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PeptideShaker Changelog

What's new in PeptideShaker 2.2.25

May 10, 2023
  • LIBRARY UPDATE: Updated utilities to version 5.0.70.

New in PeptideShaker 2.2.24 (May 8, 2023)

  • LIBRARY UPDATE: Updated utilities to version 5.0.69.

New in PeptideShaker 2.2.23 (Mar 21, 2023)

  • NEW FEATURE: Added initial support for displaying the Sage LFQ values (beta).
  • LIBRARY UPDATE: Updated utilities to version 5.0.68.

New in PeptideShaker 2.2.22 (Mar 9, 2023)

  • LIBRARY UPDATE: Updated utilities to version 5.0.67.

New in PeptideShaker 2.2.21 (Mar 7, 2023)

  • FEATURE IMPROVEMENT: Improved the MS3 support when parsing mzML files.
  • LIBRARY UPDATE: Updated utilities to version 5.0.66.

New in PeptideShaker 2.2.20 (Feb 14, 2023)

  • NEW FEATURE: Added support for extracting all spectra (and not just MS2) when parsing mzML files (beta).
  • BUG FIX: Sage results can now be opened from the command line (and from SearchGUI).
  • LIBRARY UPDATE: Updated utilities to version 5.0.65.

New in PeptideShaker 2.2.19 (Feb 2, 2023)

  • LIBRARY UPDATE: Updated utilities to version 5.0.62.

New in PeptideShaker 2.2.18 (Feb 1, 2023)

  • NEW FEATURE: Added support for parsing Sage output.
  • FEATURE IMPROVEMENT: Added high resolution versions of the charts.
  • BUG FIX: Removed a potential null pointer for custom PTMs in the mzml export.
  • LIBRARY UPDATE: Updated poi to version 5.2.3.
  • LIBRARY UPDATE: Updatedspring-webmvc to version 5.3.23.
  • LIBRARY UPDATE: Updated jackson-databind to version 2.14.0.
  • LIBRARY UPDATE: Updated jackson-annotations to version 2.14.0.
  • LIBRARY UPDATE: Updated utilities to version 5.0.61.

New in PeptideShaker 2.2.17 (Oct 26, 2022)

  • LIBRARY UPDATE: Updated utilities to version 5.0.51.

New in PeptideShaker 2.2.16 (Oct 24, 2022)

  • BUG FIX: Fixed a bug in the NewEnzymeDialog.
  • LIBRARY UPDATE: Updated utilities to version 5.0.50.

New in PeptideShaker 2.2.15 (Oct 6, 2022)

  • FEATURE IMPROVEMENT: Minor improvement to the scaling for mirrored spectra.
  • LIBRARY UPDATE: Updated utilities to version 5.0.49.

New in PeptideShaker 2.2.13 (Oct 3, 2022)

  • LIBRARY UPDATE: Updated utilities to version 5.0.48, supporting Java version numbers with + as separator.

New in PeptideShaker 2.2.12 (Sep 28, 2022)

  • LIBRARY UPDATE: Updated utilities to version 5.0.47, updating from http to https in the software setup dialogs.

New in PeptideShaker 2.2.11 (Sep 28, 2022)

  • BUG FIX: Fixed a bug in the Ensembl mappings.
  • LIBRARY UPDATE: Updated utilities to version 5.0.46, fixing a bug for Java versions without decimals, e.g. just 19.

New in PeptideShaker 2.2.10 (Sep 28, 2022)

  • FEATURE IMPROVEMENT: Updated Ensembl to version 104 and Ensembl Genomes to version 51.

New in PeptideShaker 2.2.9 (Jun 9, 2022)

  • BUG FIX:
  • Updated the link in the check for new versions.

New in PeptideShaker 2.2.8 (Apr 28, 2022)

  • LIBRARY UPDATE: Updated utilities to version 5.0.41, fixing a bug in the Total Spectrum Intensity export.

New in PeptideShaker 2.2.7 (Apr 23, 2022)

  • FEATURE IMPROVEMENT: Added support for Cl, Co, Ni and Mn.
  • LIBRARY UPDATE: Updated utilities to version 5.0.40.

New in PeptideShaker 2.2.6 (Mar 2, 2022)

  • BUG FIX: Fixed a null pointer in the algorithm matches export for tags.

New in PeptideShaker 2.2.5 (Feb 1, 2022)

  • BUG FIX: Fixed a null pointer in the algorithm matches export.
  • LIBRARY UPDATE: Updated utilities to version 5.0.39.

New in PeptideShaker 2.2.4 (Jan 14, 2022)

  • LIBRARY UPDATE: Updated utilities to version 5.0.37.

New in PeptideShaker 2.2.3 (Jan 6, 2022)

  • LIBRARY UPDATE: Updated omssa-parser to version 2.0.4.
  • LIBRARY UPDATE: Updated utilities to version 5.0.35.

New in PeptideShaker 2.2.2 (Nov 16, 2021)

  • LIBRARY UPDATE: Updated omssa-parser to version 2.0.3.
  • LIBRARY UPDATE: Updated utilities to version 5.0.34.

New in PeptideShaker 2.2.1 (Nov 9, 2021)

  • FEATURE IMPROVEMENT: Added support for TMTpro 18-plex.
  • FEATURE IMPROVEMENT: Added a command line option for setting the project type: project_type.
  • LIBRARY UPDATE: Updated utilities to version 5.0.33.

New in PeptideShaker 2.2.0 (Aug 24, 2021)

  • LIBRARY UPDATE: Updated utilities to version 5.0.29, fixing a PTM alignment issue.

New in PeptideShaker 2.1.1 (Aug 17, 2021)

  • LIBRARY UPDATE:
  • Updated utilities to version 5.0.28, fixing a multi-threading null pointer in the cache handling.

