TPP:4.4.0 Release Notes

From SPCTools

(Difference between revisions)
Jump to: navigation, search
Revision as of 18:21, 16 August 2010
JoeS (Talk | contribs)
(→Release Notes)
← Previous diff		 Current revision
Ntasman (Talk | contribs)
(→build system)
Line 6: Line 6:
-== Changes ==+== New Features/Changes ==
-=== cpaulse ===+=== Deprecation of Conversion Tools ===
-------------------------------------------------------------------------+* The mzXML conversion tools ReAdW, massWolf, trapper, and mzWiff and been deprecated and are no longer included in TPP. All users are encouraged to use the converter tool <i>msconvert</i> produced as part of the ProeoWizard project. This tool supports all the same native formats as the previous tools, is better supported, and implements the new HUPO-PSI mzML standard. For convenience a version of this tool has been included with this TPP release.
-r4974 | cpaulse | 2010-05-13 12:13:21 -0700 (Thu, 13 May 2010) | 1 line+
-fix tpp.sln for vc9+=== pepXML schema ===
-------------------------------------------------------------------------+
-r4918 | cpaulse | 2010-03-29 14:33:30 -0700 (Mon, 29 Mar 2010) | 5 lines+
-Branch visual studio 8 tpp.sln file (and dependent vcproj files) to tppvc8.sln.  
- 
-tpp.sln and dependent vcproj files converted to visual studio 2008 express, with atl/mfc dependent projects (mzwiff, trapper, masswolf, readw), msconvert, and pwiz_swig projects removed from tpp.sln (last two don't compile in 2008 express and have no internal dependencies). extern/build_boost_vc8.bat renamed. 
- 
-minor bug fix to release configuration of readmzXML.vcproj. 
------------------------------------------------------------------------- 
-r4917 | cpaulse | 2010-03-29 11:08:10 -0700 (Mon, 29 Mar 2010) | 2 lines 
- 
-Fix reading of search engine specific input data where multiple search results are present for a single spectrum. 
-Compile warning in Visual C++ (PhosphoMixtureDistr.cxx). 
------------------------------------------------------------------------- 
-r4901 | cpaulse | 2010-03-12 08:51:32 -0800 (Fri, 12 Mar 2010) | 1 line 
- 
-fix destructor semantics for iProphet 
------------------------------------------------------------------------- 
-r4899 | cpaulse | 2010-03-10 12:04:17 -0800 (Wed, 10 Mar 2010) | 1 line 
- 
-don't delete RT and PI mixtureDistr's twice. 
------------------------------------------------------------------------- 
-r4898 | cpaulse | 2010-03-10 09:13:32 -0800 (Wed, 10 Mar 2010) | 1 line 
- 
-fix memory leaks in PeptideProphetParser, and type cast warnings generated by visual studio in spectrast 
------------------------------------------------------------------------- 
-r4890 | cpaulse | 2010-02-28 14:32:24 -0800 (Sun, 28 Feb 2010) | 1 line 
- 
-undo my destruction of Peptide::mods semantics. 
------------------------------------------------------------------------- 
-r4889 | cpaulse | 2010-02-26 11:35:58 -0800 (Fri, 26 Feb 2010) | 1 line 
- 
-more missed files intended for changeset 4885 
------------------------------------------------------------------------- 
-r4887 | cpaulse | 2010-02-26 11:19:01 -0800 (Fri, 26 Feb 2010) | 1 line 
- 
-missed from changeset 4885 
------------------------------------------------------------------------- 
-r4885 | cpaulse | 2010-02-25 15:21:11 -0800 (Thu, 25 Feb 2010) | 1 line 
- 
-modernize integer definitions enough to stop visual studio 9 from issuing warnings at level 3. 
------------------------------------------------------------------------- 
-=== real_procopio === 
- 
-==== pepXML schema ==== 
* New pepXML 1.15: Adds more search engines (ProteinPilot, ProteinLynx, Spectrum Mill, greylag, Phenyx, Proteios, Crux, Tide) and activation methods (ETD/CID, HCD). * New pepXML 1.15: Adds more search engines (ProteinPilot, ProteinLynx, Spectrum Mill, greylag, Phenyx, Proteios, Crux, Tide) and activation methods (ETD/CID, HCD).
- +=== MzXML2Search ===
-==== MzXML2Search ====+
* Added "mzML" to usage statement * Added "mzML" to usage statement
- +=== Petunia ===
-==== Petunia ====+
* Moved mzXML utils to new tab * Moved mzXML utils to new tab
* Changed wording on home page to state using mzML as the standard * Changed wording on home page to state using mzML as the standard
Line 97: Line 50:
-==== xinteract ====+=== xinteract ===
* Adding isotopic peaks XPRESS option to usage statement * Adding isotopic peaks XPRESS option to usage statement
-==== readmzXML ====+=== readmzXML ===
* Add -r option to output spectrum data only; no title or extra CR's. (Replicates functionality of Jimmy's getSpectrum) * Add -r option to output spectrum data only; no title or extra CR's. (Replicates functionality of Jimmy's getSpectrum)
-==== Pep3D ====+=== Pep3D ===
* Enable viewing of MS2-only data (no elution, but at least you can see the distribution of sequencing events) * Enable viewing of MS2-only data (no elution, but at least you can see the distribution of sequencing events)
* Larger input field for filename * Larger input field for filename
Line 111: Line 64:
-==== plot-msms (spectrum viewer) ====+=== plot-msms (spectrum viewer) ===
* Added Image Size option * Added Image Size option
* Update to unified look and feel * Update to unified look and feel
-==== protxml2html (ProteinProphet viewer) ====+=== protxml2html (ProteinProphet viewer) ===
* Add command-line usage statement * Add command-line usage statement
* Took out a bunch of commented-out code. * Took out a bunch of commented-out code.
Line 123: Line 76:
** Add option not to generate Gaggle files ** Add option not to generate Gaggle files
Limited testing gives speeds up to 5x faster than previous version. Limited testing gives speeds up to 5x faster than previous version.
 +
 +
 +=== build system ===
 +
 +TPP project fully converted to be built under C++ rules (vs mix of C and C++).
 +
 +OS X (not an officially supported system)
 +* use macports vs fink search paths for extra libraries;
 +* add dectection for 64-bit OS X systems
 +
 +"win_lib" directory retired; relevant components moved into tpp/extern directory; components stored as compressed files when possible.
 +
 +=== ASAPRatio ===
 +* added experimental wavelet smoothing. Test using new ASAPRatioPeptideParser -w command line option. From WaveletQuant implmentation, http://www.biomedcentral.com/1471-2105/11/219
