The following instructors and speakers have agreed to contribute their expertise to the success of Buck Institute Course:
|Birgit Schilling, Ph.D.
Birgit is Assistant Professor and the Director of the Mass Spectrometry and Chemistry Core at the Buck Institute for Research on Aging in Novato, CA. Research projects include investigations of neurodegenerative diseases, aging, cancer, mitochondrial damage, protein posttranslational modifications including acetylation in bacteria, the role of surface glycoconjugates in bacterial pathogenesis etc., but also mass spectrometric method development. Birgit has worked in the field of protein quantitation to assess differential protein expression or changes in posttranslational modifications, particularly using selected reaction monitoring stable isotope dilution mass spectrometry (SRM-SID-MS), and other chemical and metabolic labeling quantitative workflows, i.e., iTRAQ and SILAC technologies. Birgit has participated in large multi-laboratory SRM verification studies taking advantage of Skyline’s platform independent features. In recent years, she has used more and more label free protein quantitation approaches to investigate discovery mass spectrometric data sets (Skyline MS1 Filtering), as well as newer quantitative workflows, such as high resolution data-independent acquisitions (SWATH and PRM). Birgit has co-developed some algorithms for the Skyline Tool Store and she also extensively uses the interactive data sharing features of the Panorama webserver.
|Ruth Huttenhain, Ph.D.
Ruth Huttenhain is an Assistant Adjunct Professor at University of California San Francisco (UCSF). During her Ph.D. with Prof. Ruedi Aebersold at the Institute of Molecular Systems Biology, ETH Zurich, Ruth developed high-throughput and large scale targeted mass spectrometric approaches and applied them to the verification of plasma-based biomarkers. In 2013 Ruth joined the lab of Prof. Nevan Krogan at UCSF as a Postdoctoral Scholar. Her postdoctoral and current research focuses on leveraging quantitative mass spectrometry and genetic approaches to study dynamics of protein interaction networks combining classical affinity purification and novel proximity-based biotinylation approaches.
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.
|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.
|Chris Ashwood, Ph.D.
Chris is a Postdoctoral Fellow at the Medical College of Wisconsin (MCW). During his Ph.D. with Prof. Nicolle Packer at Macquarie University, Sydney, Australia, Chris developed robust untargeted mass spectrometric approaches for glycan analysis and applied them to profiling cells and tissues of the central nervous system. In 2018, Chris joined the lab of Dr. Rebekah Gundry at MCW as a Postdoctoral Fellow. His current research focuses on further optimizing these approaches and applying them towards advancing our current understanding of protein glycosylation for human cardiac tissues and cells.
|Christie Hunter, Ph.D.
Christie is the Director of Applications at SCIEX. Christie and her team are focused on developing and testing innovative MS workflows to analyze biomolecules, and work collaboratively with the instrument, chemistry and software research groups. Her primary area of focus is the application of MS based tools for the quantitative analysis of proteins and using MRM and SWATH® Acquisition strategies.
|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).
|Matthew Rardin Ph.D.
Matt is currently a scientist in the Discovery Attribute Sciences group at Amgen where he develops discovery and quantitative proteomic workflows to understand mechanism of action, pre-clinical biomarker discovery, and target engagement. Originally from Colorado, he received a B.S. in Microbiology at Colorado State University followed by graduate studies in Jack Dixon’s group at UCSD on the role of reversible phosphorylation signaling in mitochondria. For his postdoctoral studies, Matt joined Brad Gibson’s group where he focused on developing quantitative proteomic techniques to understand the regulation of lysine acylation by sirtuins and their role in metabolic function.
Brian is a Translational Research Fellow at the Institute for Systems Biology. Brian received his chemistry BA at Reed College in 2001. In 2004, he co-founded Proteome Software with Mark Turner and Dr. Ashley McCormack to produce and distribute cutting-edge data analysis software for proteomicists. In 2014, he returned to academia to earn his PhD with Dr. Michael MacCoss at University of Washington, where he developed methods to detect and quantify proteins and phosphosites using mass spectrometry. In 2018, he joined the Institute for Systems Biology as an independent fellow to build a research program that spans the intersection of proteomics, mass spectrometry, bioinformatics, and technology development to study human genetic variation.
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.
|J. Will Thompson, Ph.D.
Will is the Assistant Director of the Duke Proteomics and Metabolomics Shared Resource, and Assistant Research Professor in the Department of Pharmacology and Cancer Biology. He received his Ph.D. in Ultrahigh Pressure Liquid Chromatography from the laboratory of Dr. Jim Jorgenson at the University of North Carolina at Chapel Hill, and subsequently joined the Disease and Biomarker Proteomics group led by Dr. Arthur Moseley at GlaxoSmithKline. In 2007, Dr. Thompson assisted Dr. Moseley in founding the Duke Proteomics Core Facility, which as of winter 2017 has 10 full time scientists. Dr. Thompson has overseen the expansion of the group's efforts into small molecule and metabolomics analysis, which now represents roughly 40% of the work of the Shared Resource. His research in part focuses on application of novel proteomics and targeted metabolomics assays to clinical and basic science research applications, with special emphasis on Alzheimer's Disease. The Core has completed over 1200 projects for nearly 200 principal investigators since 2007, and works with investigators both inside and outside the Duke School of Medicine.
|Irene van den Broek, Ph.D.
Irene has over 10 year experience in quantitative, targeted, mass spectrometry of peptides and proteins, particularly for pharmaceutical and clinical applications. After she obtained her Ph.D. in peptide bioanalysis in the Netherlands, she competed as a professional cyclist before getting back to science as a post-doctoral scientist at the department of Clinical Chemistry and Laboratory Medicine in Leiden, the Netherlands. Here, she worked on the development of mass-spectrometry based clinical assays for protein biomarkers to improve harmonization and standardization of clinical diagnostic tests. She placed particular focus on understanding the sources of error in a typical bottom-up targeted proteomics workflow. In 2015, Irene joined the laboratory of Dr. Jennifer Van Eyk at Cedars-Sinai Medical Center in Los Angeles, CA, to work on the coupling of micro sampling and at-home blood collection to high-throughout, multiplexed, quantitative mass spectrometry methods, including MRM and DIA. She currently leads the Clinical R&D of the newly founded Cedars-Sinai Precision Biomarker Laboratories in Los Angeles, CA. This mass spectrometry-based specialty laboratory is a consortium of academic, contract-based and clinical (CLIA certified) laboratories with a main aim to translate biomarker discovery into clinical tests.