TPP:5.0.0 Release Notes

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* ''tpp_models:'' * ''tpp_models:''
 +** Capture StPeter analysis values
 +** Display decoy-based ROC curves, with errorbars
* Include ''Kojak'' 1.5.1 and related conf file * Include ''Kojak'' 1.5.1 and related conf file
* Updated to ''Comet'' 2016.01.2 and related params file * Updated to ''Comet'' 2016.01.2 and related params file
 +
 +* Adding ''hardklor'' to support DISCO
* New versions of ''pepXML'' and ''protXML'' schemae. * New versions of ''pepXML'' and ''protXML'' schemae.
Line 60: Line 64:
* ''PTMProphet'': * ''PTMProphet'':
** auto-populate modifications not known to SpectraST Peptide library ** auto-populate modifications not known to SpectraST Peptide library
- 
-* ''tpp_models'' 
-** Display decoy-based ROC curves, with errorbars 
* ''PeptideProphet'': * ''PeptideProphet'':
Line 87: Line 88:
* ''Spectrum Viewer'': * ''Spectrum Viewer'':
 +** Scale all spectra to 0 < mz < 2000 unless more data present (eases comparison of spectra)
** Added ability to view up to 5 interpretations of a single spectrum in same window via js tabs, with animation control ** Added ability to view up to 5 interpretations of a single spectrum in same window via js tabs, with animation control
** Added link from Comet hits to link to this page with top 5 hits ** Added link from Comet hits to link to this page with top 5 hits
** Also used for visualization of cross-linked peptide results ** Also used for visualization of cross-linked peptide results
 +
 +* ''Comet hits viewer''
 +** Added support for cases when mz data file is in different directory than pepXML file
 +** Updated link to Lorikeet by passing mzML file, scan number, and charge
* ''SpectraST'' * ''SpectraST''
Line 143: Line 149:
** Visual Studio project files ** Visual Studio project files
** Misc .bat files. ** Misc .bat files.
-** ''fdr_plot.cpp'', ''getSpectrum.cpp'', ''mzxml2dta1.cpp'', ''plottic1.cpp'', ''prophet_png1.cpp''+** ''fdr_plot.cpp'', ''getSpectrum.cpp'', ''mzxml2dta1.cpp'', ''plottic1.cpp'', ''prophet_png1.cpp'', ''tryp_model.txt''
** Old help files ** Old help files
** Cygwin-related code and settings ** Cygwin-related code and settings

Revision as of 03:05, 30 August 2016

Trans-Proteomic Pipeline (TPP) software, release 5.0.0 is a major release of TPP that contains new features, improvements, and fixes to 4.8.0. The software is available for Windows as well as Linux (and unofficially) for OSX 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 on Linux or OS X, 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:4.8.0_Release_Notes

Contents

Major Changes and Overview

  • Heavily modified code organization, build, and installation system
  • 64-bit
  • Windows installer:
    • includes all external dependencies, including stand-alone Apache web server (uses port 10401, user configurable) and Strawberry perl
    • allows for user-configurable software and data locations
    • new (optional) TPP Tray application provides convenient shortcuts to TPP, web server control, and data and log folders
  • New major software components:
    • Kojak for cross-linking analysis
    • DISCO for analysis of DIA data without using spectral libraries
    • StPeter for label-free protein quantitation via MS2 normalized spectral indices
  • Updated user interface look and feel

More details below.


New Features

  • New PeptideMapper tool???
  • PepxMLViewer:
    • Link iProphet prob to new models page
  • ProteinProphet:
  • PTMProphet
    • Added ability to look for neutral loss ions (new command-line spec)
    • User-defined MS2 tolerance (PPMTOL)
    • MINPROB parameter to ignore low scoring spectra
  • Petunia:
  • tpp_models:
    • Capture StPeter analysis values
    • Display decoy-based ROC curves, with errorbars
  • Include Kojak 1.5.1 and related conf file
  • Updated to Comet 2016.01.2 and related params file
  • Adding hardklor to support DISCO
  • New versions of pepXML and protXML schemae.


