TPP:4.5.0 Release Notes
From SPCTools
Trans-Proteomic Pipeline (TPP) "Rapture" 4.5.0 Release Notes
Trans-Proteomic Pipeline (TPP) software, release 4.5.0 is a minor release containing new features, new programs, and addresses a number of issues found with 4.4.1. 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 webserver). For advanced users who need to customize the TPP, or for those who run high-throughput experiments, you can download the source code. As always if you have any questions or problems with this release please let us know on the spctools-discuss discussion groupspctools-discuss mailing list.
Previous release notes are available at TPP:4.4.1_Release_Notes
Contents |
New Features
- New iModelParser.cgi tpp; fpr viewing iProphet models.
- New PTMProphetParser tool.
- New RTCatalogParser tool for cataloging retention times.
- xinteract
- New features, report collision energy, report compensation voltage
- InteractParser:
- New features, report collision energy, report compensation voltage
- Adding collision energy and compensation voltage for FAIMS as
optional attributes in pepXML schema spectrum_query
- SearchHit Changes, also defines bool_hash used in RTCatalog.
- Read collision energies in all msms_run_summaries, not just the first one encountered per pepXML file.
- Allow InteractParser (or RAMP in general) to read FAIMS Compensation Voltage from mzML filter line. TODO: need to make sure this makes it into the real PWIZ.
- New feature precursor intensity in pepXML
- Option for recording the retention_time_sec in pepXML.
- Windows installer now allows you to choose which components (such as msconvert) to install. This was done to comply with the licensing requirements of Proteowizard/msconvert. The installer was also streamlined by removing some of the dialog/steps, improving the language of the instructions and changing when certain checks are done as part of the installation process.
Improvements/Changes
- The older ProteoWizard based RAMP mzML/mzXML parse was replaced with mzParser to address some performance problems in a number of different programs.
- PepXMLViewer.cgi
- Version added to index file so that old index files get regenerated instead of crashing the viewer
- Index files now use longs for offsets to support large files
- Added collision_energy, precursor_intensity and compensation_voltage support for Crux
- Added PTMProphetParser support.
- RefreshParser
- I->L conversion on peptide and proteins to map to all indistinguishable peptides in the proteins.
- ASAPRatio
- New options added to quantify only above certain probability.
- PeptideProphetParser
- tweak pI model to model only +-5 stdev from mean pI for run.
- update to correct problem with latest version of Myrimatch which removed some scores in the reports.
- XPressPeptideParser
- Allow for proper quantitation of combined files where modified masses might be off depending on search engine and use of average vs monoisotopic mass in the search.
- RAMP
- Adding parsing of compensationVoltage (FAIMS).
- iProphet
- Clear out tophit hashes before recomputing. Separate SearchHit in a different class.
- Remove any peptideprophet or prior interprophet analysis_summary tags.
- New pepXML schema update for collision_energy and compensation_voltage
- Add scan counters to use as scan numbers when this info is not available in the mzML file (e.g. Agilent QTrap Data)
- Fix boost build to work with zlib125's directory structure, delete
old zlib123-dll.tar.bz2
- Switch to zlib v1.2.5 and tweaks for MingW build
- Rules for fetching Proteowizard and copying msconvert in the Windows installer were added to the Makefile to make builds more automated.
Bug fixes
- PepXMLViewer
- Fixed crash when empty filtered set is returned.
- Fixed problem when using commandline generated index which didn't print the queryString so we fake one.
- Tandem2XML
- Filter out extension from Tandem spectrum names.
- iModelParser.cgi
- Fix bugs with getting page to display. Now displays but the overlapping colors of gnuplot don't work. For best results use gnuplot 4.4.
- InteractParser
- Fix Q[111] and E[111] modification reporting in pepXML for OMSSA, max
rank option to not report hits above a certain hit_rank.
- iProphet
- When the pepXML already contains the iProphet tags filter them out, including the end tag.
- Correct the outputting of extra </spectrum_query> tags.
- Changes to pepXML writer to correct extra tag issue when iProphet is run on pepXML that already contains iProphet tags.
- Fix parsing of Phenyx search results.
Miscellaneous
- Nothing to report
Known Issues
- None to report
Getting the TPP Software
- Download the TPP version 4.5.0 native windows installer (TPP_Setup_v4_5_RAPTURE_rev_1.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 4.5.0 source code .zip package;
or, check out the code directly from svn:
"svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-5-0"
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, 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.
SVN Log
The SVN log of all changes since the previous release are available at TPP:4.5.0_SVN_Log.
