Table of Contents

guest
2020-10-24
Skyline @ UW: Targeted Quantitative Mass Spectrometry Course
Instructor List
Course Schedule

Skyline @ UW: Targeted Quantitative Mass Spectrometry Course


Thanks!

The six annual Quantitative Targeted Mass Spectrometry Course at the University of Washington - which we have re-named as Skyline@UW - was held July 22- 26, 2019, and is wrapped up and in the books. With an engaged and inquisitive group of participants and great instructors, we had an exceptional week of focus on the methods and approaches of quantitative mass spectrometry. The feedback on the course was overwhelmingly positive with 100% of respondees saying they would recommend the course to a collaborator or colleague.

With another lovely week of weather in Seattle, we'll continue to pick dates in July to host this course in the future.  Continue to watch the Join Us section of the Skyline homepage for announcement information about this and other future targeted proteomics courses and workshops coming up! 

2019 Skyline@UW Course



Instructor List


The following instructors and speakers have agreed to contribute their expertise to the success of UW Course:

Mike MacCoss 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.

Brendan MacLean 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.

 Ariel Bensimon
Ariel is a postdoctoral fellow at Research Center for Molecular Medicine of the Austrian Academy of Sciences. During his Ph.D. with Prof. Ruedi Aebersold at ETH Zurich, Ariel developed targeted mass spectrometric approaches to investigate phosphorylation signaling networks, specializing in cancer research. In 2017, Ariel joined the group of Prof. Giulio Superti-Furga, to investigate the interactomes of membrane proteins.
Meena Choi Meena Choi Ph.D. Meena is a post-doctoral associate in the lab of Olga Vitek at Northeastern University. She holds a B.S. in Biology from the Korea Advanced Institute for Science and Technology, and a PhD in Statistics from Purdue University. Meena’s work focuses on statistical methods for quantitative proteomics. She is the lead developer and maintainer of MSstats.
 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.

Danielle Faivre Danielle Faivre
Danielle is a Genome Sciences Ph.D. student in the MacCoss lab at the University of Washington. Her research focuses on neurodegenerative diseases and uses quantitative proteomics approaches to study protein structure, turnover, and aggregation in cerebrospinal fluid and brain tissue. Before joining the MacCoss lab, Danielle received a B.S. in Biochemistry at the University of Notre Dame and worked under Dr. Norman J. Dovichi. In the Dovichi lab, her research involved method development for capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS) and using CE-ESI-MS to analyze the developmental metabolome of Xenopus laevis.

Deanna Plubell Deanna Plubell, Ph.D.
Deanna is a PhD student in the MacCoss lab at the University of Washington. A portion of her research has been the use of data-independent acquisition to aid in peptide selection for targeted assay development. Her other research interests include the use of mass spectrometry techniques for detecting proteolytic cleavage activity and small endogenous polypeptides in neurodegenerative disease. Prior to joining the MacCoss lab, Deanna worked at Oregon Health & Science University where she used both discovery and targeted proteomics methods to investigate changes to adipose tissue and lipoprotein proteomes in cardiovascular and metabolic diseases.

 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.

 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.

 Chris Shuford, Ph.D.

Chris is Technical Director for research and development at LabCorp’s Center for Esoteric Testing in Burlington, North Carolina. Chris received a B.S. in Chemistry at the Longwood University and obtained his Ph.D. from North Carolina State University under the tutelage of Professor David Muddiman, where his research focused on multiplexed peptide quantification using protein cleavage coupled with isotope dilution mass spectrometry (PC-IDMS). In 2012, Chris joined LabCorp’s research and development team as a scientist where his efforts have focused on development of multiplexed and single protein assays for clinical application, with particular interest around the effect of protein digestion on the throughput and accuracy of isotope dilution assays.

Nicholas Shulman Nicholas Shulman - development, support
Nick worked from 1995-2000 at Microsoft on the Microsoft Access team, leaving to join Westside Corporation with Brendan to create browser-based database design tools. After Westside was acquired by BEA Systems, Nick created a new graphical JSP designer for Weblogic Workshop, an award winning Integrated Development Environment for enterprise Java applications. At LabKey Corporation, Nick created the flow cytometry module and the graphical query designer. Since March, 2009 he has worked in the Maccoss lab on Skyline and Topograph, a quantitative analysis tool for protein turnover experiments.
 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.




Course Schedule


Monday: Introduction to targeted quantitative proteomics and Skyline 

  • Meet at Foege S. (between Foege South and North) at 9am
  • Welcome and intro to targeted proteomics and quantitative analysis
  • Basics of mass spectrometry for targeted MS
  • Intro to Skyline
  • Tutorial: SRM method development and refinement

Tuesday: Panorama, parallel reaction monitoring, system suitability and iRT

  • PRM method development
  • Tutorial: Working with PRM data
  • System suitability and quality control
  • Tutorial: Using Panorama for publishing data and Auto QC
  • Tutorial: SRM libraries and iRT

Wednesday: Standards, calibration, statistics for quantitative experiments and Panorama

  • Statistical considerations in study design
  • Statistical analysis of proteomics experiments
  • Standards for targeted proteomics
  • Signal calibration and absolute quantification
  • Targeting and quantifying small molecules in Skyline

Thursday: Sample prep, DIA, methods and data analysis

  • Sample prep for targeted proteomics
  • Introduction data independent acquisition (DIA)
  • Tutorial: Analysis of DIA data in Skyline

Friday: Plasma proteomics and the future

  • Plasma proteomics - Validation
  • Tutorial: Processing grouped study data in Skyline
  • Review and test
  • Conclusion:  The future of targeted proteomics

The course also includes popular morning “Sky-Jam” sessions led by Brendan MacLean with hands-on Skyline processing.

Note: As instructors update their content for this course, this list may change slightly.