The following team members have made invaluable, direct contributions to the effort to build Skyline:

Brendan MacLean Brendan MacLean - principal developer
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 Mass Spec Environment and its growing worldwide user community.

Mike MacCoss Michael J. MacCoss, Ph.D. - principal scientist
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 2008 he hired 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.

Yuval Boss Yuval Boss (University of Washington) - development
Yuval has worked on the Skyline team since leaving high school in 2013 on and off with breaks for rock climbing and salmon fishing in Alaska. He has been responsible for features in Panorama and Skyline, the Skyline tool store, several external tools and the Skyline nightly test results module tracking over 1 million tests run on Skyline each week. He is now also pursuing an undergraduate degree in CS at the University of Washington.

Nat Brace - project manager - outreach & user education
Nat worked full-time for Microsoft from 1991 through 2000 where he led a team of system engineers who were helping organizations plan for and integrate Microsoft’s advanced server solutions including network and database products, as well as software development tools. He continued at Microsoft as a consultant from 2000 to 2011, with several internal teams as a technical project owner, customer outreach lead and marketing manager. More recently, Nat joined a social innovation start-up piloting a global educational reform initiative where he served as the lead project manager in delivering a collaboration platform for use by the initiative’s participating educators, researchers and sponsors. As project manager for the Skyline team, Nat is responsible for outreach programs, like webinars, courses and user meetings, foreign language translation, and instrument vendor interactions.

Matthew Chambers Matthew Chambers - development (ProteoWizard)
Matt has worked in mass spectrometry informatics (mostly proteomics) since 2005; the first ten years he worked for David Tabb and Bing Zhang at Vanderbilt University Medical Center, and since then he has continued working as an independent consultant. He has worked in many subfields within MS, including shotgun proteomics database search, sequence tagging, spectral library search, and protein assembly. Along with Darren Kessner (director: Parag Mallick), Matt developed ProteoWizard, a free open-source library for mass spectrometry data processing. Since 2009, he has been its principal developer. The ProteoWizard tool msconvert is widely used for converting mass spectrometry data by users all over the world. For Skyline, he has focused on being able to read data directly from vendor proprietary data formats.
Jarrett D. Egertson Jarrett Egertson, Ph.D - Staff Researcher
Jarrett is a staff 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 Ph.D in 2013 from University of Washington and 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.

Brian Pratt Brian Pratt - development, support
Brian's love affair with computing started the day he and his dad unboxed that brand new Apple II. Since then he's been involved with software development for, and started a couple of companies around, such varied applications as robot-assisted surgery, circuit board manufacturing and test, internet firewalls, and proteomics. Brian's proteomics work prior to joining the Skyline team included contributions to TPP, X!Tandem, LabKey's CPAS, and ProteoWizard. He's excited to be on a team of software professionals that value performance, reliability, and usability in the support of science.
Tobias Rohde Tobias Rohde (University of Washington) - development intern
Tobias is currently a student at the University of Washington. He joined the Skyline team after graduating Roosevelt High School in 2017 and quickly developed an interest for proteomics and mass spectrometry. Tobias primarily works on graph related features and among other things has been responsible for the group comparison volcano plot and the peak area CV histogram graphs.
Birgit Schilling Birgit Schilling, Ph.D. (Buck Institute for Research on Aging) - software design, data acquisition, scientific consulting, documentation
Birgit joined the Chemistry Core and Mass Spectrometry Laboratory at the Buck Institute for Research of Aging in Novato, CA in 2000 (director: Dr. Gibson). Research projects include investigations of neurodegenerative diseases, cancer, mitochondrial damage, protein oxidative posttranslational modifications, the role of surface glycoconjugates in bacterial pathogenesis etc., but also mass spectrometric method development. Birgit is interested in oxidative damage of proteins, protein phosphorylation, glycosylation, acetylation, and other posttranslational modifications, as well as differential expression of proteins during disease and aging processes. In recent years Birgit worked extensively in the field of protein quantitation to assess differential protein expression, particularly using multiple reaction monitoring stable isotope dilution mass spectrometry (MRM-SID-MS), and other chemical labeling quantitative workflows (i.e., iTRAQ and SILAC), however she also used label free protein/peptide quantitation approaches to investigate discovery mass spectrometric data sets (based on MS1 intensity).
Vagisha Sharma Vagisha Sharma - development, support, documentation (Panorama)
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. Vagisha enjoys developing tools that help researchers get stuff done.

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.
Kaipo Tamura Kaipo Tamura - development, support
Kaipo completed a CS degree at Washington State University in 2012, where he was introduced to proteomics as part of a senior project. He developed lipid identification software at the Pacific Northwest National Laboratory in 2012 before joining the Department of Genome Sciences at the University of Washington. Kaipo helps develop Crux in the Noble Lab, and BiblioSpec in the MacCoss Lab. He also implemented the Skyline Tool Store and is responsible for the Import Peptide Search wizard.


Previous contributors:

  • Susan E. Abbatiello, Ph.D. - software design, data acquisition, scientific consulting (now Thermo Scientific)
  • Dario Amodei - development - Stanford (Baidu, Google, now OpenAI, SF)
  • Eva Baker - development (now UW Med. School)
  • Daniel Broudy - development intern - Harvard (now Google, Seattle)
  • John Chilton - development intern - UW
  • Gregory Finney, Ph.D. - development - UW (Crawdad)
  • Barbara Frewen - development - UW (BiblioSpec, Thermo BRIMS, now Zymergen)
  • Mimi Fung - development intern - UW (now Microsoft)
  • Max Horowitz-Gelb - development intern - U. Wisconsin (now Google)
  • Shannon Joyner - development intern - CMU (Cisco Meraki, now Cornell)
  • Randall Kern - development architecture consulting (Microsoft, now
  • Alana Killeen - development intern - UW (Microsoft, now DropBox)
  • Trevor Killeen - development intern - UW (now Facebook)
  • Alex MacLean - development intern - Roosevelt High School (intern - Microsoft Research)
  • Don Marsh - development (now Whitemarsh Forests)
  • Daniela Tomazela, Ph.D. - software design, data acquisition, scientific consulting (now Merck)



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