TPP:4.6.3 Release Notes
From SPCTools
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
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.