 +
 +
=== dctrud === === dctrud ===
Line 401: Line 370:
[win32 installer] temp rename of README to README.txt while building installer allows windows to know how to display the readme doc at install time. Already did this for the MSVC installer build process, forgot about mingw. [win32 installer] temp rename of README to README.txt while building installer allows windows to know how to display the readme doc at install time. Already did this for the MSVC installer build process, forgot about mingw.
------------------------------------------------------------------------ ------------------------------------------------------------------------
 +===PeptideProphetParser===
 +
 +* Replace SSRCalc with RTCalc for retention time modelling.
 +
 +* Using ppm in the accurate mass model
 +
 +* Report error and don't model spectra with assumed_charge not equal to encoded charge in the name. Fix bug reported by Ludovic.
 +
 +* Adding InspectFvalue, PHOSPHO model, TOPCAT model.
 +
 +* tuning params on Tandem's semi-parametric model
 +
 +* Inspect f-value model.
 +
 +* adjusting Myrimatch f-value params.
 +
 +* tweaking the discriminant function params for OMSSA analysis
 +
 +* Caching variable bandwidth for quicker runtime. New function varBWdensityFit now can also take an additional parameter of a pointer to a Fit object.
 +
 +* PeptideProphetParser now stores all proteins matched by a search result.
 +
 +* Make tool more robust by auto trimming whitespace from spectrum names. Tandem searches submitted by Scott Stansfield (Aug 2009) where generated with method mzXML->mgf->tandem->pepXML was adding an extra space to the end of spectrum name. This commit addresses the issue with Scott's data.
 +
 +* Fixing seg fault appearing in MALDI mode on PROBID results.
 +
 +* Fix memory leaks
 +
=== David Shteynberg === === David Shteynberg ===
Line 410: Line 407:
ASAPRatio: changes to display ratios of secondary proteins from protein groups. TODO: Next and Prev Protein buttons will take you to the next protein group not the next protein in the group, should be corrected or disabled. ASAPRatio: changes to display ratios of secondary proteins from protein groups. TODO: Next and Prev Protein buttons will take you to the next protein group not the next protein in the group, should be corrected or disabled.
- 
-PeptideProphetParser: Replace SSRCalc with RTCalc for retention time modelling. 
RefreshParser: Only map unrejected peptides. RefreshParser: Only map unrejected peptides.
ASAPRatio: changes to display ratios of secondary proteins from protein groups. ASAPRatio: changes to display ratios of secondary proteins from protein groups.
- 
-PeptideProphetParser: Using ppm in the accurate mass model 
- 
- 
-PeptideProphetParser: Report error and don't model spectra with assumed_charge not equal to encoded charge in the name. Fix bug reported by Ludovic. 
- 
InteractParser: Make sure to not strip out the enzyme info when not specified on commandline. InteractParser: Make sure to not strip out the enzyme info when not specified on commandline.
Line 445: Line 434:
ProteinProphet Store a separate value with peptide's total weight in the protein group. ProteinProphet Store a separate value with peptide's total weight in the protein group.
- 
-PeptideProphetParser: Adding InspectFvalue, PHOSPHO model, TOPCAT model. 
Line 465: Line 452:
ProteinProphet store peptide group weight (sum of peptide's weight in the protein group) separatelly from peptide's weight in the protein. ProteinProphet store peptide group weight (sum of peptide's weight in the protein group) separatelly from peptide's weight in the protein.
- 
-PeptideProphetParser tuning params on Tandem's semi-parametric model 
- 
-PeptideProphetParser Inspect f-value model. 
- 
-PeptideProphetParser adjusting Myrimatch f-value params. 
- 
-PeptideProphetParser tweaking the discriminant function params for OMSSA analysis 
- 
-Caching variable bandwidth for quicker runtime. New function varBWdensityFit now can also take an additional parameter of a pointer to a Fit object. 
- 
-PeptideProphetParser now stores all proteins matched by a search result. 
ASAPRATIO: Bug Fix, wrong masses were being computed for charge 5+, now corrected. ASAPRATIO: Bug Fix, wrong masses were being computed for charge 5+, now corrected.
ASAPCGIDisplay.cgi: BUG FIX Normalized Ratio was not getting displayed. ASAPCGIDisplay.cgi: BUG FIX Normalized Ratio was not getting displayed.
- 
-PeptideProphet: Fixing seg fault appearing in MALDI mode on PROBID results. 
RefreshParser: Bug fix with UNMAPPED peptides not showing up UNMAPPED under some conditions. Use minimum number of enzymatic termini from the search_hit num_tol_term attribute. RefreshParser: Bug fix with UNMAPPED peptides not showing up UNMAPPED under some conditions. Use minimum number of enzymatic termini from the search_hit num_tol_term attribute.
[ProteinProphet] Fix bug of indistinguishable_peptides being reported wrong with bad charge and first 2 chars stripped off. [ProteinProphet] Fix bug of indistinguishable_peptides being reported wrong with bad charge and first 2 chars stripped off.
- 
-[PeptideProphetParser] Make tool more robust by auto trimming whitespace from spectrum names. Tandem searches submitted by Scott Stansfield (Aug 2009) where generated with method mzXML->mgf->tandem->pepXML was adding an extra space to the end of spectrum name. This commit addresses the issue with Scott's data.  
[InteractParser] Fix seg fault bug when dbtype option is set -T [InteractParser] Fix seg fault bug when dbtype option is set -T
-=== henrylam ===+=== SpectraST ===
- +
-==== SpectraST ====+
* New features (SpectraST v.4.0) * New features (SpectraST v.4.0)
Line 519: Line 488:
** Various bug fixes ** Various bug fixes
-==== calctppstats.pl ====+=== calctppstats.pl ===
* Option to specify probability or FDR threshold * Option to specify probability or FDR threshold
* Option to count number of unique proteins mapped to by PSMs * Option to count number of unique proteins mapped to by PSMs
-==== xinteract ====+=== xinteract ===
