TPP:Recent Updates
From SPCTools
(Note: this is not a full changelog; please see the spctools-announce newsgroup and its archives for release announcements.)
SpectraST version 3.0 released!
September 14, 2008; TPP version 4.0.2
This new version of SpectraST includes the functionality of building spectral libraries from sequence search results, among several feature and performance upgrades.
Native Windows TPP version released!
June 3, 2008; TPP version 4.0.0
The TPP release system moved from cygwin to a true native Windows installation with the 4.0.0 release. We thank Insilicos for their continued major contributions to the project.
mzML support throughout the TPP
June 3, 2008; TPP version 4.0.0
The new mzML 1.0 standard, a joint effort of the HUPO PSI, SPC, vendors, and others, is now fully supported in throughout the TPP.
Insilicos IPP optimizations integrated into TPP
March 3, 2008; TPP version 3.5.1
With TPP version 3.5.1, many improvements to code speed from the Insilicos IPP branch were merged into the main TPP distribution. We thank Insilicos for their continued major contributions to the project.
New TPP Version Naming Scheme
November 27, 2007; TPP version 3.4.0
A new version naming scheme begins with 3.4.0. 3.4.0 introduces a new numbering scheme. .1 (minor) increments will introduce new features, while 0.0.1 (revision) increments will denote any bug fixes that change results. Cygwin packages ('a', 'b', etc) will denote updates for cygwin-only fixes (to the webserver configuration, etc.)
X!Tandem Processing Pipeline added to TPP GUI
September 25, 2007; TPP version 3.3.0
Version 3.3.0 of the TPP release includes full support for running the X!Tandem pipeline through Petunia (the TPP GUI).
Retention Time Model added to PeptideProphet
September 25, 2007; TPP version 3.3.0
A retention time model has been added to the TPP version 3.3.0 to improve peptide validation.
New TPP Tutorial added
September 18, 2007
Bryan Prazen of InSilicos has contributed his excellent TPP Tutorial to our wiki. He has completely updated his very comprehensive tutorial. We hope that the community will not only find it useful, but will join in updating and growing the tutorial as the TPP tools change and evolve. Thanks, Bryan!
TPP development moves to Subversion
July 19, 2007
For developers: The SourceForge Sashimi project, the TPP's code repository, has migrated to Subversion (SVN) from CVS. Please see the Sashimi SVN page for more information.
Open-source search engine X!Tandem included with Windows/Cygwin TPP release
June 20, 2007; TPP version 3.2.1
X!Tandem with K-Score plugin is now included as a cygwin binary. Source code can be included by selecting the X!Tandem source package under "Proteomics". Please see using X!Tandem and the TPP for more information.
TPP adds Phenyx support
May 31, 2007; TPP version 3.1.0
The TPP has been updated to allow validation of search results from GeneBio's Phenyx sequence search engine. GeneBio has updated their Phenyx product to write out search results in the TPP's native pepXML format. The TPP developers have updated PeptideProphet to read these files and generate validation models for the Phenyx search scores. All subsequent downstream tools are then able to work with these results. Please see using Phenyx and the TPP for more information.
ProteinProphet rewritten in C++
March 29, 2007; TPP version 3.0.0
Contributed by Brian Pratt of InSilicos, this new version of ProteinProphet is much faster than the previous perl code.