New in PeptideShaker 2.1.0 (Aug 14, 2021)

  • LIBRARY UPDATE: Updated xpp3 to version 1.1.6.
  • LIBRARY UPDATE: Replaced commons-lang3 with commons-text version 1.9.
  • LIBRARY UPDATE: Updated poi to version 5.0.0.
  • LIBRARY UPDATE: Updated spring-webmvc to version 5.3.9.
  • LIBRARY UPDATE: Updated jackson-databind to version 2.12.4.
  • LIBRARY UPDATE: Updated jackson-annotations to version 2.12.4.
  • LIBRARY UPDATE: Updated utilities to version 5.0.27.

New in PeptideShaker 2.0.35 (Aug 11, 2021)

  • LIBRARY UPDATE: Updated utilities to version 5.0.26.

New in PeptideShaker 2.0.34 (Aug 11, 2021)

  • LIBRARY UPDATE: Updated utilities to version 5.0.25.

New in PeptideShaker 2.0.33 (Jun 30, 2021)

  • FEATURE IMPROVEMENT: Added support for Java 16.
  • LIBRARY UPDATE: Updated utilities to version 5.0.24.

New in PeptideShaker 2.0.32 (Jun 30, 2021)

  • BUG FIX: Fixed a gene mapping issue.

New in PeptideShaker 2.0.31 (Jun 15, 2021)

  • FEATURE IMPROVEMENT: Updated the example dataset.
  • FEATURE IMPROVEMENT: Updated Ensembl to version 104 and Ensembl Genomes to version 51.
  • FEATURE IMPROVEMENT: Turned off illegal access log messages for more of the CLIs.
  • LIBRARY UPDATE: Updated utilities to version 5.0.23.

New in PeptideShaker 2.0.30 (Jun 3, 2021)

  • BUG FIX: Updated the cms file in the example dataset.

New in PeptideShaker 2.0.29 (Jun 2, 2021)

  • BUG FIX: Fixed a bug in opening the example dataset on non-Windows setups.

New in PeptideShaker 2.0.28 (May 29, 2021)

  • BUG FIX: Fixed an issue with opening the example dataset.
  • LIBRARY UPDATE: Updated utilities to version 5.0.22.

New in PeptideShaker 2.0.27 (May 23, 2021)

  • FEATURE IMPROVEMENT: Updated the PDB web service.
  • LIBRARY UPDATE: Updated utilities to version 5.0.20.

New in PeptideShaker 2.0.26 (May 20, 2021)

  • BUG FIX: Fixied an issue with the PTM scoring when there are more than 20 possible sites for the same PTM.
  • LIBRARY UPDATE: Updated utilities to version 5.0.19

New in PeptideShaker 2.0.25 (May 20, 2021)

  • BUG FIX: Fixied an issue with the PTM scoring when there are more than 20 possible sites for the same PTM.
  • LIBRARY UPDATE: Updated utilities to version 5.0.19.

New in PeptideShaker 2.0.24 (Apr 27, 2021)

  • BUG FIX: Removed a custom settings file that caused the spectrum parsing to fail.

New in PeptideShaker 2.0.23 (Apr 27, 2021)

  • BUG FIX: Fixed a backwards compatibility bug for the cms files.
  • LIBRARY UPDATE: Updated utilities to version 5.0.17.

New in PeptideShaker 2.0.22 (Apr 27, 2021)

  • BUG FIX: Fixed a bug that occurred if not using a log folder and not exporting a psdb file.

New in PeptideShaker 2.0.21 (Apr 23, 2021)

  • LIBRARY UPDATE: Updated utilities to version 5.0.16.

New in PeptideShaker 2.0.20 (Apr 22, 2021)

  • FEATURE IMPROVEMENT: Greatly sped up the parsing/indexing of the spectrum files.
  • FEATURE IMPROVEMENT: Removed the Java 1.9 requirement, i.e. only Java 1.8 is now required.
  • FEATURE IMPROVEMENT: Made sure that also the error messages are sent to the standard output when not using the log.
  • LIBRARY UPDATE: Updated utilities to version 5.0.15.

New in PeptideShaker 2.0.19 (Apr 14, 2021)

  • NEW FEATURE: Added a new command line option (use_log_folder) that makes it possible to override the log folder and send the log details directly to the standard output.

New in PeptideShaker 2.0.18 (Mar 31, 2021)

  • FBUG FIX: Fixed a bug in the check for duplicate accession numbers in FASTA files.
  • LIBRARY UPDATE: Updated utilities to version 5.0.14.

New in PeptideShaker 2.0.16 (Mar 17, 2021)

  • FEATURE IMPROVEMENT: Extended the protein exports to also include organism identifiers for UniProt headers.
  • LIBRARY UPDATE: Updated utilities to version 5.0.12.

New in PeptideShaker 2.0.15 (Mar 15, 2021)

  • BUG FIX: Fixed bugs in parsing the user-defined exports.
  • LIBRARY UPDATE: Updated utilities to version 5.0.11.

New in PeptideShaker 2.0.14 (Mar 11, 2021)

  • BUG FIX: Fixed a bug with the fragmentation setting for MS-GF+ when using the command line.
  • LIBRARY UPDATE: Updated utilities to version 5.0.10.

New in PeptideShaker 2.0.13 (Mar 9, 2021)

  • FEATURE IMPROVEMENT: Made the FASTA header parsing (slightly) more robust.
  • LIBRARY UPDATE: Updated utilities to version 5.0.9

New in PeptideShaker 2.0.12 (Feb 25, 2021)

  • FEATURE IMPROVEMENT: Added the search engine raw score for peptides and tags.
  • LIBRARY UPDATE: Updated omssa-parser to version 2.0.2.
  • LIBRARY UPDATE: Updated utilities to version 5.0.8.

