TPP:4.7.0 Release Notes

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Trans-Proteomic Pipeline (TPP) software, release 4.7.0 is a minor release of TPP that contains changes to 4.6.3. 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. Trans-Proteomic Pipeline (TPP) software, release 4.7.0 is a minor release of TPP that contains changes to 4.6.3. 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.
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== New Features == == New Features ==
 +* '''compareProts_ClusterHM.pl''':
 +** tool for building heatmaps comparing different ProteinProphet results
 +** can be launched via Petunia
 +* '''ShowXIC.cgi''':
 +** tool for visualizing Single Ion Current traces.
 +** launched via the precursor ion link in PepXMLViewer
-* TBD+* New '''ProtXML Viewer''' (beta):
 +** It is ''much'' faster
 +** Uses simple graphical elements, and has a clean interface.
 +** Colored horizontal bars used for most values, with mouse-over information
 +** Uses index to retrieve selected entries
 +** Displays protein annotation via AJAX call, with show/hide divs
 +** Auto-scroll main window to last clicked-on protein entry when switching tabs
 +** Sort and filter by various values
 +** Peptide probability histograms that are not contributing evidence are grayed out
 +** Graphical cues for uniquely mapping sequences, and ntt in sequences view
 +** Links to MODELS file, if present
 + 
 +* Upgraded to r51 of '''X!Tandem''' (Jackhammer updates)
 +* Added the following additional parameters for TPP's version of X!Tandem so that you no longer have to use a taxonomy.xml but instead can just directly specify the paths:
 + 
 + tpp list path, peptide
 + tpp list path, saps
 + tpp list path, mods
 + 
 +* '''RNA-Seq functionality''' (alpha): contains a script for building a database from RNA-Seq data for use with TPP.
 + 
 +* Replaced updateAllPaths.pl with a new program, '''updatepaths.pl''', that applies a more intelligent remapping of paths in pep.xml/prot.xml files by parsing the XML and updates attributes on the element based on its name.
 + 
 +* '''Mayu''' version 1.07 is now bundled with the TPP and can be invoked using the Petunia web interface
 + 
 +* '''Petunia''':
 +** Added ability to terminate a running job
 +** Added Comet launch page, including ability to run on the Amazon cloud
 +** Added new useSGE and useSudo options to run commands as authenticated user and/or to run on grid platforms such as the Sun Grid Engine (SGE). Caveat emptor.
 +** Added utility to edit Tandem parameters files:
 +*** Page allows users to change values, delete them, and add new ones
 +*** Flag duplicated parameters and non-existent default files
 +*** Include "I'm feeling lucky" google link to GPM for each parameter for extra help
 +*** User is able to save parameters under a different file name
 +*** No longer requiring that Tandem params filenames end in ".xml"; instead Petunia can recognize it from its contents
== Improvements/Changes == == Improvements/Changes ==
 +* '''indexmzXML''':
 +** Allow more upto 100K scans per mzXML file
 +* '''get_prot.pl''':
 +** filter by probability and any filter out filter_out string
 +* '''PTMProphet''':
 +** support for more modifications
 +** improved modification recognition and performance on N-glyco capture data.
 +** handle static terminal modifications, whether of not the mod is written in the modified_peptide attribute of pepXML file.
 +* '''xinteract''':
 +** Allow xinteract to keep running even if -nI is used to disable InteractParser, for using xinteract on previously interacted files (e.g. to do Quantitation separately with xinteract
 +** If PTMProphet was enabled, xinteract will run quantitation on the PTMProphet results.
 +** More Descriptive Usage statements
 +* '''PeptideProphetParser''':
 +** print usage and exit when invoked without arguments.
 +** write directory to inputfile tag when the file path is not absolute, and check for extension...add one if needed.
 +* InterProphetParser ('''iProphet'''):
 +** Added optional LENGTH model, and reporting of estimated number of corrects.
 +** KDModel: added more flexibility in bandwidth control.
 +* '''iModelParser.cgi''':
 +** added display of iProphet estimates of total correct PSM and total correct peptides in the results.
 +* '''InteractParser''':
 +** write directory to inputfile tag when the file path is not absolute.
-* PTMProphet :+* '''PepXMLViewer.cgi''':
 +** Add start scan back as a sortable column.
 +** Allow iProphet results to link out to the correct search_summary thereby allowing to a link on each spectrum to display the results depending on the best scoring search engine.
 +** Display friendly 'spectrum' link when no matched ions information is available from pepXML
 +** Display MSGF+ and (correct) Myrimatch search scores, and added corresponding filter options.
 +** Minor reformatting of filters for PeptideProphet and OMSSA
 +** Add ppm option to XPRESS
 +** Minor text changes to ASAP and XPRESS entry fields
--- support for more modifications+* Updated '''Lorikeet''' to r61:
 +** Label iTraq/TMT peaks
 +** Label precursor ion and m/z
 +** Label immonium ions
 + 
 +* '''Petunia''':
 +** Added ability to list files by wildcard, not just by filename extension/ending
 +** Use a different color when choosing files vs. browsing
 +** Added auto page refresh when submitting a job in Linux (avoids accidental job resubmission if refreshing the jobs page)
 +** Added link to beta ProtXMLViewer
 +** Use clear wording when user needs to select a directory vs a file
 +** Added option to run xinteract on each individual input file (i.e. not combine them into a single interact.*.xml)
 +** Align speclibs panes to top of table
 + 
 +* '''Miscellaneous''':
 +** Added "no enzyme" (OMSSA) and "no cleavage" (Myrimatch) as alternatives to the "nonspecific" enzyme entry in TPP.
 +** Applied David Trudgian's recent changes to support clang 5.0/MacOSX
 +** Don't emit warnings about amino acid codes in X!Tandem if it is a stop ('*') code.
 +** Make a better guess as to the linux platform we're on when building from the source.
 +** Output a warning message in the Apache log if WEBSERVER_ROOT isn't set and we are being run by a web server.
 +** Updated comet to 2013022
 +** Now includes ProteoWizard's qtofpeakpicker
== Bug fixes == == Bug fixes ==
 +* '''InterProphetParser''':
 +** BUGFIX with DECOY= option
 +* '''InteractParser''':
 +** BUGFIX write closing tags when last spectrum query is empty.
 +* '''xinteract''':
 +** BUGFIX with -MONO option being incorrectly parsed as a PTMProphet command.
 +** BUGFIX pep.xml was being appended twice due to typo.
 +
 +* '''TPP Models''':
 +** Got rid of ''qw as parentheses is deprecated'' warnings
 +** Fixed tick marks for nmc and ntt models
 +** Fixed minor filename bug
 +** Added quantitation summary and parameters to 'Run Options' tab.
 +** Create full filepaths when generating models for all files in a given directory
 +* Removed confusing ''confidence'' metric from '''protxml2html.pl'''
 +* Fixed '''Mayu''' to produce true 'csv' output (as opposed to tab-delimited)
-* TBD+* Added '''comet-pepxml.cgi''' to Windows installer so it gets installed.
 +* Fixed the link in the '''PepXMLViewer''' to use the pep.xml file instead of using the basename location of the input spectrum
 +* Uses '/' then a '\' when separating the file from the spectrum
 +* Fixed perl dependency issue in '''Petunia''' where the authors of IO::Compress::Zip renamed the option FilterEnvelope to FilterContainer without making it backwards compatible. Changed to use the more recent rendition and also added a minimum version of IO::Compress::Zip allowed.
 +* Addressed many of the issues brought up in this blog http://www.viva64.com/en/b/0212/
== Miscellaneous == == Miscellaneous ==
-* TBD+* Removed '''PepC''' from TPP
== Known Issues == == Known Issues ==