* Allow specification of protein database for RefreshParser (and hence for ProteinProphet) by -D option (in case that information is not in the pepXML file). * Allow specification of protein database for RefreshParser (and hence for ProteinProphet) by -D option (in case that information is not in the pepXML file).
* Skip RefreshParser, rather than crashing, if the database is not specified or not found. * Skip RefreshParser, rather than crashing, if the database is not specified or not found.
-=== eng_jk ===+=== XPRESS ===
-<b>XPRESS</b>+* Added support for intensity ratios (versus area based ratios) and specifying negative mass offsets. XPRESS includes better support for highres data by optionally summing individual isotope peaks for chromatogram reconstruction.
-Added support for intensity ratios (versus area based ratios) and specifying negative mass offsets. XPRESS includes better support for highres data by optionally summing individual isotope peaks for chromatogram reconstruction.+* Added minimum chromatrogram ion count parameter -c<num>. This parameter filters out entries from being quantified unless the reconstruction chromatogram meets the minimum number of peaks specified.
-Added minimum chromatrogram ion count parameter -c<num>. This parameter filters out entries from being quantified unless the reconstruction chromatogram meets the minimum number of peaks specified.+* Added -l label free option. This option will calculate stats on precursor ions only. Resulting analysis is labeled as 'xpresslabelfree' in pep.xml.
-Added -l label free option. This option will calculate stats on precursor ions only. Resulting analysis is labeled as 'xpresslabelfree' in pep.xml.+=== MzXML2Search ===
 +* Added -N option to print out top N most intense peaks in a spectrum. Needed for large peaklists from new instrument as Mascot will complain if input peak list exceeds 10,000 count.
-<b>MzXML2Search</b> 
-Add -N option to print out top N most intense peaks in a spectrum. Needed for large peaklists from new instrument as Mascot will complain if input peak list exceeds 10,000 count. 
-=== zhisun === 
- 
------------------------------------------------------------------------- 
-r4784 | zhisun | 2009-11-30 13:02:05 -0800 (Mon, 30 Nov 2009) | 1 line 
- 
-Chris Paulse modified the script and made it more permissive regarding the precursorCharge target string (doesn’t expect space immediately after the close quote.) 
------------------------------------------------------------------------- 
-r4545 | zhisun | 2009-08-07 15:02:14 -0700 (Fri, 07 Aug 2009) | 1 line 
- 
-solve memory problem 
------------------------------------------------------------------------- 
=== Full Integration of MaRiMba === === Full Integration of MaRiMba ===
* Completion of the full integration of MaRiMba into the TPP. * Completion of the full integration of MaRiMba into the TPP.
-=== spacepod === 
-------------------------------------------------------------------------+=== New "High Performance Computing" Tools ===
-r4972 | spacepod | 2010-05-10 12:24:18 -0700 (Mon, 10 May 2010) | 2 lines+
-[build process] 1) add dectection for 64-bit OS X systems; 2) use macports vs fink search paths for extra libraries (can add detection, if requested)+Two new tool sets for high performance computing have been added to the extern/ directory of TPP. Both of these
 +sets can be downloaded and installed to provide greater functionality to TPP.
-------------------------------------------------------------------------+* Grid (../extern/hpctools/grid)
-r4971 | spacepod | 2010-05-10 12:21:03 -0700 (Mon, 10 May 2010) | 2 lines+
-[PepXMLViewer] adding casts to work under boost 1.43.0+The intend of this project was to share to the community the set of bash scripts used by ISB to submit various TPP jobs to a compute cluster. These scripts where designed to work for either the open source version of the portable batch system (PBS) or the Sun Grid Engine. The scripts where written in bash for portability between
 +cluster platforms are are intended to be modified to suite you site's particular needs.
-------------------------------------------------------------------------+* AWS Search Tool (..extern/hpctools/aws)
-r4967 | spacepod | 2010-05-04 17:20:10 -0700 (Tue, 04 May 2010) | 2 lines+
-[ASAPRatioPeptideParser] adding experimental wavelet smoothing. Test using new ASAPRatioPeptideParser -w option. From WaveletQuant implmentation, http://www.biomedcentral.com/1471-2105/11/219+Set of programs and services which can be used to run MS/MS peptide spectra searches on Amazon Web Services. Currently supports X!Tandem, OMSSA, and Inspect. For each search algorithm a single control program is
 +provided which manages all aspects of connecting to Amazon Web Services, starting and stopping EC2 compute nodes
-------------------------------------------------------------------------+===tpp.sln (Windows only)===
-r4922 | spacepod | 2010-03-31 16:21:57 -0700 (Wed, 31 Mar 2010) | 2 lines+
-[Makefile] removing extra tab character+ported solution and vcproj files to Visual Studio 2008 express (necessitates the exclusion of ATL/MFC dependent projects, in this case the raw data file converters -- to be succeeded by proteowizard msconvert).
-------------------------------------------------------------------------+== Other bug fixes and improvements ==
-r4921 | spacepod | 2010-03-31 11:53:14 -0700 (Wed, 31 Mar 2010) | 2 lines+
-[linux install] generalizing ubuntu 9.04 install to 9.10 as well (tested)+* Fixed basePeak m/z and intensity bug for centroided data in ReAdW for Thermo Interface.
-------------------------------------------------------------------------+== Known Issues ==
-r4872 | spacepod | 2010-02-10 16:19:05 -0800 (Wed, 10 Feb 2010) | 1 line+
-[OS requirements] updating ubuntu 8.10 install+* None to report
-------------------------------------------------------------------------+
-r4785 | spacepod | 2009-11-30 17:46:38 -0800 (Mon, 30 Nov 2009) | 1 line+
-[mingw build] updates for mingw build+== Getting the TPP Software ==
-------------------------------------------------------------------------+
-r4660 | spacepod | 2009-09-28 14:17:22 -0700 (Mon, 28 Sep 2009) | 3 lines+
-[c to c++ cleanup] catching a few files that svn got confused on the first time.+* Download the TPP version 4.4.0 native windows installer (TPP_Setup_v4_4.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