New in PeptideShaker 2.0.11 (Jan 31, 2021)

  • FEATURE IMPROVEMENT: The Java version warning now appears if using Java 8 or older.
  • LIBRARY UPDATE: Updated utilities to version 5.0.7.

New in PeptideShaker 2.0.10 (Jan 22, 2021)

  • BUG FIX: Fixed a bug in the export of non-enzymatic peptides.
  • LIBRARY UPDATE: Updated utilities to version 5.0.6.

New in PeptideShaker 2.0.9 (Jan 19, 2021)

  • BUG FIX: Fixed a bug in the protein inference graphs for displaying non-enzymatic peptides.
  • LIBRARY UPDATE: Updated utilities to version 5.0.5.

New in PeptideShaker 2.0.8 (Dec 22, 2020)

  • BUG FIX: Fixed an issue with indexing mgf files with empty spectra.
  • LIBRARY UPDATE: Updated utilities to version 5.0.4.

New in PeptideShaker 2.0.7 (Dec 18, 2020)

  • BUG FIX: Fixed an issue with checking for new versions when running in Conda.
  • LIBRARY UPDATE: Updated utilities to version 5.0.3.

New in PeptideShaker 2.0.5 (Nov 20, 2020)

  • FEATURE IMPROVEMENT: Added support for parsing spectrum titles with leading or trailing white space.
  • FEATURE IMPROVEMENT: Hid the kryo illegal reflective access warning messages.
  • BUG FIX: Added missing mgf file extensions in the follow up exports.
  • LIBRARY UPDATE: Updated utilities to version 5.0.1.

New in PeptideShaker 2.0.4 (Nov 19, 2020)

  • BUG FIX: Fixed bugs with locating moved FASTA and spectrum files.
  • BUG FIX: The out option is now mandatory for the PeptideShakerCLI command line if the zip option is used.

New in PeptideShaker 2.0.3 (Nov 18, 2020)

  • BUG FIX: Fixed a drawing bug in the validation plots.

New in PeptideShaker 2.0.2 (Nov 12, 2020)

  • BUG FIX: Fixed a bug in opening the example dataset.

New in PeptideShaker 2.0.1 (Nov 11, 2020)

  • BUG FIX: Fixed bugs in the gzip options for the MzidCLI and ReportCLI command lines.

New in PeptideShaker 2.0.0 (Nov 6, 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. Note that Java 9 or newer is now required to run PeptideShaker!
  • 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.

New in PeptideShaker 1.16.45 (Apr 24, 2020)

  • BUG FIX: Peptides and spectra occurring in only one spectrum file are no longer excluded.

New in PeptideShaker 1.16.44 (Feb 7, 2020)

  • BUG FIX: Fixed a bug in the Unipept export where unnecessary white space was added in the XML.

New in PeptideShaker 1.16.43 (Jan 18, 2020)

  • NEW IMPROVEMENT: Added support for exporting peptide sequences to Unipept.

New in PeptideShaker 1.16.42 (Jul 11, 2019)

  • FEATURE IMPROVEMENT: Updated the example dataset.

New in PeptideShaker 1.16.41 (Jul 11, 2019)

  • FEATURE IMPROVEMENT: Re-implemented the PRIDE Reshake to not show all projects but rather the results of the user’s search.
  • LIBRARY UPDATE: Updated utilities to version 4.12.15.

New in PeptideShaker 1.16.40 (May 16, 2019)

  • BUG FIX: Fixed a bug in the use of user-defined terminal PTMs.
  • LIBRARY UPDATE: Updated utilities to version 4.12.14

New in PeptideShaker 1.16.39 (May 9, 2019)

  • BUG FIX: The paths are now updated before the IdentificationParametersCLI is executed.

New in PeptideShaker 1.16.38 (Feb 1, 2019)

  • FEATURE IMPROVEMENT: Made the -out option non-mandatory, making it possible to, for example, only generate an mzid file as output.
  • BUG FIX: Fixed a bug in the closing of the PeptideShaker db when ran via the command line.

New in PeptideShaker 1.16.37 (Feb 1, 2019)

  • FEATURE IMPROVEMENT: Non-standard characters in the submitter details (i.e. the Person and Organization elements) are now escaped when exporting to mzIdentML.

New in PeptideShaker 1.16.36 (Dec 14, 2018)

  • FEATURE IMPROVEMENT:
  • Changed the order of the files in zip for faster access to reports and indexes when read as a stream.
  • Included the path to the log file in the error message printed if the command line fails.

New in PeptideShaker 1.16.35 (Nov 19, 2018)

  • FEATURE IMPROVEMENT: Added support for hyperplexing combining SILAC and TMT.
  • LIBRARY UPDATE: Updated utilities to version 4.12.13.

New in PeptideShaker 1.16.34 (Nov 14, 2018)

  • FEATURE IMPROVEMENT: Added support for Iron atoms.
  • FEATURE IMPROVEMENT: Added support for iodoTMT.
  • FEATURE IMPROVEMENT: Added Heme B as a default PTM.
  • LIBRARY UPDATE: Updated utilities to version 4.12.12.

New in PeptideShaker 1.16.33 (Nov 11, 2018)

  • BUG FIX: Fixed issues with http/https when accessing UniProt.
  • LIBRARY UPDATE: Updated utilities to version 4.12.10.

New in PeptideShaker 1.16.31 (Oct 9, 2018)

  • BUG FIX: Removed a reference to GUI code in the PathSettingsCLI.

New in PeptideShaker 1.16.30 (Oct 4, 2018)

  • BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
  • BUG FIX: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.

