We are proud to offer an update to the Trans-Proteomic Pipeline (TPP) software, release 4.3.1 (4.3 revision 1). 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 webserver). 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.
Trans-Proteomic Pipeline (TPP) 4.3.1 release notes (Changes since the last official release, 4.3.0) == Contents == - full mzML 1.1 and 1.0 support - important note for using mscovert and PWIZ on Windows - Petunia bug fix - XPRESS bug fixes - ProteinProphet bug fix - mergeCharges utility memory usage improvement - updatePaths utility bug fixes - improved perl scripts - known issues - Getting the TPP software == full mzML 1.1 and 1.0 support== * mzML parsing code updated for full mzML 1.1 compatibility, including full 1.0 backwards compatiblity. Includes a fix to X!Tandem's custom mzXML parser, which now correctly handles mzML 1.0 and 1.1 data. == important note for using mscovert and PWIZ on Windows== * PWIZ and mscovert require the free "Microsoft Visual C++ 2008 SP1 Redistributable Package" to be installed on your computer before use. You can download this package from http://www.microsoft.com/downloads/details.aspx?familyid=A5C84275-3B97-4AB7-A40D-3802B2AF5FC2&displaylang=en * For processing Thermo RAW files, PWIZ and mscovert require the free "MSFileReader" download, which can be found here: http://sjsupport.thermofinnigan.com/public/detail.asp?id=586 == Petunia bug fix == * correct Analysis Pipeline now displays when selected (previously was always displaying Sequest interface in 4.3.0) == XPRESS bug fixes == * fixed bug which caused N15 metabolic labeling option to run incorrectly (introduced when C13 option added). * XPressCGIProteinDisplayParser.cgi bug fix: a counter/index variable was re-used in an inner loop causing outer loop to exit prematurely resulting in the CGI not displaying peptide ratios from all input files; problem appears to be present in all previous releases == ProteinProphet bug fix == * handle missing description lines for IPI database searches == mergeCharges utility memory usage improvement == * improved memory usage == updatePaths utility bug fixes == * it will actually update root and database paths at the same time, if specified. Cleaned-up output too. == improved perl scripts == * better handling of non-standard TPP installation location == known issues == * mzWiff: charge state information is not recorded in output mzXML * massWolf: charge state information is not recorded in output mzXML * trapper: if dual-mode file is processed, the resulting file is possibly always converted as centroid (even if centroid is not selected.) == Getting the TPP software == * Download the TPP version 4.3.1 native windows installer (TPP_Setup_v4_3_JETSTREAM_rev_1.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 4.3.1 source code .zip package; or, check out the code directly from svn: "svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-3-1"; For building from source, please refer to the readme file in TPP/src as well as the wiki. The TPP Team: Luis, David, Brian, and Natalie, 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. --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
