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

Contents

primary authors (active)

  • David Shteynberg (ISB): statistical tools within the TPP
  • Joe Slagel (ISB): cloud-based (AWS) workflow management
  • Luis Mendoza (ISB): graphic interface (Petunia)
  • 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)
  • Alexey Nesvizhskii (University of Michigan): statistical tools
  • Brian Pratt (Insilicos): optimization, data formats, windows installation

other primary authors

  • Natalie Tasman: cross-platform build and release and installation, data visualization, raw format conversion
  • 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
  • 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
  • Laurel Feltz (ISB): manager of the Seattle Proteome Center (SPC) grant from NHLBI which was the primary source of funding for the majority of the TPP work.
  • 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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