-r4659 | spacepod | 2009-09-28 14:07:53 -0700 (Mon, 28 Sep 2009) | 3 lines+ "http://tools.proteomecenter.org/wiki/"
-[c to c++ cleanup] catching a few files that svn got confused on the first time.+* 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 4.4.0 source code .zip package;
 +or, check out the code directly from svn:
 + "svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-4-0"
-------------------------------------------------------------------------+ For building from source, please refer to the readme file in TPP/src as well as the wiki.
-r4658 | spacepod | 2009-09-28 14:02:07 -0700 (Mon, 28 Sep 2009) | 3 lines+
-[c to c++ cleanup] catching a few files that svn got confused on the first time.+The TPP Team: Luis, David, Brian, Natalie, 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.
- +
- +
-------------------------------------------------------------------------+
-r4657 | spacepod | 2009-09-28 13:44:33 -0700 (Mon, 28 Sep 2009) | 4 lines+
- +
-[c to c++ rename] merging changes to convert file extensions and build process from c to c++, from cpprename. fully +
-tested in 'cpprename' branch.+
- +
- +
-------------------------------------------------------------------------+
-r4656 | spacepod | 2009-09-28 13:19:44 -0700 (Mon, 28 Sep 2009) | 1 line+
- +
-[windows builds] updating paths for boost, expat dependencies; from cpprename branch+
-------------------------------------------------------------------------+
-r4655 | spacepod | 2009-09-28 12:25:19 -0700 (Mon, 28 Sep 2009) | 1 line+
- +
-[restoring trunk/tpp to cleaner history, before c->c++ thrashing+
-------------------------------------------------------------------------+
-r4587 | spacepod | 2009-08-24 12:13:54 -0700 (Mon, 24 Aug 2009) | 1 line+
- +
-[mingw build] adding script for building TPP under mingw, so that it's easier to get this going from outside the mingw/msys environment.+
-------------------------------------------------------------------------+
-r4573 | spacepod | 2009-08-13 17:48:57 -0700 (Thu, 13 Aug 2009) | 1 line+
- +
-[pwiz] attempting re-adding local copies in stages+
-------------------------------------------------------------------------+
-r4572 | spacepod | 2009-08-13 17:47:42 -0700 (Thu, 13 Aug 2009) | 1 line+
- +
-[pwiz] attempting re-adding local copies in stages+
-------------------------------------------------------------------------+
-r4571 | spacepod | 2009-08-13 17:46:34 -0700 (Thu, 13 Aug 2009) | 1 line+
- +
-[pwiz] attempting re-adding local copies in stages+
-------------------------------------------------------------------------+
-r4570 | spacepod | 2009-08-13 17:45:39 -0700 (Thu, 13 Aug 2009) | 1 line+
- +
-[pwiz] attempting re-adding local copies in stages+
-------------------------------------------------------------------------+
-r4569 | spacepod | 2009-08-13 17:45:09 -0700 (Thu, 13 Aug 2009) | 1 line+
- +
-[pwiz] attempting re-adding local copies in stages+
-------------------------------------------------------------------------+
-r4568 | spacepod | 2009-08-13 17:43:43 -0700 (Thu, 13 Aug 2009) | 1 line+
- +
-[pwiz] attempting re-adding local copies in stages+
-------------------------------------------------------------------------+
-r4567 | spacepod | 2009-08-13 17:39:50 -0700 (Thu, 13 Aug 2009) | 2 lines+
- +
-[pwiz] grr, trying again+
- +
-------------------------------------------------------------------------+
-r4566 | spacepod | 2009-08-13 16:56:51 -0700 (Thu, 13 Aug 2009) | 1 line+
- +
-[pwiz] adding local copy, staging as sourceforge keeps rejecting large checkins+
-------------------------------------------------------------------------+
-r4565 | spacepod | 2009-08-13 16:56:05 -0700 (Thu, 13 Aug 2009) | 1 line+
- +
-[pwiz] adding local copy+
-------------------------------------------------------------------------+
-r4564 | spacepod | 2009-08-13 15:59:03 -0700 (Thu, 13 Aug 2009) | 3 lines+
- +
-[pwiz] zapping pwiz method using svn extern; will be replaced with sashimi's own copy+
- +
- +
-------------------------------------------------------------------------+
-r4563 | spacepod | 2009-08-13 11:44:15 -0700 (Thu, 13 Aug 2009) | 2 lines+
- +
-[pwiz] moving and updating pwiz notes to tpp/extern in prep for compressing pwiz+
- +
-------------------------------------------------------------------------+
-r4560 | spacepod | 2009-08-12 17:23:22 -0700 (Wed, 12 Aug 2009) | 3 lines+
- +
-[moving win_lib into tpp/extern] moving files and making changes to reflect new locations. Followups likely.+
- +
- +
-------------------------------------------------------------------------+
-r4557 | spacepod | 2009-08-12 14:23:21 -0700 (Wed, 12 Aug 2009) | 3 lines+
- +
-[win_lib cleanup] part 1 of 2: merging changes from "win_lib-cleanup" branch to deal with compressed win_lib directories+
- +
- +
-------------------------------------------------------------------------+
- +
-=== New "High Performance Computing" Tools ===+
- +
-Two new tool sets for high performance computing have been added to the extern/ directory of TPP. Both of these+
-sets can be downloaded and installed to provide greater functionality to TPP. +
- +
-* Grid (../extern/hpctools/grid)+
- +
-The intend of this project was to share to the community the set of bash scripts used by ISB to submit various TPP jobs to a compute cluster. These scripts where designed to work for either the open source version of the portable batch system (PBS) or the Sun Grid Engine. The scripts where written in bash for portability between+
-cluster platforms are are intended to be modified to suite you site's particular needs.+
- +
-* AWS Search Tool (..extern/hpctools/aws)+
- +
-Set of programs and services which can be used to run MS/MS peptide spectra searches on Amazon Web Services. Currently supports X!Tandem, OMSSA, and Inspect. For each search algorithm a single control program is+
-provided which manages all aspects of connecting to Amazon Web Services, starting and stopping EC2 compute nodes+
- +
-------------------------------------------------------------------------+
- +
-=== Other bug fixes and improvements ===+
- +
-* Fixed basePeak m/z and intensity bug for centroided data in ReAdW for Thermo Interface.+

