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.
- New Javascript-based spectrum viewer (Lorikeet)
- Petunia:
- Added direct access to switch a directory in File Browser
- Added user input to pass parameters directly to the command-line (certain executables at this time), including simple validation
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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.
- Petunia:
- Make Tandem the default pipeline;
- Added option to run Tandem2XML immediately after searching;
- Added support for two missing enzymes in ->pepXML, as well as semi-enzyme support;
- Added IPROPHET option to ProteinProphet
- Adjusted Xpress defaults;
- Centralized code that creates links to open files in respective viewers;
- Moved "timeout" link to the right to avoid overlap with update page link;
- Added confirmation message when switching pipeline type;
- Shortened some menu titles to save space;
- Added mouse-over tooltips for menu items and navigation tabs;
- Added NIGMS logo and credits; replacing NHLBI's
- Took out obsolete SpectraST user options; added decoy-related options and Append To Library feature
- Minor formatting fix to PepC page
- Small code formatting/alignment changes.
- Updated meaning of $in_windows and introduced $in_cygwin vars;
- Removed some seemingly unused code.
- Protein Sequence Viewer:
- Added html comments for easier scrubbing of page (by exporTPP.pl)
- Peptide-Protein Weights Viewer:
- Fixed page format to fit page width, got rid of wasted space;
- Minor HTML tweaks;
- Added svn rev;
- Code clean-up: took out unused code, re-tabbed/formatted.
[edit]
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.
- Petunia:
- Minor bug fix when file is not present (as opposed to unreadable).
- Fixed broken Set Working Dir feature, also fixed link when output is a directory;
- Fixed bug that FileChooser to fail when pressing 'Enter' to switch directory
[edit]
Miscellaneous
- Nothing to report
[edit]
Known Issues
- There is an issue with using the 64bit version of ActiveState's Perl. While the installer recognizes that it is installed all of the Perl programs and scripts are hard-coded to use C:\perl\bin\perl -- the default location for 32bit installations of ActiveState perl. You can either install the 32bit version, or modify all of the scripts to use the 64 bit location (C:\perl64\bin\perl).
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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/"
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