New in PeptideShaker 1.16.29 (Sep 18, 2018)

  • FEATURE IMPROVEMENT: Added default protein, peptide and PSM reports that also include the non-validated hits. Note: Some of the numbers used ro refer to the previous reports have changed and that you may need to update your command lines.

New in PeptideShaker 1.16.28 (Sep 17, 2018)

  • BUG FIX: The accuracy slider in the spectrum panel now works again.
  • BUG FIX: Improved the way the gene and GO mappings are checked and updated.
  • LIBRARY UPDATE: Updated utilities to version 4.12.8.

New in PeptideShaker 1.16.27 (Jul 9, 2018)

  • BUG FIX: Fixed a bug in the algorithm details features export.

New in PeptideShaker 1.16.26 (Jun 24, 2018)

  • BUG FIX: Fixed a bug where the PathSettingsCLI options where not supported when using the ReportCLI.

New in PeptideShaker 1.16.25 (Jun 15, 2018)

  • FEATURE IMPROVEMENT: Updated the example dataset.
  • BUG FIX: Fixed a bug in the clear filter feature in the PRIDE Reshake dialog.

New in PeptideShaker 1.16.24 (Jun 14, 2018)

  • Ensured that Novor results can be loaded across operating systems, e.g. run on Windows and open on Linux.
  • LIBRARY UPDATE: Updated utilities to version 4.12.7.

New in PeptideShaker 1.16.23 (May 8, 2018)

  • LIBRARY UPDATE: Updated utilities to version 4.12.6.

New in PeptideShaker 1.16.22 (May 3, 2018)

  • BUG FIX: Fixed a bug in the search setting dialog regarding the use of semi-specific enzymes.
  • LIBRARY UPDATE: Updated utilities to version 4.12.5.

New in PeptideShaker 1.16.21 (Apr 28, 2018)

  • BUG FIX: Fixed a bug in the IdentificationParametersInputBean where a break was missing when setting the cleavage preferences for MS-GF+ and MyriMatch.
  • BUG FIX: Fixed a bug where upper case mgf file endings resulted in a null pointer when indexing such files.
  • LIBRARY UPDATE: Updated utilities to version 4.12.4.

New in PeptideShaker 1.16.19 (Apr 24, 2018)

  • BUG FIX: Fixed bugs in the automatic detection of enzyme specificity that failed if non-enzymatic digestion was used.
  • LIBRARY UPDATE: Updated utilities to version 4.12.2.

New in PeptideShaker 1.16.18 (Apr 12, 2018)

  • BUG FIX: Updated the parsing of the organism information from UniProt headers (after UniProt added the NCBI tax id to the headers)
  • BUG FIX: Fixed backwards compatibility issues with opening old projects.
  • LIBRARY UPDATE: Updated utilities to version 4.12.1.

New in PeptideShaker 1.16.17 (Apr 12, 2018)

  • BUG FIX: Fixed backwards compatibility issues with opening old projects.
  • LIBRARY UPDATE: Updated utilities to version 4.12.0.

New in PeptideShaker 1.16.16 (Mar 12, 2018)

  • BUG FIX: Fixed issues with the PRIDE Reshake.
  • LIBRARY UPDATE: Updated the PRIDE web-service-model to version 1.0.2.

New in PeptideShaker 1.16.15 (Nov 10, 2017)

  • FEATURE IMPROVEMENT: Fixed issues with getting data from PRIDE (changed from http to https).

New in PeptideShaker 1.16.14 (Oct 9, 2017)

  • FEATURE IMPROVEMENT: Fixed issues with getting data from QuickGO (changed from http to https).

New in PeptideShaker 1.16.13 (Sep 5, 2017)

  • FEATURE IMPROVEMENT: Fixed issues with getting data from the new QuickGO, mainly required in the GO Analysis tab.

New in PeptideShaker 1.16.12 (Jul 18, 2017)

  • BUG FIX: Fixed a broken link to the PDB for getting the protein structure information.
  • LIBRARY UPDATE: Updated utilities to version 4.11.19.

New in PeptideShaker 1.16.10 (Jun 9, 2017)

  • FEATURE IMPROVEMENT: Updated Ensembl to version 89.
  • FEATURE IMPROVEMENT: Cleaned up the help files. (work in progress)
  • BUG FIX: Corrected errors in the mzIdentML export where only one modification was exported when having multiple modifications with the same mass shift.
  • BUG FIX: Fixed bugs in the mzid export where only the main modifications were exported.
  • BUG FIX: Fixed a bug where the default project name in the PRIDE Reshake could end up as too long.
  • BUG FIX: Fixed a bug in the PRIDE Reshake that occurred if the enzyme was extracted from the mzid file but not mapped to utilities.
  • LIBRARY UPDATE: Updated utilities to version 4.11.15.

New in PeptideShaker 1.16.9 (May 16, 2017)

  • FEATURE IMPROVEMENT: Added a check for quotation marks in accession numbers when parsing FASTA files.
  • BUG FIX: Corrected the links to the compomics.github.io wiki pages.
  • LIBRARY UPDATE: Updated utilities to version 4.11.12.

New in PeptideShaker 1.16.8 (May 15, 2017)

  • FEATURE IMPROVEMENT: Made it possible to export mzIdentML from the command line.
  • LIBRARY UPDATE: Updated utilities to version 4.11.11.

New in PeptideShaker 1.16.7 (May 9, 2017)

  • BUG FIX: Fixed a typo in the “Dimethylation of K 2H4” PTM.
  • LIBRARY UPDATE: Updated utilities to version 4.11.9.

New in PeptideShaker 1.16.6 (May 8, 2017)

  • FEATURE IMPROVEMENT: Added “Dimethylation of K 2H4” to the standard list of PTMs.
  • LIBRARY UPDATE: Updated utilities to version 4.11.8.

