Trans-Proteomic Pipeline (TPP) 4.5.0 release

http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.5.0_Release_Notes

 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.

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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

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Miscellaneous

• Nothing to report

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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/"