The following instructors and speakers have agreed to contribute their expertise to the success of UW Course:
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Michael J. MacCoss, Ph.D. Mike 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 vetted by the mass spectrometry community. |
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Brendan MacLean 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 LakKey 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. |
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Josh Eckels Josh has lead development on proteomics related projects for LabKey Server over the past 10+ years, and he currently oversees Panorama development. He is experienced in security-related projects, client-side end user applications, and server-side development. Prior to joining LabKey, Josh worked most recently on Amazon.com's data warehouse, developing the software that schedules and executes loading and querying of more than 30 terabytes of data. Before that, he was the team lead for the debugger for BEA System's WebLogic Workshop. At LabKey, he focuses on mass spectrometry, other assay types, experimental annotations and general infrastructure. Josh has a BS in Computer Engineering from Northwestern University. |
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Jarrett Egertson, Ph.D. Jarrett is a postdoctoral researcher at the University of Washington Department of Genome Sciences. He works in the MacCoss Lab and primarily focuses on developing new data acquisition methods and software in support of these methods. Jarrett earned his undergraduate degree (B.S. in Molecular, Cell, and Developmental Biology) from UCLA in 2008. While earning his undergraduate degree, Jarrett researched at the Spielberg Family Center for Applied Proteomics at the Cedars-Sinai Medical Center. |
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Andy Hoofnagle, MD, Ph.D. Andy is an Associate Professor in the Department of Laboratory Medicine at the University of Washington. His laboratory focuses on developing CLIA-certified assays for small molecules using mass spectrometry. They also investigate the function of high density lipoproteins in patients at increased risk for cardiovascular disease and the translation of proteomics technologies into the clinical laboratory. |
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Christina Ludwig, Ph.D. Tina is heading the proteomics section at the Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS) at the Technical University Munich (www.baybioms.wzw.tum.de). Her current research interests are focused on technical development projects related to targeted and data-independent mass spectrometry, including Selected Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM) and SWATH-MS. During her postdoc in the laboratory of Professor Ruedi Aebersold at the ETH Zürich Christina was involved in projects aiming for specific site-localization of post-translational modifications and estimation of absolute protein abundances from label-free, targeted mass spectrometric data. |
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Lindsay K. Pino
Lindsay is a Ph.D. candidate at the University of Washington’s Department of Genome Sciences in the MacCoss lab. Her research interests include the development of large-scale proteomics assays using data independent acquisition-MS to investigate complex mixtures and applying computational techniques to mine the resulting high-dimensional data. Prior to joining the MacCoss lab, she worked as a research associate at the Broad Institute of MIT and Harvard in Dr. Steve Carr’s Proteomics Platform, where she worked under Dr. Susan Abbatiello to improve the speed and selectivity of targeted proteomics assays using high-field asymmetric waveform ion mobility spectrometry (FAIMS). |
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Brian Searle Brian Searle is the co-founder and chairman of the board of Proteome Software, Incorporated. Following an undergraduate degree in chemistry from Reed College, Brian was mentored in MS/MS-based proteomics by Ashley McCormack and software development by Mark Turner in Srinivasa Nagalla’s lab at Oregon Health and Science University. In 2004 Brian co-founded Proteome Software with Mark and Ashley to produce and distribute cutting-edge data analysis software for proteomicists. As the owner of Proteome Software, Brian has produced numerous innovations in the analysis of MS/MS-based proteomics data. Brian is a member of the American Society for Mass Spectrometry (ASMS) and served on the board of directors for that organization. Brian also co-founded the Proteome Informatics Research Group of the Association of Biomolecular Resource Facilities (ABRF) society and is active in ABRF committees. In addition to furthering the goals of Proteome Software, Brian is concurrently pursuing a PhD at University of Washington. |
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Vagisha Sharma Vagisha got involved with proteomics at UC San Diego where she worked with Prof. Vineet Bafna. During that time she built her first tools for visualizing Mass Spectrometry data while working at ActivX Biosciences. Since moving to Seattle Vagisha has worked on Mass Spectrometry pipelines for the Aebersold group at the Institute for Systems Biology, and developed a data management system while at the University of Washington Proteomics Resource and the Yeast Resource Center. She joined the Skyline team in October 2011 where she has been the lead developer for the Panorama Targeted Proteomics Knowledge Base. |
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Sandi Spencer, Ph.D. Sandi is currently a postdoctoral researcher in the MacCoss lab at the University of Washington working on method development for targeted proteomics and improvement of nanoLC robustness. She earned her Ph.D. from the University of North Carolina at Chapel Hill working in the Glish lab on real-time analysis of compounds in organic aerosol particles. |
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Olga Vitek, Ph.D. Olga is a Sy and Laurie Sternberg Associate Professor in the College of Science and the College of Computer and Information Science at Northeastern University. Olga holds a PhD in Statistics from Purdue University. Her group develops statistical methods and algorithms for quantitative proteomics. The methods optimize the experimental design, and ensure accurate and objective interpretation of the resulting large and complex datasets. The tools developed by her group include MSstats, an open-source software for statistical analysis of quantitative shotgun, targeted and data-independent proteomic experiments. |