Current revision

Trans-Proteomic Pipeline (TPP) "Vuvuzela" 4.4.0 release notes

(Changes since the last official release, 4.3.1)

We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 4.4.0 (4.4 revision). 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.


Contents

[edit]

New Features/Changes

[edit]

Deprecation of Conversion Tools

  • The mzXML conversion tools ReAdW, massWolf, trapper, and mzWiff and been deprecated and are no longer included in TPP. All users are encouraged to use the converter tool msconvert produced as part of the ProeoWizard project. This tool supports all the same native formats as the previous tools, is better supported, and implements the new HUPO-PSI mzML standard. For convenience a version of this tool has been included with this TPP release.
[edit]

pepXML schema

  • New pepXML 1.15: Adds more search engines (ProteinPilot, ProteinLynx, Spectrum Mill, greylag, Phenyx, Proteios, Crux, Tide) and activation methods (ETD/CID, HCD).
[edit]

MzXML2Search

  • Added "mzML" to usage statement
[edit]

Petunia

  • Moved mzXML utils to new tab
  • Changed wording on home page to state using mzML as the standard
  • Added indexmzXML page
  • Optionally authenticate against an .htpasswd entry (from J.Slagel)
  • Fix tabs (from 4.3 branch)

New options

  • PeptideProphet:
    • Use Phospho model
  • XPRESS:
    • Allow passing of negative mass offsets
    • Min Points needed
    • Sum N isotopic peaks)
  • MzXML2Search:
    • Output N Top Peaks
    • Max Charge State
    • Output Precision
    • Removed ion mass option

Technical changes:

  • Minor corrections to session handling
  • Add trailing slash to tppbin definition
  • Added a variable to hold location of tpp-bin
  • Refer to tpp_hostname by full path
  • Silence perl warning (more to go...)
  • Provide path to plotspectrast.cgi when calling Lib2HTML
  • Minor form closing changes to avoid mis-formatting in IE


[edit]

xinteract

  • Adding isotopic peaks XPRESS option to usage statement


[edit]

readmzXML

  • Add -r option to output spectrum data only; no title or extra CR's. (Replicates functionality of Jimmy's getSpectrum)


[edit]

Pep3D

  • Enable viewing of MS2-only data (no elution, but at least you can see the distribution of sequencing events)
  • Larger input field for filename
  • Use dhtml to print/display messages (also simplify error messages so they display correctly).


[edit]

plot-msms (spectrum viewer)

  • Added Image Size option
  • Update to unified look and feel


[edit]

protxml2html (ProteinProphet viewer)

  • Add command-line usage statement
  • Took out a bunch of commented-out code.
  • Performance improvements:
    • Define several 'global' variables in xsl to avoid costly lookups
    • Add option not to generate Gaggle files

Limited testing gives speeds up to 5x faster than previous version.


[edit]

build system

TPP project fully converted to be built under C++ rules (vs mix of C and C++).

OS X (not an officially supported system)

  • use macports vs fink search paths for extra libraries;
  • add dectection for 64-bit OS X systems

"win_lib" directory retired; relevant components moved into tpp/extern directory; components stored as compressed files when possible.

[edit]

ASAPRatio


[edit]

dctrud

r4884 | dctrud | 2010-02-25 02:42:00 -0800 (Thu, 25 Feb 2010) | 1 line

[ASAPRatioProteinRatioParser] Implement PepXML cacheing as XPRESS

[edit]

pcbrefugee

r5043 | pcbrefugee | 2010-06-24 08:22:26 -0700 (Thu, 24 Jun 2010) | 1 line

[Mascot2XML] fatal error messages about enzyme definition issues are always useful, ignore the state of verbose_ flag for these

r5036 | pcbrefugee | 2010-06-14 16:16:26 -0700 (Mon, 14 Jun 2010) | 1 line

[pwiz] sync up to latest from ProteoWizard, their rev 2047

r4995 | pcbrefugee | 2010-05-28 10:56:11 -0700 (Fri, 28 May 2010) | 1 line

[pwiz] get current with ProteoWizard codebase - sync to pwiz commit number 2005

r4992 | pcbrefugee | 2010-05-28 10:21:54 -0700 (Fri, 28 May 2010) | 1 line

[indexmzXML] light changes to accomodate ever-stricter GCC's handling of long long (it doesn't like that), also fix and off-by-one error that left the last entry in the index untested.

r4954 | pcbrefugee | 2010-04-20 13:12:51 -0700 (Tue, 20 Apr 2010) | 1 line

[various] add a bunch of missing initializations - stack and dynamically allocated memory cannot be expected to be zeroed out. Also, don't call delete on malloc'd memory, use free instead.

r4937 | pcbrefugee | 2010-04-09 17:03:15 -0700 (Fri, 09 Apr 2010) | 1 line

[MzXMLSearch] change a variable size stack allocation of peak structs to new/delete allocation (some older compilers don't like that syntax, and it risks stack overflow too)

r4935 | pcbrefugee | 2010-04-09 15:39:07 -0700 (Fri, 09 Apr 2010) | 1 line

[MzXML2Search] fix a crash when WEBSERVER_ROOT env variable isn't set

r4929 | pcbrefugee | 2010-04-06 12:50:50 -0700 (Tue, 06 Apr 2010) | 1 line

[Pepc] update GWT and GChart to current versions and tweak color select code to satisfy IE8

r4928 | pcbrefugee | 2010-04-05 15:07:46 -0700 (Mon, 05 Apr 2010) | 1 line

[pwiz] add a missing pwiz source file for ABI_T2D that was tripping up the xtandem build on linux

r4926 | pcbrefugee | 2010-04-01 10:28:53 -0700 (Thu, 01 Apr 2010) | 1 line

[pwiz] handful of pwiz files missed again(!) in the previous commit (something's up with my TortoiseSVN installation?)

r4925 | pcbrefugee | 2010-04-01 09:59:20 -0700 (Thu, 01 Apr 2010) | 1 line

[pwiz] handful of pwiz files missed in the previous commit

r4924 | pcbrefugee | 2010-04-01 08:34:04 -0700 (Thu, 01 Apr 2010) | 1 line

synch up to Proteowizard rev 1925

r4920 | pcbrefugee | 2010-03-30 16:11:50 -0700 (Tue, 30 Mar 2010) | 1 line

Finish various renames of VC8 project files for the VC8 build.

r4919 | pcbrefugee | 2010-03-30 15:57:47 -0700 (Tue, 30 Mar 2010) | 1 line

tidy up notes to match current code

r4914 | pcbrefugee | 2010-03-23 16:15:51 -0700 (Tue, 23 Mar 2010) | 1 line

tweaks for MSVC build

r4913 | pcbrefugee | 2010-03-23 15:41:24 -0700 (Tue, 23 Mar 2010) | 1 line

[PepC] allow more seperator types in CSV files (comma, tab, semicolon, colon, space) and properly handle error cases where none of those are present. Also tweak IntelliJ project file to be directory location independent.

r4912 | pcbrefugee | 2010-03-22 15:47:43 -0700 (Mon, 22 Mar 2010) | 1 line

adding externals for rebuilding PepC jar file

r4911 | pcbrefugee | 2010-03-22 14:19:40 -0700 (Mon, 22 Mar 2010) | 1 line

integrate PepC statistical peptide counting into TPP GUI (commandline version was added in commit 4886). Somewhat underdocumented at the moment, will add link to accompanying paper as soon as it becomes available.

r4888 | pcbrefugee | 2010-02-26 11:34:57 -0800 (Fri, 26 Feb 2010) | 1 line

[PepC] - some documentation tweaks

r4886 | pcbrefugee | 2010-02-25 15:58:56 -0800 (Thu, 25 Feb 2010) | 1 line

initial commit of "PepC: Proteomics software for identifying differentially expressed proteins based on spectral counting." developed by Insilicos with Lev Becker et al at the UW Heinecke lab (paper has been submitted to Bioinformatics). Changes for integration with Petunia will come in a different commit - what's here is sufficient for commandline usage.

