ReleaseNotes - CompOmics/peptide-shaker-2.0-issue-tracker GitHub Wiki

ReleaseNotes

Changes in SearchGUI 4.0.0-beta (November 2. 2020):

  • NEW FEATURE: Added support for MetaMorpheus (version 0.0.312).
  • NEW FEATURE: Added support for spectrum files in mzML format.
  • NEW FEATURE: Added ThermoRawFileParser for support for Thermo raw file conversion.
  • NEW FEATURE: The user can now edit the enzymes via the graphical user interface.
  • FEATURE IMPROVEMENT: Updated MS-GF+ to version 2020.08.05.
  • FEATURE IMPROVEMENT: Updated Comet to version 2019.01 rev. 5.
  • FEATURE IMPROVEMENT: Updated MS Amanda to version 2.0.0.14828.
  • FEATURE IMPROVEMENT: Moved the FASTA file out of the search parameters.
  • FEATURE IMPROVEMENT: Search and de novo engines results are now gzipped upon completion.
  • FEATURE IMPROVEMENT: Added support for TMTpro (i.e. TMT 16-plex).
  • FEATURE IMPROVEMENT: Added support for the X! Tandem parameter "spectrum, parent monoisotopic mass isotope error", previously hard coded to "yes".
  • FEATURE IMPROVEMENT: Updated Ensembl to version 101 and Ensembl Genomes to version 48.
  • FEATURE IMPROVEMENT: Refactored the command lines.
  • FEATURE IMPROVEMENT: Moved the code to Java 14.
  • FEATURE IMPROVEMENT: The time stamp is now also included in the PeptideShaker output file name (if selected in the advanced settings).
  • FEATURE IMPROVEMENT: The last user selected spectrum and output folders are now remembered in the same way as the FASTA file folder.
  • FEATURE IMPROVEMENT: Added support for parsing the new NCBI FASTA headers.
  • FEATURE IMPROVEMENT: Added taxonomy name to the protein export options.
  • FEATURE IMPROVEMENT: Added coverage including the non-validated peptides to the protein export options.
  • BUG FIX: Fixed a bug with unspecific searches and missed cleavages for MS Amanda.
  • BUG FIX: Better handling of exceptions thrown if MyriMatch runs out of symbols to represent variable modifications.
  • LIBRARY UPDATE: Updated jsparklines to version 1.0.12.
  • LIBRARY UPDATE: Updated junit to version 4.13.1.
  • LIBRARY UPDATE: Updated utilities to version 5.0.0.

Changes in PeptideShaker 2.0.0-beta (November 2. 2020):

  • NEW FEATURE: Added support for spectrum files in mzML format.
  • NEW FEATURE: Added support for loading Morpheus mzIdentML files files.
  • FEATURE IMPROVEMENT: Novor results are now parsed as tags instead of complete peptides.
  • FEATURE IMPROVEMENT: New faster and more memory efficient database backend.
  • FEATURE IMPROVEMENT: Enabled launching of several instances on one computer.
  • FEATURE IMPROVEMENT: Decreased file sizes when storing PS projects.
  • FEATURE IMPROVEMENT: Increased GUI performance.
  • FEATURE IMPROVEMENT: Sped up and reduced the memory load when parsing several of the search and de novo engine file formats.
  • FEATURE IMPROVEMENT: Added support for gzipped search and de novo result files.
  • FEATURE IMPROVEMENT: Moved the FASTA file out of the search parameters.
  • FEATURE IMPROVEMENT: Added support for loading IdentiPy pep.xml files.
  • FEATURE IMPROVEMENT: Added support for TMTpro (i.e. TMT 16-plex).
  • FEATURE IMPROVEMENT: Updated Ensembl to version 101 and Ensembl Genomes to version 48.
  • FEATURE IMPROVEMENT: Updated the validation icons and added a new icon for "Not Validated".
  • FEATURE IMPROVEMENT: Refactored the command lines.
  • FEATURE IMPROVEMENT: Enabled partial projects processing (i.e. PSMs or peptide and PSMs only).
  • FEATURE IMPROVEMENT: Moved the code to Java 14.
  • FEATURE IMPROVEMENT: Removed charge/modification grouping of PSM/peptides during scoring.
  • FEATURE IMPROVEMENT: Better use of secondary hits.
  • FEATURE IMPROVEMENT: Filtered hits are now visible in the interface.
  • FEATURE IMPROVEMENT: Refactored the PTM alignment between peptides.
  • FEATURE IMPROVEMENT: Improved the use of multiple threads.
  • LIBRARY UPDATE: Updated utilities to version 5.0.0.

Changes in Reporter 0.8.0-beta (January 17. 2020):

Note: not yet compatible with utilities to version 5.0.0...

  • FEATURE IMPROVEMENT: Added support for TMTpro (i.e. TMT 16-plex).
  • FEATURE IMPROVEMENT: Moved the code to Java 8.
  • LIBRARY UPDATE: Updated PeptideShaker to version 2.0.0-beta.
  • LIBRARY UPDATE: Updated utilities to version 5.0.0.
  • LIBRARY UPDATE: Updated apache.poi to version 4.1.1.