Improvements/Changes

  • InteractParser:
    • Add option to record ion_injection_time in pepXML
  • ASAPRatio:
    • Write xml-compliant 'NaN' string when applicable
    • Removed obsolete .bof files code
  • PTMProphet:
    • auto-populate modifications not known to SpectraST Peptide library
  • PeptideProphet:
    • Expanded N-Glyc model
    • Expanded mass models to allow for search offsets
  • ProteinProphet:
    • More user and progress feedback
  • RespectParser:
    • New options to remove peaks (instead of attenuate) and for output file suffix
  • Libra
    • Boosted performance of protein ratio calculation by 100x or more by doing a single pass over source pepXML files
    • Use higher precision for channels in order to support TMT-10 tags
    • Added progress bar
    • Record version in XML file after analysis
  • Petunia
    • Use Digest::MD5 to calculate md5 checksum instead of system call
  • Sequence viewer:
    • Attempt to map peptides via I/L substitution when first pass fails
  • Spectrum Viewer:
    • Scale all spectra to 0 < mz < 2000 unless more data present (eases comparison of spectra)
    • Added ability to view up to 5 interpretations of a single spectrum in same window via js tabs, with animation control
    • Added link from Comet hits to link to this page with top 5 hits
    • Also used for visualization of cross-linked peptide results
  • Comet hits viewer
    • Added support for cases when mz data file is in different directory than pepXML file
    • Updated link to Lorikeet by passing mzML file, scan number, and charge
  • SpectraST
    • Multi-threaded search
    • Added selenium-related modifications
    • Glyco-peptide support


Bug fixes

  • Fixed definition for lysn_promisc enzyme (to [X]|[KR])
  • InteractParser:
    • Do not crash when protein descriptions are blank
    • Upgrade scan numbers to long
    • Fix instances where 'scan=' is not found within nativeSpectrumID
    • Fix recording of variable mods if they were not listed in order in source pepXML
  • PTMProphet
    • Fixed memory leak
  • PepxMLViewer:
    • regenerate index when a new column is added, and keep the column always in display
    • corrected issue with bad byte offsets in large files
  • ProteinProphet:
    • Synced usage statement, removed obsolete XML option
    • Check for existence of input files before attempting to open them; provide meaningful feedback to user
  • Spectrum Viewer:
    • Faster rendering of spectra from MS2-only files
  • Mascot2XML
    • Fix mass error due to differing masses for proton
  • Tandem2XML
    • Corrections to modifications problems when using lots of mods

Miscellaneous

  • Major code reorganization and standardization:
    • Updated path furnishing utilities, as some paths are user-settable post-compilation
    • Renamed all ".cxx" C++ source files as ".cpp"
    • Harmonize directory names
    • Moved Enzyme code to Common/
    • moved COVERAGE/ folder into src/Util and renamed it batchcoverage (its target name)
    • Moved xtandem out of extern/ and into src/Search
    • Updated boost


  • Removed no longer needed or supported components:
    • refresh_interact, runperl, run_in
    • Visual Studio project files
    • Misc .bat files.
    • fdr_plot.cpp, getSpectrum.cpp, mzxml2dta1.cpp, plottic1.cpp, prophet_png1.cpp, tryp_model.txt
    • Old help files
    • Cygwin-related code and settings
  • Using Inno to produce Windows installer


Known Issues

  • Kojak graphical models in PeptideProphet are not displaying correctly on the MODELS page.


Getting the TPP Software

  • Download the TPP version 5.0.0 native windows installer (TPP_Setup_v5_0_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 5.0.0 source code .tgz package;
  • Or, check out the code directly from svn: 
 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_5-0-0
  • For building from source, please refer to the README and INSTALL files in src/ directory of TPP as well as this wiki.

Acknowledgements

The TPP Team: David, Luis, Mike, Jimmy, and our old colleague 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:5.0.0_SVN_Log.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:5.0.0_Release_Notes"
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