r4877 | pcbrefugee | 2010-02-22 08:46:38 -0800 (Mon, 22 Feb 2010) | 1 line

properly escape FASTA protein descriptions containing reserved XML characters in pepXML output

r4856 | pcbrefugee | 2010-01-15 17:01:37 -0800 (Fri, 15 Jan 2010) | 1 line

[ProteoWizard] a handful more missed commits from recent ProteoWizard code reorg

r4855 | pcbrefugee | 2010-01-15 16:12:00 -0800 (Fri, 15 Jan 2010) | 1 line

[ProteoWizard] add a few things I missed from the most recent ProteoWizard code tree reorganization, update to ProteoWizard rev 1707

r4854 | pcbrefugee | 2010-01-15 14:44:15 -0800 (Fri, 15 Jan 2010) | 1 line

[proteowizard] sync up with proteowizard rev 1699, which includes my fix for reading mzXML files with nested scans (only affects TPP when reading mzXML without newlines, in which case RAMP passes off to pwiz).

r4852 | pcbrefugee | 2010-01-15 13:25:47 -0800 (Fri, 15 Jan 2010) | 1 line

[xinteract] skip the iprophet stuff for LabKey purposes (currently internally identified as "non interactive mode", which becomes a misnomer now, since this has nothing to do with interactivity and is a more general config issue)

r4851 | pcbrefugee | 2010-01-15 13:23:17 -0800 (Fri, 15 Jan 2010) | 1 line

[xtandem] No functional change, just a couple of standard include file adds/drops for crossplatform purposes, and identify the build as our own variant: VERSION "2009.10.01.1 (LabKey and ISB) " instead of just "2009.10.01.1".

r4814 | pcbrefugee | 2010-01-11 11:46:52 -0800 (Mon, 11 Jan 2010) | 1 line

[tpp_gui/win32] consistent use of single quotes so perl_paths build step can find and replace /usr/bin with windowsy default path

r4795 | pcbrefugee | 2009-12-14 08:38:47 -0800 (Mon, 14 Dec 2009) | 1 line

[mzXML] a copy of http://sashimi.sourceforge.net/schema_revision/mzXML_3.0/mzXML_3.0.xsd for convenience, it's surprisingly difficult to locate online if you don't know where to look already

r4793 | pcbrefugee | 2009-12-10 17:45:24 -0800 (Thu, 10 Dec 2009) | 1 line

[pwiz] silence some gcc 4.2.4 warnings about assigning string constant to non-const char *

r4792 | pcbrefugee | 2009-12-10 16:20:39 -0800 (Thu, 10 Dec 2009) | 1 line

[pwiz mzML reader code] sync up with ProteoWizard project at their rev 1608, for mzML CV version 2.29.0. Missed a handful of adds in previous commit.

r4790 | pcbrefugee | 2009-12-10 15:54:38 -0800 (Thu, 10 Dec 2009) | 1 line

[pwiz mzML reader code] sync up with ProteoWizard project at their rev 1608, for mzML CV version 2.29.0. Changes are not a drastic as length of commit list might seem to imply, much of that is just changes in header comments due to an author's change of institution

r4789 | pcbrefugee | 2009-12-10 12:18:32 -0800 (Thu, 10 Dec 2009) | 1 line

[ASAPRatio CGI] don't mistake "cidIndx" for "Indx" while parsing html field values, per user dctrud in https://mail.google.com/a/insilicos.com/#label/spctools-discuss/125795e322f2433b

r4788 | pcbrefugee | 2009-12-09 16:46:10 -0800 (Wed, 09 Dec 2009) | 1 line

[pwiz] tidy up the MSVC build for pwiz JNI bindings (no more win_lib), add a clean-pwiz_swig target to Makefile.pwiz.incl

r4787 | pcbrefugee | 2009-12-04 16:59:09 -0800 (Fri, 04 Dec 2009) | 1 line

[pwiz] create the java bindings output directory if need be

r4786 | pcbrefugee | 2009-12-04 16:54:12 -0800 (Fri, 04 Dec 2009) | 1 line

[pwiz] add an optional target "pwiz_swig" to generate JNI wrappers for pwiz's RAMPAdapter. Not actually used by TPP, but useful for other projects that use TPP components.

r4781 | pcbrefugee | 2009-11-24 09:28:39 -0800 (Tue, 24 Nov 2009) | 1 line

[MzXML2Search] tweak the usage statement, "-T" sets maximum MH+ mass, not "maximum MH+ scan".

r4780 | pcbrefugee | 2009-11-23 09:23:25 -0800 (Mon, 23 Nov 2009) | 1 line

[ProteinProphet] call to writeErrorAndSens is still needed even when running non-interactively, as in LabKey Server usage

r4776 | pcbrefugee | 2009-11-17 14:27:00 -0800 (Tue, 17 Nov 2009) | 1 line

[out2xml] add a cast (int)strlen for quiet compile

r4774 | pcbrefugee | 2009-11-16 11:58:31 -0800 (Mon, 16 Nov 2009) | 1 line

[xtandem] remove an unneeded (and, to some compilers, offensive) class declaration within class definition of the same

r4773 | pcbrefugee | 2009-11-16 10:36:32 -0800 (Mon, 16 Nov 2009) | 1 line

[windows build] tweak the readme to remove references to win_lib

r4761 | pcbrefugee | 2009-11-12 15:05:48 -0800 (Thu, 12 Nov 2009) | 32 lines

[xtandem] updates from labkey guys to get us at least partly up to date with GPM - see attachment in my email to spctools-dev of Nov 12 2009, the crucial part of which is copied here with total loss of formatting:

2. Details 2.1 Make TPP fork current (jeckels)


Item Change Justification 2.1.A mscore.cpp To mimic SEQUEST-like scoring, a scoring plugin has to modify the theoretical fragment ion series to adjust intensities and add appropriate neutral losses. To allow this make mscore::load_seq virtual under #ifdef PLUGGABLE_SCORING


2.2 Consider merging additional changes from GPM tree into TPP fork (jeckels) These are the changes in the current GPM sources that seem unrelated to our changes and relatively useful.

Item Change Justification

2.2.a tandem.cpp p3.cpp Current source code in the GPM has implements a round-robin allocation of work to threads that results in better balance of execution time between threads. Requested by Matt Fitzgibbon. Note the 2 files are almost identical, they compile under different flags

2.2.b mscore.cpp , GPM version at lines 530 and 1573 Current GPM builds have added support for including doubly charged y-ions in the scoring. This will raise some scores to make them more accurate. Requested by Matt Fitzgibbon.