New in PeptideShaker 1.16.5 (Apr 27, 2017)

  • FEATURE IMPROVEMENT: Updated Ensembl Genomes to version 35.
  • LIBRARY UPDATE: Updated utilities to version 4.11.7.

New in PeptideShaker 1.16.4 (Apr 7, 2017)

  • Feature improvement:
  • Updated Ensembl to version 88
  • Library update:
  • Updated JSparklines to version 1.0.9.
  • Updated utilities to version 4.11.5.

New in PeptideShaker 1.16.2 (Mar 6, 2017)

  • Feature improvement:
  • Updated the Example Dataset

New in PeptideShaker 1.13.6 (Oct 21, 2016)

  • BUG FIX: Fixed a bug in the annotation of spectra with variable modifications.
  • LIBRARY UPDATE: Updated utilities to version 4.7.5.

New in PeptideShaker 1.13.5 (Oct 21, 2016)

  • FEATURE IMPROVEMENT: Updated Ensembl to version 86.
  • FEATURE IMPROVEMENT: Added an export to file option for the default and user modifications.
  • LIBRARY UPDATE: Updated utilities to version 4.7.4.

New in PeptideShaker 1.13.4 (Sep 28, 2016)

  • FEATURE IMPROVEMENT: Added the option to include the protein sequences in the mzid export.
  • FEATURE IMPROVEMENT: Speedups to the spectrum annotation processing.
  • BUG FIX: Made sure that the log parameter is recognized when using the command line.
  • BUG FIX: Corrected some exit process values with non zero on error conditions.
  • BUG FIX: Minor correction in the tag mapper.
  • LIBRARY UPDATE: Updated utilities to version 4.7.3.

New in PeptideShaker 1.13.3 (Sep 12, 2016)

  • FEATURE IMPROVEMENT: Export the spectrum as an array list formatted as a string (via the identification feature export).
  • BUG FIX: Fixed a null pointer that occurred if PeptideShakerCLI was used with path settings options.
  • LIBRARY UPDATE: Updated utilities to version 4.7.2.

New in PeptideShaker 1.13.1 (Aug 19, 2016)

  • NEW FEATURE: Added support for loading PEAKS Studio mzIdentML files.
  • NEW FEATURE: Added support for loading Protein Pilot mzIdentML files.
  • FEATURE IMPROVEMENT: Speed-ups in the use of the cache.
  • BUG FIX: Fixed potential multithreading issues.
  • LIBRARY UPDATE: Updated utilities to version 4.7.1.

New in PeptideShaker 1.13.0 (Aug 15, 2016)

  • NEW FEATURE: Added support for loading Morpheus pepXML files.
  • NEW FEATURE: Made it possible to export the fragment ions of secondary matches.
  • FEATURE IMPROVEMENT: Updated GO and gene mappings to Ensembl 85 and 32.
  • FEATURE IMPROVEMENT: Made the probability estimation of intermediate scores more conservative.
  • FEATURE IMPROVEMENT: The consensus score is now estimated based on the confidence.
  • FEATURE IMPROVEMENT: Spectra are now batch loaded prior to tag mapping.
  • FEATURE IMPROVEMENT: The cache size is now set according to the memory available.
  • FEATURE IMPROVEMENT: Attempt at making the command line exit codes follow the Unix convention.
  • FEATURE IMPROVEMENT: Removed the upper limit for the number of amino acids shown before/after the peptide sequence.
  • BUG FIX: Moved the instantiation of factories to after the setting of temporary paths in the CLIs.
  • LIBRARY UPDATE: Updated utilities to version 4.7.

New in PeptideShaker 1.12.3 (Jul 28, 2016)

  • BUG FIX: Fixed issues in the mzid export: made the file paths valid URIs and corrected a CV term name.

New in PeptideShaker 1.12.2 (Jul 8, 2016)

  • FEATURE IMPROVEMENT: Fixed an issue in the mgf reader where lines ending with r could cause problems.
  • BUG FIX: Corrected a bug in the pepxml parser where start_scan was used instead if index to extract the spectrum number.
  • BUG FIX: Corrected issues in the mzid export with regards to the annotation of neutral losses in mzid v1.1.
  • LIBRARY UPDATE: Updated utilities to version 4.6.3.

New in PeptideShaker 1.12.1 (Jun 27, 2016)

  • BUG FIX: Corrected errors in the command line documentation and parameter testing.
  • LIBRARY UPDATE: Updated utilities to version 4.6.2.

New in PeptideShaker 1.12.0 (Jun 27, 2016)

  • FEATURE IMPROVEMENT: Updated the URIs for the PSI-MS and UO ontologies in the mzid export.
  • FEATURE IMPROVEMENT: Removed the “final PSM list” CV term as it is no longer required.
  • FEATURE IMPROVEMENT: Added amino acid before/after and position to the default PSM export, and position to the default peptide export.
  • BUG FIX: Corrected the annotation of neutral losses in the mzid export.
  • BUG FIX: Fixed a minor formatting bug in the position output in the peptide export.
  • BUG FIX: Corrected typos in the documentation for the Validation terms in the custom exports at the peptide and PSM level.
  • LIBRARY UPDATE: Updated utilities to version 4.6.1.

