Table of Contents

Course Canceled
Instructor List
Course Schedule


Dear Skyline Users:

**The 2020 Buck Institute Targeted Proteomics Course on April 13 - 17, 2020 in the Northern San Francisco Bay Area, California (Novato)  is fully suscribed at this point. To join the waitlist please fill out the form from the link below.**

The course schedule will address emerging quantitative proteomics strategies.  This will include the use of Skyline in the context of different quantitative targeted workflows, assay development, generation of acquisit
ion methods, processing of quantitative data sets, as well as using statistical and R software packages and tools in Skyline.  Data examples will cover high through-put SRM, MS1 Filtering, parallel reaction monitoring (PRM) and data-independent acquisition (DIA/SWATH).  Data examples will range from analysis of posttranslational modifications, work with human plasma for biomarker analysis and projects involving protein-protein interactions. In addition, Skyline support for ion mobility separation and small molecules will be presented.

The instructor list includes researchers and software developers wie th a wealth of combined experience in targeted and quantitative proteomics, and both using and creating Skyline to meet the needs of this research approach.

Space is limited.  However, all applications and course fees must be submitted by the deadline of January 10, 2020. 

We hope you will join us for this exciting week.

-- Birgit Schilling, Ph.D.; (Buck Institute, Novato)
Workshop coordinator

-- Ruth Huttenhain, Ph.D. (UCSF/Gladstone Institutes, San Francisco)
Workshop coordinator

-- Brendan MacLean, (UW, Seattle)
Skyline Project Lead

When: April 13 - 17, 2020
Where: Buck Institute is in Novato, California (north of San Francisco) (map) (photo
Cost: $500 academic, $1,600 industry 

Latest cancelation date: February 28, 2020
Participants: ~30
Room & Board: Not included
Lunch Provided daily

[registration closed]

Related Links:
Course Schedule
Instructor List


Course Canceled

Dear Skyline Users,

With the rapid developments of the coronavirus spread, the co-organizers of the Buck Institute Targeted Proteomics Course have made the difficult decision to cancel the Skyline Buck Institute Course April 13–17 in Novato, California (San Francisco Bay Area). The health and safety of all involved is our top priority.

We have closely monitored the spread of the COVID-19 (coronavirus disease) ( Based on the latest guidance from public health officials, the travel bans implemented by different institutions and the state of emergency declared in California a few days ago, it became clear to us that canceling was the right course of action. We thank you for understanding the extreme difficulty of this decision.


Birgit Schilling, Ph.D.
Associate Professor
Director of the Mass Spectrometry Core
The Buck Institute

Instructor List

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

  Birgit Schilling, Ph.D.
Birgit is Associate 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 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.

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.

Kendra Adams   Kendra Adams, Ph.D.
Kendra is a joint postdoctoral associate between Dr. Arthur Moseley’s lab, the Duke Proteomics and Metabolomics Shared Resource, and Dr. Carol Colton in the Department of Neurology at Duke University. She currently uses mass spectrometry to study Alzheimer’s disease in new mouse models. Kendra earned her PhD in Dr. Francisco Fernandez-Lima’s Lab at Florida International University where she analyzed small molecules using LC-TIMS-MS. Her current research focuses on method development for targeted biomarker analysis and stable isotope tracing for Alzheimer’s disease.

Chris Ashwood   Chris Ashwood, Ph.D.
During Dr. Ashwood’s graduate studies with Dr. Nicolle Packer, he developed expertise in the structural analysis of released glycans from mammalian glycoproteins using porous graphitized carbon (PGC)-based LC-MS/MS. In his post-doctoral training in Dr. Gundry’s laboratory, Dr. Ashwood, has applied these methods to develop the first N- and O- glycan maps of primary human cardiomyocytes and stem cell-derived cardiomyocytes, characterizing glycans that are potentially useful for identifying cells of various cell culture stages and cell types. With a long-term goal of developing automated analytical workflows for characterization and quantification of glycans, he also actively works to improve the bioinformatic analysis of glycan and glycopeptide MS data.To date, his scientific contributions include 8 peer reviewed publications and one manuscript in revision, of which he is first author on 4. He has also recently received a prestigious Postdoctoral Career Development Award from the American Society for Mass Spectrometry.
Brett Phinney   Brett Phinney, Ph.D.
Brett has been researching the analysis and measurement of complex mixtures of proteins and peptides using mass spectrometry since 1996, where as a grad student he used mass spectrometry to study the protein dynamics of viral structural proteins. After graduate school he then did a post doc with noted mass spectrometrist Jack Watson at Michigan State University and then went on to co-found and co-direct the Michigan Proteome consortium is 2002. In 2005 Brett founded the UC Davis Genome Center proteomics core and currently directs its research and oversees its staff. The UC Davis proteomics core is currently researching ways to increase efficiency, sensitivity & quantitative accuracy in bottom-up proteomics applications.Dr. Phinney has been an member of ABRF where he is/was a member of several international research groups that develop proteomics standards and methods for the proteomics community.

Lindsay Pino   Lindsay K. Pino, Ph.D.
Lindsay is a postdoctoral researcher in Dr. Ben Garcia’s lab at the University of Pennsylvania where she uses quantitative mass spectrometry to study epigenetics. Before going to the University of Washington for graduate school, she spent two years in South Korea as a Fulbright scholar and three years working as a research associate in Dr. Steve Carr's Proteomics Platform at the Broad Institute of MIT and Harvard. She earned her PhD under the joint advisorship of Drs. Michael J. MacCoss and William Stafford Noble. There, she developed techniques for data independent acquisition mass spectrometry, in particular the challenges associated with scaling up quantitative mass spectrometry experiments. Her research interests are in the roles proteins play in nuclear organization and the maintenance of genomic stability.
  Brian Searle, Ph.D.
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 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.

van den Broek
  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.

Course Schedule

Buck Institute Targeted Proteomics Course - Buck Institute April 13 - 17, 2020

 Introduction to targeted quantitative proteomics and Skyline

  • Meet at Buck Institute at 9 am
  • Welcome and intro to quantitative analysis
  • Basics of mass spectrometry and SRM
  • From discovery to targeted proteomics
  • Intro to Skyline
  • Tutorial: SRM method development
  • From discovery to targeted quantification

PRM and quantification

  • Introduction to iRT
  • Tutorial: iRT
  • Absolute quantification adn calibration curves
  • Tutorials: Manual data analysis and grouped studies
  • PRM method development
  • Hands-on: PRM data analysis

Computational methods, statistics for quantitative experiments and Panorama

  • Statistical considerations in study design
  • MSstats and its integration with Skyline
  • Tutorials: Using MSstats R package for analysis and applications
  • Data Independent Acquisition (DIA) - cross lab study and new advances
  • Statistical analysis of proteomics experiments
  • Intro to Panorama 
  • Panorama autoQC, calibration curves and reporting

DIA, methods and integrated data analysis

  • Biomarker Studies - design and applications
  • Skyline processing of DDA data (MS1 filtering) 
  • Intro to DIA
  • Tutorial: Analysis of DIA data in Skyline
Small molecule research and the future of targeted experiments
  • Small molecule applications 
  • Tutorial: Small molecule research in Skyline
  • Small molecule iomers
  • Skyline and industry applications
  • The future of targeted proteomics

The course includes voluntary but very popular morning (8am!) "Sky-Jam" sessions led by Brendan MacLean with hands-on Skyline processing.