TPP:4.1 Release Notes

TPP 4.1 Release Notes

To developers: Please add anything you want to be sent out here. I'll take out the author attribution in the actual announcement. We can keep this page (or something similar) on the Wiki, as well.

(from Luis:)

• Added options to protxml2html to write out HTML or Excel (tab-delimited) from command line;
• New file downloading tool, fileDownloader.pl, with (optional) md5 verification and unzip;
• Fixed bug in findsubsets.pl that prevented it from running properly;
• Added tar (to windows distro);
• Apache defaults to 5-hour timeout;
• In Petunia:
  • New page for management (download) of Spectral Libraries;
  • New page to generate Libra condition files - for up to 8 channels (with updated isotopic correction factors);
  • Fixed bug when generating xtandem xml input file;
  • Implemented minimum peptide length option and expanded size of prob. cutoff field for PeptideProphet;
  • Option to pre-run generation of ProteinProphet results in html format;
  • Support for other mzXML converters: mzWiff, massWolf, and trapper (not all options yet);
  • Launch plot-msms when viewing spectra (instead of former dtaviewer);
  • Misc options for MzXML2Search.

(From Natalie)

• Spectrum Viewer updated to automatically select appropriate ion series for display
• linux build options: many parameters added to Makefile.config.incl (see Makefile.incl)
• massWolf: thresholding and (experimental) centroiding options
• ReAdW: calls msconvert for mzML output

(From Brian)

• TPP’s build of X!Tandem now reads mzML, mzXML3, and anything else that the PWIZ library can read.
• ReadMZXML now reads mzML and anything else that the PWIZ library can read.
• TPP GUI settings can now be changed by editing tpp_gui_config.pl so your changes to Mascot Server location etc don’t get blown away on each software update.