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.
Josh Aldrich Josh Aldrich development
Josh began working in mass spectrometry (proteomics) starting in 2010 as a Research Associate at Pacific Northwest National Laboratory under Liljana Pasa-Tolic. Here he developed software aiding identification and post translational modification site detection as well as developing pipelines to aid in large scale reproducible data analysis. Following this he joined Amazon, building backend and frontend software for what eventually became Amazon:Go, the cashierless grocery store. Now he has returned to the field of proteomics on the Skyline team to help the team grow into the cloud in addition to other work.

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.
Rita Chupalov Rita Chupalov development
Rita’s experience with software and computers goes back to a Russian clone of DEC’s PDP-11 in 1991. She finished her degree in Organic Chemistry from Saint-Petersburg State University in 1996 where she wrote her first mass-spectrometry software: identification of halogen isotopic multiplets in low-resolution mass-spectra. Since then she worked for multiple software development companies specializing on database-centric applications, analytics and data warehousing. Her most recent job was with Amazon where she learned big data and cloud technologies.

Brian Connolly Brian Connolly - IT
Over the years Brian has worked for a number of companies in the Seattle area including Microsoft, BEA Systems and Cray. In 2007 Brian joined LabKey where he wore a number of hats. He helped LabKey's customers design and operate their LabKey Servers and pipelines. He architected and operated all of LabKey's Servers running in the public cloud (AWS and other cloud vendors) and became an expert in FISMA and HIPAA regulations. As part of the Skyline Team, Brian is responsible for managing growth of the and servers and helping the team grow its use of the AWS cloud.
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 and is now director of that department. 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.


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
  • Jarrett Egertson - develpment - UW (MSX and overlapped demux)
  • 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)
  • Kaipo Tamura - development (spectral library building and import peptide search wizard)
  • Daniela Tomazela, Ph.D. - software design, data acquisition, scientific consulting (now Merck)
Rita Chupalov

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