Seattle Proteome Center (SPC) - Proteomics Tools
NHLBI Proteomics Center at the Institute for Systems Biology

Trans-Proteomic Pipeline (TPP) Software Distribution: Windows Installation

Please refer to the TPP Windows installation guide on the SPCTools wiki.

Current: release 2.1-0a, dated 3/29/2007: Installs the latest Trans-Proteomic Pipeline (TPP - v3.0.0 SQUALL) Many improvements, including switch to C++ version of ProteinProphet. Please see our spctools-disucss message board for more information.

OLD: release 2.0-0 dated 11/29/2006: Installs the latest Trans-Proteomic Pipeline (TPP - v2.9.5 GALE) Improved access to the tools by links on the Desktop and the Start->Programs->TPP.

OLD: release 1.9-7 dated 10/18/2006: Installs the latest Trans-Proteomic Pipeline (TPP - v2.9.4 GALE) Addresses problems with Apache configuration during the install.

OLD: release 1.9-5 dated 10/11/2006: Installs the latest Trans-Proteomic Pipeline (TPP - v2.9.4 GALE), New installation which doesn't require any configuration, New viewer for pepXML documents, updates to the quantitation tools, various other enhancements and bug fixes.

OLD: release 1.9-4 dated 08/29/2006: Installs the latest Trans-Proteomic Pipeline (TPP - v2.9.3 GALE), ...

OLD: release 1.9-2 dated 07/27/2006: Installs the latest Trans-Proteomic Pipeline (TPP - v2.9.2 GALE), Improvements to the quantitation tools ...

OLD: release 1.9-0a dated 06/14/2006: Installs Trans-Proteomic Pipeline (TPP - v2.9.0 GALE), TPP GUI (Petunia updated with more options for running PeptideProphet and Quantitation Tools, Petunia Mascot support improvements, accurate mass binning option in PeptideProphet, small tweaks to the pI model algorithm in PeptideProphet, Libra now operates on data in profile mode

OLD: release 1.8-3 dated 05/23/2006: Installs the latest Trans-Proteomic Pipeline (TPP - v2.8.3 THAW), Various improvements over 1.8-0 including: corrected H/L peptide and protein ratio, ignores zoom scans for quantitation, improvements to quantitation tools, updated modification list, improved user interface.

OLD: release 1.8-2 (minor updates of 1.8-0) dated 04/06/2006: Installs the latest fully XML-based Trans-Proteomic Pipeline (TPP - v2.8.2 THAW), New features for quantitation, corrected calculation of inverted ratios, PeptideAtlas link from PeptideProphet results, pI model improvements, NMC calculation updated for special cases near the termini, updated web interface, other small correction

OLD: release 1.7-3 dated 01/13/2006: Installs the latest fully XML-based Trans-Proteomic Pipeline (TPP - v2.7.3 MIST), RefreshParser now calculates the n-terminus of a peptide that starts right after the start codon Met as an enzymatically tolerable terminus, Mascot2XML corrected handling of Mascot standard modifications when the modification corresponds to a specific amino acid the location of which must be terminal on the peptide, msxml2other -mgf changes to improve compatibility of Mascot searches with the TPP, same improvements as release 1.7-2 listed below.
OLD: release 1.7-2 dated 01/06/2006: Installs the latest fully XML-based Trans-Proteomic Pipeline (TPP - v2.7.2 MIST), Correct version number displayed by the various programs, same improvements as release 1.7-1, listed below.
OLD: release 1.7-1 dated 01/05/2006: Installs the latest fully XML-based Trans-Proteomic Pipeline (TPP - v2.7.1 MIST), Improved pI model, Improved Mascot support, new commandline option -x to force extra iterations of PeptideProphet, improvements to Libra quantitation, additional enhancements to improve the user experience.
OLD: release 1.6-2 dated 10/07/2005: Installs the latest fully XML-based Trans-Proteomic Pipeline (TPP - v2.6.1 QPF), New Web Interface, ASAPRatio protein display page now shows Normalized Ratio as pre-TPP tool, additional information printed on the PeptideProphet model display page, other enhancements and improvements.
OLD: release 1.6-1 dated 09/20/2005: Installs the latest fully XML-based Trans-Proteomic Pipeline (TPP - v2.6 Quantitative Percipitation Forecast), fixes some problems with XPress quantitation observed in older version where the protein level ratios were being incorrectly computed, provides somes small enhancements and improvements.
OLD: release 1.5-2 dated 09/09/2005: Installs the latest fully XML-based Trans-Proteomic Pipeline (TPP - v2.5 ConvergenceZone rev.1), fixes a problem with new installs that used to require creating a tpp-bin directory by hand.
OLD: release 1.4-3 dated 01/26/2005: fixed ProteinProphet web interface bug that was causing no output files to be generated
OLD: release 1.4-2 dated 01/20/2005: fixed various small bugs and broken links issues
OLD: release 1.4-1 dated 01/18/2005 : adds spctools_web interface (beta)
OLD: release 1.3-5 dated 10/29/2004 : adds Pep3D; readw.exe replaces t2x.exe
OLD: release 1.3-4 dated 09/10/2004

Source Code

You can find the source code for the ISB Proteomics projects from the Sashimi project File Release page on SourceForge.