TPP:4.6.2 Release Notes
From SPCTools
Trans-Proteomic Pipeline (TPP) software, release 4.6.2 is a maintenance release of TPP that contains several fixes to 4.6.1. 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 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. Again, most users don't need build from source, and should use the Windows installer.
Previous release notes are available at TPP:4.6.1_Release_Notes
Contents |
New Features
- New dashboard page for the various prophets: visualize all pertinent models, error tables, run parameters, etc (uses same javascript plot libraries as Lorikeet.) Automatically called by xinteract. Will displace current models page in next release.
- New decoy database generation tool:
- decoy sequences are randomized
- decoy proteins are interleaved with targets
- two independent sets of decoys are generated
- tryptic peptides randomized once will be remembered and retained in all occurence within each independent set
- Support for latest Comet
- Support for MSGF+
- Support for high-resolution X!Tandem k-score
- New iProphet Feature
- Number of Sibling Peptides model computation
- semi-supervised iProphet
- InteractParser
- detects OMSSA and fixes protein names and pyro mods
- corrects data file (mzML/mzXML) references when found
- removes empty spectrum_queries
- automatically changes spectrum names to 5 digit scan numbers
- Auto update ntt and nmc info based on sample_enzyme tag when recognized
Improvements/Changes
- No longer producing shtml files. Petunia provides the appropriate link to open pepXML and protXML files in their respective viewers.
- Updated to latest Lorikeet MS/MS viewer. This corrected various bugs (i.e. fragment ion calculations) in the old viewer. Functionality also improved by optional peak picking algorithm for ion labeling which is checked on by default.
- Petunia now recognizes OMSSA generated pepXML files and displays a link to view the file in the PepXMLViewer. (OMSAA writes the older DOCTYPE DTD declaration in its XML output instead of using the XML schema declaration that Petunia was looking for.)
- TPP now recognizes the enzyme string "Trypsin/P".
- Stop file checking in PepXMLViewer once a) file has been detected as changed on server, or b) 4 failed attempts at getting status.
- Read in Mascot's expectation score when present
- Improved error messages to be more descriptive of the problem
- iProphet:
- Added multi-threading option
- Added progress bars
- Added command-line options to its Petunia page
- PTMProphet
- version reporting
- autodetect and report when in ETD mode
- default output file in the input file unless specified
- fixed bug with n-term modified peptides
- static mod containing peptides
- ProteinProphet outputs a prot.xml file with 0 proteins on pep.xml input with 0 peptides
Bug fixes
- Fixed bug with wrong protein descriptions being displayed in ProteinProphet
- Added a patch for the version of Boost bundled with TPP so that it will compile using gcc 4.7 (Ubuntu 10.12)
- Corrected an issue in ASAPRatio discovered when compiling with gcc 4.7 (Ubuntu 10.12). It was using of strcpy() and the source and destination overlapped in memory. According to the strcpy() reference one shouldn't do this so it was replaced with memmove().
- Added a patch for the version of HDF bundled with TPP so that it will compile using gcc 4.7 (Ubuntu 10.12)
- Corrected a issue with compiling under MingW/Windows with newer versions of g++. With Linux g++ version 4.1.2 the overloaded constructor construct is allowed but with g++ 4.6.2 on MingW it complains about having a constructor call itself. Regardless its unnecessary to have both constructors since the definition is assigning a default value to the last parameter anyhow.
- InteractParser no longer writes the alternate protein twice. This addresses an issue when running InteractParser on OMSSA results and then getting duplicate alternate proteins for a peptide.
- Updated the link to UniProtKB and removed the dead link to SGD from the protein page of the Comet viewer.
- ProtXML Viewer: Fixed links in tab-delimited output; got rid of ineffectual if statements; fixed a number of bad usage of variables (misnamed, uninitialized, redeclared, and unused); removed some old stale code and local (regis) path comparisons.
- Fixed a reported buffer overflow bug in Mascot2XML
- Do not error out and crash in case of unknown enzyme in Comet protein sequence viewer; give a warning instead and forget about enzyme. Also, implemented on-page error reporting via javascript.
- Display a meaningful error if input file is not found in ModelParser
- Fixed bugs identified by http://www.viva64.com/en/b/0156/ :
- Fix potential bug with peptide sequence comparison in SpectraST
- Corrected a logic error in path insertion in Tandem2XML
- Fix faulty substring search in PepXMLViewer and in Dta2mzXML
- Fix erroneous index in crypt
- Fix logic error in Mascot2XML
- Fix incorrect increment operator in Comet spectrum viewer
- Use correct size for array in Out2XML
- Properly initialize a variable in RTCalculator and in MixtureModel
- Remove unused if/else logic in KernelDensityRTMixtureDistr
- Removed a bare pointer and redundant logic in NXST check in Comet protein sequence viewer
Miscellaneous
- No miscellaneous issues to report
Known Issues
- No known issues to report
Getting the TPP Software
- Download the TPP version 4.6.2 native windows installer (TPP_Setup_v4_6_2.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 4.6.2 source code .tgz package;
or, check out the code directly from svn:
"svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-6-2"
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.
SVN Log
The SVN log of all changes since the previous release are available at TPP:4.6.2_SVN_Log.
