TPP:4.6.0 Release Notes

From SPCTools

Trans-Proteomic Pipeline (TPP) "Occupy" 4.6.0 Release Notes

Trans-Proteomic Pipeline (TPP) software, release 4.6.0 is a minor release of TPP that contains several new features. 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.

Previous release notes are available at TPP:4.5.2_Release_Notes

1 New Features
2 Improvements/Changes
3 Bug fixes
4 Miscellaneous
5 Known Issues
6 Getting the TPP Software
7 SVN Log

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New Features

PTMProphet: new tool for assigning probabilities to PTM-sites

MSGFDB support

Support for .mz5 format

New Petunia features:
- Support for use of Amazon Web Services, including basic Amazon account management and monitoring
- Option to launch X!Tandem searches on the Amazon cloud (using amztpp)
- Keep history of launched commands and output; option to delete old output
- Launch and monitor multiple commands (don't overwhelm your CPU!)
  - New self-updating jobs page shows all jobs run by user, including old sessions
  - Number of running jobs shows up on window title, updates every few seconds
  - Basic monitoring of Amazon cloud jobs
- No longer hangs after submitting a job in Windows (self-redirects to jobs page in 200ms)
- Added a button to download a file or a zip archive of files directly from the browser.

Add support for quick acetyl mods from X!Tandem in Tandem2XML

PepXMLViewer ions (ions2) link goes to Lorikeet viewer by default; old one is still an option

Added column in excel ouput of protXML viewer that indicates if peptide ion is used as evidence

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Improvements/Changes

Updated X!Tandem to the latest release: CYCLONE (2011.12.01)

Increased the number of threads allowed in X!Tandem from 16 to 256. We don't recommend running 256 threads unless you have a really really big computer.

Display human readable file sizes in Petunia

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Bug fixes

Various security enhancements

Fixed bugs associated with updateAllPaths.pl

Fixed double counting bug (under specific conditions) in ProphetModels.pl

Fixed bug causing XPressPeptideParser to run slowly

Petunia:
- Fix bug when converting multiple files to pepXML using semi-cleavage specificity
- Specify SpectraST output to have correct '.pep.xml' suffix

Fixed mzXML output of dta2mzxml

decoyFASTA now gracefully deals with empty lines in input fasta file

Include charge and file downloder perl utilities in Linux make install step

Lorikeet:
- Do not attempt to populate ms1 data unless we are reading an mz[X]ML file
- Fix typos on parameter names for n- and c-terMods

Added error message to mascotout.pl if input file not found; also added html footer with TPP version

Fix webserver accessible file path in PepXMLViewer

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Miscellaneous

No miscellaneous issues to report

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Known Issues

No known issues to report

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Getting the TPP Software

Download the TPP version 4.6.0 native windows installer (TPP_Setup_v4_6_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 4.6.0 source code .zip package;

or, check out the code directly from svn:

 "svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-6-0"

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

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

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