Current revision

Trans-Proteomic Pipeline (TPP) software, release 4.7.0 is a minor release of TPP that contains changes to 4.6.3. 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:4.6.3_Release_Notes

Contents

[edit]

New Features

  • compareProts_ClusterHM.pl:
    • tool for building heatmaps comparing different ProteinProphet results
    • can be launched via Petunia
  • ShowXIC.cgi:
    • tool for visualizing Single Ion Current traces.
    • launched via the precursor ion link in PepXMLViewer
  • New ProtXML Viewer (beta):
    • It is much faster
    • Uses simple graphical elements, and has a clean interface.
    • Colored horizontal bars used for most values, with mouse-over information
    • Uses index to retrieve selected entries
    • Displays protein annotation via AJAX call, with show/hide divs
    • Auto-scroll main window to last clicked-on protein entry when switching tabs
    • Sort and filter by various values
    • Peptide probability histograms that are not contributing evidence are grayed out
    • Graphical cues for uniquely mapping sequences, and ntt in sequences view
    • Links to MODELS file, if present
  • Upgraded to r51 of X!Tandem (Jackhammer updates)
  • Added the following additional parameters for TPP's version of X!Tandem so that you no longer have to use a taxonomy.xml but instead can just directly specify the paths: 
  tpp list path, peptide
  tpp list path, saps
  tpp list path, mods
  • RNA-Seq functionality (alpha): contains a script for building a database from RNA-Seq data for use with TPP.
  • Replaced updateAllPaths.pl with a new program, updatepaths.pl, that applies a more intelligent remapping of paths in pep.xml/prot.xml files by parsing the XML and updates attributes on the element based on its name.
  • Mayu version 1.07 is now bundled with the TPP and can be invoked using the Petunia web interface
  • Petunia:
    • Added ability to terminate a running job
    • Added Comet launch page, including ability to run on the Amazon cloud
    • Added new useSGE and useSudo options to run commands as authenticated user and/or to run on grid platforms such as the Sun Grid Engine (SGE). Caveat emptor.
    • Added utility to edit Tandem parameters files:
      • Page allows users to change values, delete them, and add new ones
      • Flag duplicated parameters and non-existent default files
      • Include "I'm feeling lucky" google link to GPM for each parameter for extra help
      • User is able to save parameters under a different file name
      • No longer requiring that Tandem params filenames end in ".xml"; instead Petunia can recognize it from its contents
[edit]