New in PeptideShaker 1.11.0 (Jun 27, 2016)

  • NEW FEATURE: Added an export to PepXML as follow-up file.
  • NEW FEATURE: It is now possible to skip the peptide PTM alignment step.
  • NEW FEATURE: Added the possibility to tune the protein inference.
  • FEATURE IMPROVEMENT: Significantly sped up the peptide to protein mapping.
  • FEATURE IMPROVEMENT: PSM PTM site inference is now done after PTM site scoring.
  • FEATURE IMPROVEMENT: Multithreaded the estimation of PSM scores.
  • FEATURE IMPROVEMENT: Corrected potential threading issues and improved the multithreaded performance of the input and target decoy map.
  • FEATURE IMPROVEMENT: Peptides that are shorter or longer than the min/max peptide length allowed in the filters are now filtered out before the peptide validation starts.
  • FEATURE IMPROVEMENT: Changed the CV term for the immonium ions to the generic immonium ion CV term in the mzid export.
  • FEATURE IMPROVEMENT: Precursor ions (also with H20 and NH3 neutral losses) are now annotated in the mzIdentML export.
  • FEATURE IMPROVEMENT: Extended the list of supported neutral losses in the mzid export.
  • FEATURE IMPROVEMENT: Added CV terms for the TMT and iTRAQ reporter ions in the mzid export.
  • BUG FIX: Fixed a bug in the mzid export that could occur if a PSM had different PTM locations and/or PTM confidences than the parent peptide.
  • LIBRARY UPDATE: Updated xtandem parser to version 1.11.0, fixing a bug in the parsing of doubly modified terminals.
  • LIBRARY UPDATE: Updated utilities to version 4.5.20.

New in PeptideShaker 1.10.3 (May 22, 2016)

  • BUG FIX: Fixed a potential null pointer in the gene factory that could occur if there were no valid species in the FASTA file.
  • LIBRARY UPDATE: Updated utilities to version 4.5.17.

New in PeptideShaker 1.10.2 (May 22, 2016)

  • BUG FIX: Corrected a bug in the setting of the precursor mass filter.
  • BUG FIX: Corrected a bug in the Gene Preferences dialog resulting in an error when no internet connection was available.
  • LIBRARY UPDATE: Updated utilities to version 4.5.16.

New in PeptideShaker 1.10.1 (Apr 28, 2016)

  • FEATURE IMPROVEMENT: Non-html characters are now escaped when exporting to protein descriptions in mzIdentML files.
  • BUG FIX: The maximum number of missed cleavage is now included in the certificate of analysis.

New in PeptideShaker 1.10.0 (Apr 28, 2016)

  • FEATURE IMPROVEMENT: Set the mass filter based on the search settings.
  • BUG FIX: Corrected a bug in PhosphoRS leading to rounding errors.
  • BUG FIX: Corrected potential threading issues in the estimation of masses.
  • BUG FIX: Corrected an error in the parsing of the maximal precursor deviation allowed in the import filters.
  • BUG FIX: Minor correction in the command line documentation for the import_precurosor_mz and import_precurosor_mz_ppm parameters.
  • BUG FIX: Corrected a bug in the annotation of confident sites.
  • BUG FIX: Corrected the target/decoy histogram plot.
  • LIBRARY UPDATE: Updated utilities to version 4.5.13.

New in PeptideShaker 1.9.3 (Apr 8, 2016)

  • FEATURE IMPROVEMENT: Multiple fixes and enhancements in PhosphoRS as suggested by @david-bouyssie.
  • BUG FIX: Corrected CV terms in the mzIdentML export.
  • LIBRARY UPDATE: Updated utilities to version 4.5.11.

New in PeptideShaker 1.9.2 (Apr 2, 2016)

  • BUG FIX: Re-added the example dataset to the zip file.

New in PeptideShaker 1.9.1 (Apr 2, 2016)

  • FEATURE IMPROVEMENT: Updated Ensembl Genomes to version 31.
  • BUG FIX: Fixed bugs in the modification type for “Dimethylation of peptide N-term 2H(4)” and “Dimethylation of peptide N-term”.
  • LIBRARY UPDATE: Updated utilities to version 4.5.8.

New in PeptideShaker 1.9.0 (Mar 26, 2016)

  • FEATURE IMPROVEMENT: Speed improvements for the PTM scoring.
  • FEATURE IMPROVEMENT: Speed improvements for some of the exports.
  • FEATURE IMPROVEMENT: Added new PTM: Dimethylation of K 2H(6) 13C(2), also corrected “Dimethylation of peptide N-term K” to “Dimethylation of peptide N-term” and “Dimethylation of peptide N-term K 2H4” to “Dimethylation of peptide N-term 2H4”.
  • FEATURE IMPROVEMENT: Updated the Ensembl mappings to version 84.
  • BUG FIX: Fixed bugs in the PTM scoring that could occur in rare cases.
  • BUG FIX: Fixed a bug in the background color for the drop down menus with tooltips.
  • BUG FIX: Fixed a bug in the PTM dialog where empty patterns were not handled correctly for user defined PTMs.
  • BUG FIX: Corrected a bug in the phosphorylation exports.
  • BUG FIX: Fixed bugs in the validation of the following parameters when given as input on the command line: IMPORT_PRECURSOR_MZ_PPM, PREC_PPM, FRAG_PPM. Note that that the input is now binary (0 for Da and 1 for ppm, instead of 2 for Da and 1 for ppm as before).
  • LIBRARY UPDATE: jsparklines to version 1.0.8.
  • LIBRARY UPDATE: Updated utilities to version 4.5.7.

New in PeptideShaker 1.8.1 (Mar 5, 2016)

  • FEATURE IMPROVEMENT: Updated the default PTM localization settings.
  • BUG FIX: Correction in the iTRAQ 4-plex 115 mass.
  • BUG FIX: It is now possible to open the ProteinInferenceSettingsDialog even if the FASTA file is not set.
  • BUG FIX: The check for comma in PTM names now actually works.
  • BUG FIX: Fixed bugs in the loading of de novo data.
  • LIBRARY UPDATE: Updated utilities to version 4.5.3.

