TPP:4.6.3 Release Notes

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* New tool for comparing pairs of ProteinProphet result files * New tool for comparing pairs of ProteinProphet result files
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== Improvements/Changes == == Improvements/Changes ==

Revision as of 22:03, 24 July 2013

Trans-Proteomic Pipeline (TPP) "Occupy" 4.6.3 Release Notes

** DRAFT DRAFT DRAFT DRAFT DRAFT **

Contents

New Features

  • Inclusion of the Comet search engine in the TPP distribution
  • Support for importing data in the PSI mzIdentML format
  • Ability to sync data to/from Amazon S3 via Petunia, which now also supports basic (browser) user authentication
  • Addition of FPKM models in iProphet and ProteinProphet
  • New tool for generating randomized decoy databases
  • New tool for comparing pairs of ProteinProphet result files
  • Multi-threaded iProphet

Improvements/Changes

  • Support for Comet, MSGF+, and high-resolution X!Tandem k-score search results
  • Performance enhancements to PTMProphet and iProphet
  • Improved support for OMSSA, Myrimatch, and InsPecT search results, including a utility that fixes pepXML files
  • Support for unidentified spectra in spectrum viewer, updated to latest Lorikeet, and retired old Pep3D spectrum viewer
  • X!Tandem now issues a warning if invalid amino acids characters are spotted in in the fasta formatted database
  • [SpectraST] Different m/z tolerance for alignment and annotation; By default don't print top hits with zero f-value.
  • Added filter line and centroid status to ramp interface for mzML, mzXML, and mz5.
  • Added utility to grab the uniprot proteomes databases and append contaminants

Bug fixes

  • Bug fixes and improvements to the user interfaces
  • Fixed issue with InteractParser generating some bad results on Comet data with missing search_hits
  • InteractParser: large memory issue fixed
  • Addressed a compiler issue iwth latest Windows/MingW and Ubuntu

Miscellaneous

  • Comet2XML has been removed from TPP
  • Parse 'r' for rapid scan in filter line; add Velos Pro instrument

Known Issues

Getting the TPP Software

TBD

SVN Log

The SVN log of all changes since the previous release are available at TPP:4.6.3_SVN_Log.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.6.3_Release_Notes"
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