2.2.c mscore.cpp Other changes in the GPM appear to be for compiler issues. E.g. surrounding a float literal with parenthesis. If we take all the changes in GPMs version the only different that remains will be the change from 2.1.A above.

2.2.d mpmods.cpp mprocess.cpp msequtilities.cpp GPM ads support for annotation files for enumerating possible mods Tags are refine, use annotations protein, use annotations GPM defaults to yes on both but we could default to no

2.2.e mscorepam.h GPM's mscorepam.h has a change with comment "WCH: wrong pair attribute checking"


r4751 | pcbrefugee | 2009-11-11 16:22:13 -0800 (Wed, 11 Nov 2009) | 1 line

[xinteract] when creating or running regression tests, ignore the WEBSERVER_TMP environment variable - tempfile use and the temporary renames that come with it whacks out the regression test files.

r4634 | pcbrefugee | 2009-09-23 14:49:57 -0700 (Wed, 23 Sep 2009) | 1 line

[installers] hunt down and remove any manual steps required to get all new and former pepXML and protXML schemas into the windows installer, and the *nix "make install"

r4625 | pcbrefugee | 2009-09-18 11:10:33 -0700 (Fri, 18 Sep 2009) | 1 line

[ProteinProphet] more informative error message when pepXML simply contains no analyses from peptideProphet (or interProphet, as appropriate)

r4618 | pcbrefugee | 2009-09-11 11:27:03 -0700 (Fri, 11 Sep 2009) | 1 line

[Mascot2XML] handle yet another title variant, example: "title=spectrumId=3774 Polarity=Positive ScanMode=MassScan TimeInSeconds=3710.73"

r4597 | pcbrefugee | 2009-08-31 14:11:34 -0700 (Mon, 31 Aug 2009) | 1 line

[xtandem / mzML 1.0 backward compatibility] - tweaks to pwiz RAMPAdapter to handle mzML 1.0 description of precursor ions

r4583 | pcbrefugee | 2009-08-18 17:50:33 -0700 (Tue, 18 Aug 2009) | 1 line

[plot-msms] deal with a signed/unsigned warning (with a probably unmeasurable performance improvement)

r4581 | pcbrefugee | 2009-08-18 17:20:33 -0700 (Tue, 18 Aug 2009) | 1 line

[xtandem] tandem's custom mzXML parser wasn't expecting compressionType="none"

r4580 | pcbrefugee | 2009-08-18 17:01:17 -0700 (Tue, 18 Aug 2009) | 1 line

[mzML reading] get current with pwiz 1.6 branch to fix a problem with reading WIFF-originated mzML files (was throwing an exception due to complicated nativeID, now we just use the index as scan number instead)

r4579 | pcbrefugee | 2009-08-18 13:11:08 -0700 (Tue, 18 Aug 2009) | 1 line

[amazon ec2 builds] add ubuntu 9.10 as a supported OS, using the 9.04 config scripts

r4578 | pcbrefugee | 2009-08-18 13:00:41 -0700 (Tue, 18 Aug 2009) | 1 line

[xtandem] tweak for building under GCC 4.4.0 (including fake stdint.h for win32 builds)

r4577 | pcbrefugee | 2009-08-18 12:25:21 -0700 (Tue, 18 Aug 2009) | 1 line

[perl scripts] use $FindBin::Bin to locate tpp_hostname executable

r4529 | pcbrefugee | 2009-08-05 15:08:55 -0700 (Wed, 05 Aug 2009) | 1 line

[indexmzXML] add this tool to the standard install, use RAMP interface to get 64 bit file pointers for proper indexing on win32

r4517 | pcbrefugee | 2009-08-04 14:07:39 -0700 (Tue, 04 Aug 2009) | 1 line

[pwiz build] add a couple of files which our use of RAMPAdapter doesn't actually require, but which are missed by some library managers as unresolved references

r4514 | pcbrefugee | 2009-08-04 10:00:35 -0700 (Tue, 04 Aug 2009) | 1 line

[mzML handling] cutting over to latest ProteoWizard code, to pick up mzML 1.1 capability (including mzML 1.0 read capability)

r4511 | pcbrefugee | 2009-08-03 13:36:34 -0700 (Mon, 03 Aug 2009) | 1 line

[fileDownloader.pl] tweak to make this compatible with the win32-specific perl_paths make step that removes hardcoded /usr/bin path to wget etc - no effect on linux usage

r4510 | pcbrefugee | 2009-08-03 12:55:41 -0700 (Mon, 03 Aug 2009) | 1 line

[mzML handling] update ProteoWizard external references to rev 1132, to include changes for mzML 1.0 read capability

r4508 | pcbrefugee | 2009-08-02 16:46:39 -0700 (Sun, 02 Aug 2009) | 1 line

[petunia] on win32, prepend full install path to commands (should help with .pl files as commands, which the win32 path mechanism doesn't know to search for)

r4502 | pcbrefugee | 2009-07-30 14:53:56 -0700 (Thu, 30 Jul 2009) | 1 line

[win32 installer] temp rename of README to README.txt while building installer allows windows to know how to display the readme doc at install time. Already did this for the MSVC installer build process, forgot about mingw.

[edit]

PeptideProphetParser

  • Replace SSRCalc with RTCalc for retention time modelling.
  • Using ppm in the accurate mass model
  • Report error and don't model spectra with assumed_charge not equal to encoded charge in the name. Fix bug reported by Ludovic.
  • Adding InspectFvalue, PHOSPHO model, TOPCAT model.
  • tuning params on Tandem's semi-parametric model
  • Inspect f-value model.
  • adjusting Myrimatch f-value params.
  • tweaking the discriminant function params for OMSSA analysis
  • Caching variable bandwidth for quicker runtime. New function varBWdensityFit now can also take an additional parameter of a pointer to a Fit object.
  • PeptideProphetParser now stores all proteins matched by a search result.
  • Make tool more robust by auto trimming whitespace from spectrum names. Tandem searches submitted by Scott Stansfield (Aug 2009) where generated with method mzXML->mgf->tandem->pepXML was adding an extra space to the end of spectrum name. This commit addresses the issue with Scott's data.
  • Fixing seg fault appearing in MALDI mode on PROBID results.
  • Fix memory leaks
[edit]

David Shteynberg

RTCalc new tool for RT prediction

Out2XML: Use all of the last part of the encoded spectrum name for the charge not just one character, for multi character charge states

PepXMLViewer: Display only top ranked search_hit. Populate fields with search scores from any of the engines used in the analysis (useful for iProphet viewing).