New in PeptideShaker 1.8.0 (Mar 5, 2016)

  • FEATURE IMPROVEMENT: Sped up and corrected bugs in the PhosphoRS PTM scoring.
  • FEATURE IMPROVEMENT: Extended the reports to include more information on peptide uniqueness.
  • FEATURE IMPROVEMENT: Avoided very long mgf files missing warnings when selecting the id files.
  • BUG FIX: Corrected a bug in the display of PTM scores in the PTMs tab.
  • BUG FIX: Improved the test for checking if a user selected Java home folder contains a valid Java installation or not.
  • LIBRARY UPDATE: Updated utilities to version 4.5.1.

New in PeptideShaker 1.7.6 (Feb 12, 2016)

  • BUG FIX: Fixed a bug in the command line for locating FASTA files in other locations than the one in the parameter file.
  • BUG FIX: Updated the certificate of analysis export.

New in PeptideShaker 1.7.5 (Feb 12, 2016)

  • FEATURE IMPROVEMENT: Extended the peptide and PSM reports.
  • BUG FIX: Fixed bugs in the PSM export that resulted in null pointers when exporting the algorithm scores.
  • BUG FIX: If the output file on the command line is given as the file name only, this is now picked up and an error displayed.
  • BUG FIX: Fixed GUI alignment issues in the Welcome dialog.
  • BUG FIX: Minor correction in the command line documentation for the comet_num_ptms option.
  • BUG FIX: Corrected an error in the definition of the iTRAQ 8plex 115 ion.
  • BUG FIX: Made sure that the variable PTM names are checked (for if a PTM with that name exists) when setting up the identification parameters from the command line (the fixed PTM names were already checked).
  • BUG FIX: Fixed a bug in the ProteinInferencePreferences that resulted in a null pointer if the database was not set (for example when the parameter file was created in DeNovoGUI).
  • BUG FIX: Fixed a bug in the command line for displaying the list of supported PTMs, where the -out parameter was required.
  • BUG FIX: Renamed the PTM “Dimethylation of K 2H(4)” to “Label of K 2H(4)”.
  • LIBRARY UPDATE: Updated utilities to version 4.3.22.

New in PeptideShaker 1.7.4 (Feb 8, 2016)

  • BUG FIX: Fixed bugs in the PSM export that resulted in null pointers when exporting the algorithm scores.

New in PeptideShaker 1.7.3 (Feb 8, 2016)

  • BUG FIX: Fixed a bug in the mass deviation filter where min and max isotope had gotten mixed up.
  • LIBRARY UPDATE: Updated utilities to version 4.3.21.

New in PeptideShaker 1.7.2 (Feb 6, 2016)

  • BUG FIX: Fixed a bug in the loading of the user PTMs in the SearchSettingsDialog
  • BUG FIX: User defined neutral losses and reporter ions are now loaded correctly when reading the PTM factory
  • BUG FIX: The PTM Dialog now checks if reporter ion and neutral loss names are unique before adding them
  • BUG FIX: Fixed a bug in the PTM Dialog where user defined neutral losses where always of type fixed
  • BUG FIX: Fixed a bug in the isSameAs method in ReporterIon that relied on theoretical mass and not composition
  • BUG FIX: Fixed bugs in the Gene Details dialog where protein groups was not supported
  • BUG FIX: Fixed a bug in the command line where a moved FASTA file could not be found even when in the SearchGUI zipped output
  • BUG FIX: Fixed a bug that resulted in it not being possible to sort on the Chromosome column
  • LIBRARY UPDATE: Updated jsparklines to version 1.0.7
  • LIBRARY UPDATE: Updated utilities to version 4.3.20

New in PeptideShaker 1.7.1 (Feb 6, 2016)

  • BUG FIX: Fixed an uncommon issue in the PTM scoring that could cause the processing of the data to fail.

New in PeptideShaker 1.7.0 (Jan 30, 2016)

  • FEATURE IMPROVEMENT: Added support for Arg-N.
  • FEATURE IMPROVEMENT: Updated the Andromeda web page link.
  • BUG FIX: Solved a potential threading issue in the peptide mass estimation.
  • BUG FIX: Improved the handling of target only databases.
  • BUG FIX: Corrected bugs in the PTM localization.
  • BUG FIX: Corrected the text relative to precursor filtering.
  • LIBRARY UPDATE: Updated utilities to version 4.3.18.

New in PeptideShaker 1.6.0 (Jan 27, 2016)

  • FEATURE IMPROVEMENT: Added support for isotope filtering.
  • FEATURE IMPROVEMENT: Added the possibility to export neighboring amino acids in the PSM export.
  • FEATURE IMPROVEMENT: Corrected the name of the precursor m/z deviation in the assumption filter.
  • LIBRARY UPDATE: Updated utilities to version 4.3.17.

New in PeptideShaker 1.5.1 (Jan 27, 2016)

  • LIBRARY UPDATE: Updated X!Tandem Parser to version 1.10.0, fixing a bug in the handling of multiple fixed PTMs of the same type on the same peptide.

New in PeptideShaker 1.5.0 (Jan 27, 2016)

  • NEW FEATURE: Added peptide level modification QC plots.
  • FEATURE IMPROVEMENT: Added support for Semi-GluC-(DE).
  • BUG FIX: Improved the parsing of PTMs when parsing pepxml files.
  • BUG FIX: Fixed an issue that resulted in the tools not starting if a custom Java home was set and it could not be found.
  • BUG FIX: Fixed issues in the mzIdentML and PRIDE XML exports in the escaping if quotes.
  • BUG FIX: Fixed bugs in the protein coverage display.
  • BUG FIX: Corrected bug in the PTM localization.
  • BUG FIX: Fixed a bug in the related ions where not all ions where added to the list.
  • LIBRARY UPDATE: Updated X!Tandem Parser to version 1.9.0, fixing bugs in the ID file reader in the way multiple PTMs targeting the same residue was handled, in particular when one PTM was fixed and the other variable, e.g. as in variable TMT on n-term and fixed TMT on (n-term) K.
  • LIBRARY UPDATE: Updated utilities to version 4.3.16.

