TPP:5.0.0 Release Notes

From SPCTools

Trans-Proteomic Pipeline (TPP) software, release 5.0.0 is a major release of TPP that contains new features, improvements, and fixes to 4.8.0. The software is available for Windows as well as Linux (and unofficially) for OSX 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 on Linux or OS X, 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:4.8.0_Release_Notes

Contents 1 Major Changes and Overview 2 New Features 3 Improvements/Changes 4 Bug fixes 5 Miscellaneous 6 Known Issues 7 Getting the TPP Software 8 Acknowledgements 9 SVN Log

Major Changes and Overview

• Heavily modified code organization, build, and installation system

• 64-bit

• Windows installer:
  • includes all external dependencies, including stand-alone Apache web server (uses port 10401, user configurable) and Strawberry perl
  • allows for user-configurable software and data locations
  • new (optional) TPP Tray application provides convenient shortcuts to TPP, web server control, and data

• New major software components:
  • Kojak for cross-linking analysis
  • DISCO for analysis of DIA data without using spectral libraries
  • StPeter for label-free quantitation

• Updated user interface look and feel

More details below.

New Features

• ProteinProphet:
• Petunia:
• tpp_models:

Improvements/Changes

• Comet: updated to version 2014.02 rev. 2

• ASAPRatio:
  • Enable wavelet option
  • Write pvalue raw data and model into protXML file
  • Lowered bin size on pvalue modeling from 0.05 to 0.02 (to get finer-grained model and values)

Bug fixes

• PepXMLViewer.cgi:
  • Fix detection of libra result in current spectrum node (used for passing the Isobaric parameter to Lorikeet)
  • Fix link to plotspectrast
  • Fix reference to analysis file for spectrum name link (displays N top hits from engine) in Comet; use comet hits viewer for Sequest links

Miscellaneous

• Renamed all ".cxx" C++ source files as ".cpp" for standardization purposes within TPP.

Known Issues

• Kojak graphical models in PeptideProphet are not displaying correctly on the MODELS page.

Getting the TPP Software

• Download the TPP version 5.0.0 native windows installer (TPP_Setup_v5_0_0.exe) from the Sashimi SourceForge project file release page:

 http://sourceforge.net/projects/sashimi/files/

• Everyone is encouraged to read and contribute to our wiki, at

 http://tools.proteomecenter.org/wiki/

• For guides to installing and using our software, please see our wiki:

 http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP

• For downloading the source code, please go to the following link:

 http://sourceforge.net/projects/sashimi/files/ and find the 5.0.0 source code .tgz package;

• Or, check out the code directly from svn:

 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_5-0-0

• For building from source, please refer to the README and INSTALL files in src/ directory of TPP as well as this wiki.

Acknowledgements

The TPP Team: David, Luis, Mike, Jimmy, and our old colleague Joe, 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.

SVN Log

The SVN log of all changes since the previous release are available at TPP:5.0.0_SVN_Log.