ASAPRatio: changes to display ratios of secondary proteins from protein groups. TODO: Next and Prev Protein buttons will take you to the next protein group not the next protein in the group, should be corrected or disabled.

RefreshParser: Only map unrejected peptides.

ASAPRatio: changes to display ratios of secondary proteins from protein groups.

InteractParser: Make sure to not strip out the enzyme info when not specified on commandline.

InteractParser: BUGFIX prevent double delete of tag pointer.


InteractParser: Fix crash when -E option is not specified.

Tandem2XML: Handle multiple variable mods on same AA


RefreshParser: report the prev_aa and next_aa for top NTT match in the protein, not just the first entry. Test that db defn line actually has a '|' before testing if it comes before a ' '.

InteractParser: When an enzyme is given on the commandline overwrite the current sample_enzyme tag with the enzyme specified, old behaviour introduced competing sample_enzyme tags creating an inconsistency under certain conditions of use.


InterProphetParser - better usage statement, new option to output only peptides above a certain probability value.


InterProphetParser - adding computation of observed fits among initially low and high probability results, using variable bandwidths from the modeled fits.


ProteinProphet Store a separate value with peptide's total weight in the protein group.


xinteract PHOSPHO model and enable option InteractParser -P for correcting protein names in omssa output.

PeptideProphetParser new PHOSPHO model. Check all matching proteins for a peptide and count it as decoy only if all are decoys. Tuning max reward parameters for ACCMASS model. Print warning if not decoys are found. Count decoys and forward PSMs found. PeptideProphetParser new PHOSPHO model. Also fix the output when there are multiple top_hits so the probability is reported with the top most hit.


InterProphetParser Compute and report observed distributions in addition to the modeled distributions already reported.


InterProphetParser Filter out any old iProphet results from the final output file.


InterProphetParser Compute and report observed distributions in addition to the modeled distributions already reported.


ProteinProphet store peptide group weight (sum of peptide's weight in the protein group) separatelly from peptide's weight in the protein.

ASAPRATIO: Bug Fix, wrong masses were being computed for charge 5+, now corrected.

ASAPCGIDisplay.cgi: BUG FIX Normalized Ratio was not getting displayed.

RefreshParser: Bug fix with UNMAPPED peptides not showing up UNMAPPED under some conditions. Use minimum number of enzymatic termini from the search_hit num_tol_term attribute.

[ProteinProphet] Fix bug of indistinguishable_peptides being reported wrong with bad charge and first 2 chars stripped off.

[InteractParser] Fix seg fault bug when dbtype option is set -T

[edit]

SpectraST

  • New features (SpectraST v.4.0)
    • ETD support
    • iProphet support
    • Artificial decoy spectrum generation (-cAD, -cc, -cy options. Ref. Lam et al., J. Proteome Res. 9, 605-610 (2010))
    • MRM transition list generation (-cM option. Ref. Sherwood et al., J. Proteome Res. 8, 4396-4405 (2009))
    • User-defined modifications (-M option)
    • Semi-empirical spectrum generation based on user-specified modifications (-cAM, -cx options)
    • Searching MGF (Mascot Generic Format) files
    • Clickable (HTML) search output format
    • Gzipped (.gz) file support
    • Non-peptide and unidentified entries
    • Combining libraries by appending (-cJA option)
    • Searching all charges (ignore specified query charge state) (-sz option)
    • Lib2HTML option to display by sorted precursor m/z
    • "Butterfly" plot for two library spectra using plotspectrast
    • Several other advanced options
  • Other changes and bug fixes
    • Modernized library statistics reporting to stdout and in .pepidx file
    • Better book-keeping: fragmentation method, precursor intensity, and collision energy stored with library spectra
    • Improved annotation algorithm
    • Various bug fixes
[edit]

calctppstats.pl

  • Option to specify probability or FDR threshold
  • Option to count number of unique proteins mapped to by PSMs
[edit]

xinteract

  • Allow specification of protein database for RefreshParser (and hence for ProteinProphet) by -D option (in case that information is not in the pepXML file).
  • Skip RefreshParser, rather than crashing, if the database is not specified or not found.
[edit]

XPRESS

  • Added support for intensity ratios (versus area based ratios) and specifying negative mass offsets. XPRESS includes better support for highres data by optionally summing individual isotope peaks for chromatogram reconstruction.
  • Added minimum chromatrogram ion count parameter -c<num>. This parameter filters out entries from being quantified unless the reconstruction chromatogram meets the minimum number of peaks specified.
  • Added -l label free option. This option will calculate stats on precursor ions only. Resulting analysis is labeled as 'xpresslabelfree' in pep.xml.
[edit]

MzXML2Search

  • Added -N option to print out top N most intense peaks in a spectrum. Needed for large peaklists from new instrument as Mascot will complain if input peak list exceeds 10,000 count.


[edit]

Full Integration of MaRiMba

  • Completion of the full integration of MaRiMba into the TPP.


[edit]

New "High Performance Computing" Tools

Two new tool sets for high performance computing have been added to the extern/ directory of TPP. Both of these sets can be downloaded and installed to provide greater functionality to TPP.

  • Grid (../extern/hpctools/grid)

The intend of this project was to share to the community the set of bash scripts used by ISB to submit various TPP jobs to a compute cluster. These scripts where designed to work for either the open source version of the portable batch system (PBS) or the Sun Grid Engine. The scripts where written in bash for portability between cluster platforms are are intended to be modified to suite you site's particular needs.

  • AWS Search Tool (..extern/hpctools/aws)

Set of programs and services which can be used to run MS/MS peptide spectra searches on Amazon Web Services. Currently supports X!Tandem, OMSSA, and Inspect. For each search algorithm a single control program is provided which manages all aspects of connecting to Amazon Web Services, starting and stopping EC2 compute nodes

[edit]

tpp.sln (Windows only)

ported solution and vcproj files to Visual Studio 2008 express (necessitates the exclusion of ATL/MFC dependent projects, in this case the raw data file converters -- to be succeeded by proteowizard msconvert).

[edit]

Other bug fixes and improvements

  • Fixed basePeak m/z and intensity bug for centroided data in ReAdW for Thermo Interface.
[edit]

Known Issues

  • None to report
[edit]

Getting the TPP Software

  • Download the TPP version 4.4.0 native windows installer (TPP_Setup_v4_4.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 4.4.0 source code .zip package;

or, check out the code directly from svn: 

 "svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-4-0"

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

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

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.4.0_Release_Notes"
Personal tools