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.
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 computing career extends all the way back to the days of the Apple II and TRS-80. Along the way there have been a couple of startups, with forays into robot-assisted surgery, circuit board manufacturing and test, internet firewalls, and, most recently, mass spec. 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.
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
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.
Jason Wang   Jason Wang - development
Jason came to the US from China in 2018 to pursue a Ph.D. in Genetics at Dr. Mark Hargrove's lab, in the Biochemistry Department of Iowa State University. In 2017, after getting his degree followed by 2 years of post doctoral research, he worked at the animal health company Zoetis in Kalamazoo Michigan as a fermentation scientist. With a keen interest in lab automation, he started writing software to automate workflows in lab hardware and data processing workflows. He joined an online master's program in Computer Science at Georgia Tech while working at Zoetis. In early 2020, at the beginning of the pandemic, he joined Amazon Web Services as a software engineer in Seattle. In 2022, he joined Google Cloud as a software engineer. In May 2024, he joined the Skyline team to help build software for scientists - following a passion for facilitating and optimizing scientific research.
Mark Belanger   Mark Belanger - project manager - outreach & user education
Mark had a full career in communications across a number of industries including travel, start-ups, games and more. During that time, he brought technology solutions to legacy businesses and cutting-edge enterprises alike. He implemented a range of web sites, from first-generation web presence to full ecommerce and social platforms, taking companies from the pre-digital era into the modern age. He established email and mobile communication programs, and managed outreach teams and projects. Mark has an MBA in Information Systems from Seattle University. As a project manager for the Skyline team, Mark is responsible for outreach programs, like webinars, courses, and user meetings, foreign language translation, and website presence.


Previous contributors:

Previous interns:

  • Yuval Boss - development intern - UW (NOAA, now Amazon)
  • Clark Brace - development intern - UPS
  • Daniel Broudy - development intern - Harvard (now Google, Seattle)
  • John Chilton - development intern - UW
  • Henry Estberg - development intern - UC Santa Cruz (now HashiCorp)
  • Mimi Fung - development intern - UW (now Microsoft)
  • Max Horowitz-Gelb - development intern - U. Wisconsin (now Google, Seattle)
  • Shannon Joyner - development intern - CMU (Cisco Meraki, Cornell, now Afresh)
  • Hanna Kidanemariam - development intern - Dartmouth College (now Microsoft)
  • Alana Killeen - development intern - UW (Microsoft, Dropbox, Nautilus Biotech, now ACLU)
  • Trevor Killeen - development intern - UW (Facebook, now Stripe)
  • Aaron Igra - development intern - Brown
  • Alex MacLean - development intern - Roosevelt High School (Cal Poly CS, Dropbox intern, now NVIDIA)
  • Surya Mani - development intern - Hamilton College (Talus Bio intern)
  • Ali Marsh - development intern - MIT (now Tern)
  • Nate Mercer-Garber - development intern - Northeastern University
  • Rohith Mondavilli - web development intern - Dartmouth College (Apple intern, Facebook intern, now Rippling)
  • Sophie Pallanck - development intern - Western Washington University (now Amazon)
  • Tobias Rohde - development intern - UW (AI2 Incubator intern, now Amazon)
  • Henry Sanford - development intern - UW (Regeneron intern, now Vinogradova lab at Rockefeller University)
  • Pradyoth Vemulapati - development intern - UW (OpenMarket, now Uber)

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