MS, MacLean B, Tomazela DM, Liebler DC, MacCoss MJ. The development of selected reaction monitoring methods for targeted proteomics via empirical refinement. Proteomics (2012) Apr;12(8):1134-41.
  • Stergachis AB, et al. Rapid empirical discovery of optimal peptides for targeted proteomics. Nat Methods. (2011) Nov 6;8(12):1041-3. doi: 10.1038/nmeth.1770.