TPP:4.6.3 Release Notes

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Trans-Proteomic Pipeline (TPP) software, release 4.6.3 is a maintenance release of TPP that contains changes to 4.6.2. The software is available for Windows as well as Linux (and unofficially) through OSX source from all the usual locations (please see the section below, "Getting the software"). Most users are recommended to use the Windows installer, which installs and configures the TPP and other required software (such as a web server). For advanced users who need to customize the TPP, or for those who run high-throughput experiments, you can download the source code. Again, most users don't need build from source, and should use the Windows installer.

Previous release notes are available at TPP:4.6.2_Release_Notes


New Features

  • Inclusion of the Comet search engine in the TPP distribution
  • Support for importing data in the PSI mzIdentML format
  • Addition of FPKM models in iProphet and ProteinProphet
  • New tool for comparing pairs of ProteinProphet result files
  • Petunia
    • Ability to sync data to/from Amazon S3
    • Added support for basic (browser) user authentication
    • Added PTMProphet section to xinteract page
    • Added new options to MzXML2Search to remove precursor, iTRAQ, and TMT peaks, as well as ones for HCD and 'no activation'.


  • Support for Comet, MSGF+, and high-resolution X!Tandem k-score search results
  • Performance enhancements to PTMProphet and iProphet
  • Improved support for OMSSA, Myrimatch, and InsPecT search results, including a utility that fixes pepXML files
  • X!Tandem now issues a warning if invalid aminoacid characters are spotted in in the fasta formatted database
  • SpectraST
    • Different m/z tolerance for alignment and annotation
    • By default, don't print top hits with zero f-value.
  • Added filter line and centroid status to ramp interface for mzML, mzXML, and mz5.
  • Added utility to grab the uniprot proteomes databases and append contaminants
  • Spectrum Viewer
    • Support for unidentified spectra
    • Updated to latest Lorikeet
    • Retired old Pep3D spectrum viewer
    • Added support for passing an mz[X]ML file + scan number and charge in the URL
    • If precursor m/z is passed, then do not compute it from sequence and charge
    • Better error reporting
    • Added TPP version footer

Bug fixes

  • Bug fixes and improvements to the user interfaces
  • InteractParser
    • Fixed large memory issue
    • Fixed issue with generating some bad results on Comet data with missing <search_hit> tags
  • Addressed a compiler issue with latest Windows/MingW and Ubuntu


  • Comet2XML has been removed from TPP
  • Parse 'r' for rapid scan in filter line; add Velos Pro instrument

Known Issues

  • No known issues to report

Getting the TPP Software

  • Download the TPP version 4.6.3 native windows installer (TPP_Setup_v4_6_3.exe) from the Sashimi SourceForge project file release page:
  • Everyone is encouraged to read and contribute to our wiki, at
  • For guides to installing and using our software, please see our wiki:
  • For downloading the source code, please go to the following link: and find the 4.6.3 source code .tgz package;

or, check out the code directly from svn:

 svn checkout svn://
    • For building from source, please refer to the readme file in TPP/src as well as the wiki.

The TPP Team: Luis, David, Mike, Joe, and Jimmy plus all other developers who contributed to this release from the ISB. Thanks to developers and users from the TPP's user community who provided feedback and code contributions.


The SVN log of all changes since the previous release are available at TPP:4.6.3_SVN_Log.

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