TPP:Authors and Contributors

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The Trans-Proteomic Pipeline (TPP) is a collaborative open-source project. It was originally started at the Institute for Systems Biology (ISB) in the Aebersold Lab. The project has since grown, with active contributors from institutions all over the world. The ISB continues to provide primary support for the project, with other primary collaborators and contributors at Insilicos LLC, the University of Washington, Hong Kong University of Science and Technology, and Fred Hutch Cancer Research Center.

The listings are alphabetical by last name (with current affiliation, if known), followed by a short description of relevant major work


primary authors (active)

  • David Shteynberg (ISB): statistical tools within the TPP
  • Luis Mendoza (ISB): user interfaces (Petunia, etc), performance, tools integration
  • Michael Hoopmann (ISB): search engines, high resolution data, mzML parsing, and label-free analysis
  • Jimmy Eng (University of Washington): MS/MS spectra-to-peptide identification (SEQUEST)
  • Henry Lam (Hong Kong University of Science and Technology): spectral library search (SpectraST)

other primary authors

  • Joe Slagel (ISB): cloud-based (AWS) workflow management
  • Natalie Tasman: cross-platform build and release and installation, data visualization, raw format conversion
  • Brian Pratt (Insilicos): optimization, data formats, windows installation
  • James Eddes: MS spectra curation and quality assesment (QualScore)
  • Carly Holstein: MaRiMba project: creation of MRM lists from spectral libraries
  • Robert Hubley: original creator of cygwin-based Windows TPP distribution
  • Andrew Keller: statistical tools
  • Alexey Nesvizhskii (University of Michigan): statistical tools
  • Nichole King: iTRAQ-labeled quantification (Libra)
  • Xiao-jun Li: quantification (ASAPRatio)
  • Brendan MacLean: X!Tandem integration, testing, Visual Studio build
  • Patrick Pedrioli: mzXML open format creator, original work on file conversion
  • Ning Zhang: ProbID search engine
  • Ted Holzman: MRM support in massWolf
  • Lukas Reiter: protein identification false discovery rates (Mayu)
  • Chee-Hong Wong: data format conversion (mzWiff)

significant contributors and collaborators

  • Robert Moritz (ISB): PI of group which TPP is continually developed since 2008
  • Eric Deutsch (ISB): Testing and quality control in TPP; lead open standards development (PSI mzML), lead PeptideAtlas director
  • Ruedi Aebersold and the Aebersold Lab (Zurich): support, testing, feedback; Ruedi Aebersold was the PI under whose lab the TPP was originally developed.
  • PeptideAtlas project: testing, feedback; PeptideAtlas processes their library with the TPP and is thus one of the main drivers of the TPP project.
  • ProteoWizard project: file format conversion. Included in TPP; TPP authors contribute back to main project.
  • LabKey Software: Optimization, TPP testing
  • X!Tandem: open-source MS/MS search engine. Included in TPP. TPP authors update and offer improvements to original code.

other contributors

  • Sergey Doronin: CProbID: c-language implementation of ProbID search engine
  • Rune Schjellerup Philosof: special processing in massWolf
  • and all of the many people from the newsgroup who have contributed patches, bug reports, testing, and feedback.
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