TPP 4.7.0 is now available

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Joseph Slagel

Feb 28, 2014, 6:56:34 PM2/28/14
Announcing the official release of Trans-Proteomic Pipeline (TPP) 4.7.0 "Polar Vortex"

We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 4.7.0 (4.7 revision).  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.

In addition to this release, the Seattle Proteome Center (SPC) is pleased to offer another hands-on course on the Trans-Proteomic Pipeline (TPP) this year. It will be held in Seattle from March 31st-April 4th.


We will focus on the use of our open-source software tools for the analysis, validation, storage and interpretation of data obtained from large-scale quantitative proteomics experiments and methods, multi-dimensional chromatography and tandem mass spectrometry. Through daily lectures and hands-on tutorials, course participants should become proficient in the use of these tools, including PeptideProphet, iProphet, ProteinProphet, PTMProphet, and other components of the TPP. We will show how you can use Amazon Web Services cloud computing to expand your computing capacity via the TPP. There will also be instruction on using SPC resources such as PeptideAtlas, SRMAtlas, and related tools and other software packages.

More information and registration is available at:

== Release Nodes ==

* Release notes on the most important new features, changes, and known issues are available at:


== Getting the TPP Software ==

* Download the TPP version 4.7.0 native windows installer from the Sashimi SourceForge project file release page:

  " Pipeline (TPP)"

* 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 4.7.0 source code .tgz package;
or, check out the code directly from svn:
  "svn co"

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

The TPP Team: Luis, David, Mike, and 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.

Joe Slagel
Institute for Systems Biology

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