Improvements/Changes

  • indexmzXML:
    • Allow more upto 100K scans per mzXML file
  • get_prot.pl:
    • filter by probability and any filter out filter_out string
  • PTMProphet:
    • support for more modifications
    • improved modification recognition and performance on N-glyco capture data.
    • handle static terminal modifications, whether of not the mod is written in the modified_peptide attribute of pepXML file.
  • xinteract:
    • Allow xinteract to keep running even if -nI is used to disable InteractParser, for using xinteract on previously interacted files (e.g. to do Quantitation separately with xinteract
    • If PTMProphet was enabled, xinteract will run quantitation on the PTMProphet results.
    • More Descriptive Usage statements
  • PeptideProphetParser:
    • print usage and exit when invoked without arguments.
    • write directory to inputfile tag when the file path is not absolute, and check for extension...add one if needed.
  • InterProphetParser (iProphet):
    • Added optional LENGTH model, and reporting of estimated number of corrects.
    • KDModel: added more flexibility in bandwidth control.
  • iModelParser.cgi:
    • added display of iProphet estimates of total correct PSM and total correct peptides in the results.
  • InteractParser:
    • write directory to inputfile tag when the file path is not absolute.
  • PepXMLViewer.cgi:
    • Add start scan back as a sortable column.
    • Allow iProphet results to link out to the correct search_summary thereby allowing to a link on each spectrum to display the results depending on the best scoring search engine.
    • Display friendly 'spectrum' link when no matched ions information is available from pepXML
    • Display MSGF+ and (correct) Myrimatch search scores, and added corresponding filter options.
    • Minor reformatting of filters for PeptideProphet and OMSSA
    • Add ppm option to XPRESS
    • Minor text changes to ASAP and XPRESS entry fields
  • Updated Lorikeet to r61:
    • Label iTraq/TMT peaks
    • Label precursor ion and m/z
    • Label immonium ions
  • Petunia:
    • Added ability to list files by wildcard, not just by filename extension/ending
    • Use a different color when choosing files vs. browsing
    • Added auto page refresh when submitting a job in Linux (avoids accidental job resubmission if refreshing the jobs page)
    • Added link to beta ProtXMLViewer
    • Use clear wording when user needs to select a directory vs a file
    • Added option to run xinteract on each individual input file (i.e. not combine them into a single interact.*.xml)
    • Align speclibs panes to top of table
  • Miscellaneous:
    • Added "no enzyme" (OMSSA) and "no cleavage" (Myrimatch) as alternatives to the "nonspecific" enzyme entry in TPP.
    • Applied David Trudgian's recent changes to support clang 5.0/MacOSX
    • Don't emit warnings about amino acid codes in X!Tandem if it is a stop ('*') code.
    • Make a better guess as to the linux platform we're on when building from the source.
    • Output a warning message in the Apache log if WEBSERVER_ROOT isn't set and we are being run by a web server.
    • Updated comet to 2013022
    • Now includes ProteoWizard's qtofpeakpicker
[edit]

Bug fixes

  • InterProphetParser:
    • BUGFIX with DECOY= option
  • InteractParser:
    • BUGFIX write closing tags when last spectrum query is empty.
  • xinteract:
    • BUGFIX with -MONO option being incorrectly parsed as a PTMProphet command.
    • BUGFIX pep.xml was being appended twice due to typo.
  • TPP Models:
    • Got rid of qw as parentheses is deprecated warnings
    • Fixed tick marks for nmc and ntt models
    • Fixed minor filename bug
    • Added quantitation summary and parameters to 'Run Options' tab.
    • Create full filepaths when generating models for all files in a given directory
  • Removed confusing confidence metric from protxml2html.pl
  • Fixed Mayu to produce true 'csv' output (as opposed to tab-delimited)
  • Added comet-pepxml.cgi to Windows installer so it gets installed.
  • Fixed the link in the PepXMLViewer to use the pep.xml file instead of using the basename location of the input spectrum
  • Uses '/' then a '\' when separating the file from the spectrum
  • Fixed perl dependency issue in Petunia where the authors of IO::Compress::Zip renamed the option FilterEnvelope to FilterContainer without making it backwards compatible. Changed to use the more recent rendition and also added a minimum version of IO::Compress::Zip allowed.
  • Addressed many of the issues brought up in this blog http://www.viva64.com/en/b/0212/
[edit]

Miscellaneous

  • Removed PepC from TPP
[edit]

Known Issues

  • No known issues to report
[edit]

Getting the TPP Software

  • Download the TPP version 4.7.0 native windows installer (TPP_Setup_v4_7_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 4.7.0 source code .tgz package;

or, check out the code directly from svn: 

 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_4-7-0
    • For building from source, please refer to the readme file in TPP/src as well as the wiki.

The TPP Team: Luis, David, Mike, Joe, and Jimmy 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.

[edit]

SVN Log

The SVN log of all changes since the previous release are available at TPP:4.7.0_SVN_Log.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.7.0_Release_Notes"
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