New in PeptideShaker 1.4.0 (Jan 15, 2016)

  • NEW FEATURE: Added support for related ions in the spectrum annotation.
  • FEATURE IMPROVEMENT: Improved the handling of datasets where variable modifications targeting termini and amino acids are searched together.
  • FEATURE IMPROVEMENT: Updated the documentation of the peptide export.
  • FEATURE IMPROVEMENT: Improved the handling of backed-up PTMs.
  • BUG FIX: Fixed a bug where PTM names could be incorrectly assigned between PTMs of same mass.
  • BUG FIX: Fixed a bug resulting in a duplicate key exception when not using PhosphoRS.
  • BUG FIX: Fixed a bug in the neutral losses map where the reverse neutral losses were not added.
  • LIBRARY UPDATE: Updated utilities to version 4.3.11.

New in PeptideShaker 1.3.6 (Jan 8, 2016)

  • FEATURE IMPROVEMENT: Updated the ISAS logo in the Welcome and Getting Started dialogs
  • BUG FIX: Fixed an issue in the pepxml parser where peptides with both a fixed and a variable modification on the same residue (for example carbamidomethyl and pyro-c on the n-term) were not parsed correctly
  • LIBRARY UPDATE: Updated utilities to version 4.3.8

New in PeptideShaker 1.3.5 (Jan 7, 2016)

  • BUG FIX: Fixed bugs in the escaping of non-standard characters in the mzIdentML and PRIDE XML exports, which resulted in invalid files.

New in PeptideShaker 1.3.4 (Jan 7, 2016)

  • BUG FIX: Fixed a bug in the command line link between SearchGUI and PeptideShaker.
  • BUG FIX: Fixed an issue where the enzyme could be reset to Trypsin when using the command line.
  • BUG FIX: Corrected the mass for the pY reporter ion.
  • LIBRARY UPDATE: Updated utilities to version 4.3.7.

New in PeptideShaker 1.3.3 (Jan 7, 2016)

  • FEATURE IMPROVEMENT: Added support for the number of missed cleavages filters to the command line.
  • FEATURE IMPROVEMENT: Corrected minor issues with the command line documentation and made it more readable.
  • BUG FIX: Fixed a bug in the creation of parameter files from the command line.
  • LIBRARY UPDATE: Updated utilities to version 4.3.6.

New in PeptideShaker 1.3.2 (Jan 4, 2016)

  • NEW FEATURE: Added import filter for the number of missed cleavages for the peptides.
  • FEATURE IMPROVEMENT: Made sure that the 24 hour format is used in all time stamps.
  • FEATURE IMPROVEMENT: Updated the ISAS logo in the splash screen.
  • BUG FIX: Fixed possible issues in the methods for checking if a peptide is at the protein terminals.
  • LIBRARY UPDATE: Updated utilities to version 4.3.5.

New in PeptideShaker 1.3.1 (Dec 31, 2015)

  • BUG FIX: Fixed a bug in the creation of an identification settings file via the GUI.
  • LIBRARY UPDATE: Updated utilities to version 4.3.4.

New in PeptideShaker 1.3.0 (Dec 31, 2015)

  • NEW FEATURE: A log folder can now be selected when operating in command line.
  • FEATURE IMPROVEMENT: Added options for starting PRIDE Reshake with a given PX accession from the command line.
  • FEATURE IMPROVEMENT: Added support for Semi-Arg-C.
  • FEATURE IMPROVEMENT: Added links to PRIDE Inspector and ProteomeXchange in the mzIdentML export complete dialog.
  • FEATURE IMPROVEMENT: The protein inference database is now also updated if it is the same as the search database and not found when loading search result files.
  • FEATURE IMPROVEMENT: Updated the Ensembl mappings to version 83.
  • FEATURE IMPROVEMENT: Updated the Ensembl Genomes mapping to version 30.
  • FEATURE IMPROVEMENT: Improved the names of the plots in the Validation tab and updated the help text accordingly.
  • FEATURE IMPROVEMENT: First attempt at supporting fragment ion tolerance in ppm.
  • FEATURE IMPROVEMENT: The precursor and fragment ion tolerance types are now extracted from PRIDE XML files when using PRIDE Reshake.
  • BUG FIX: Improved the mzIdentML reader to be able to distinguish fixed and variable terminal modifications with the same accession and mass.
  • BUG FIX: The UniProt taxonomy mapping is now loaded before working with the identification parameters avoiding a null pointer when loading files containing search parameters only.
  • BUG FIX: Fixed a bug in the Filter dialogs where it was impossible to add filters unless there was at least one filter already in the table.
  • BUG FIX: Fixed a minor bug in the canceling of the Filter dialogs.
  • BUG FIX: Fixed bugs in the reprocessing of private PRIDE data.
  • BUG FIX: Added a fix for a Java bug where the button for the scroll bar could disappear on certain Java versions.
  • BUG FIX: Corrected the escaping if illegal characters when exporting to PRIDE XML and mzIdentML.
  • BUG FIX: The H2O neutral losses are now back in the FragmentIonTable.
  • BUG FIX: The bubble plots now react to the user annotation settings.
  • BUG FIX: Fixed an error in the “Thermolysin, no P rule” enzyme, where the P rule was actually added.
  • BUG FIX: Corrected a bug where the Tide format was not displayed properly.
  • BUG FIX: Fixed a bug where the processing of the neutral losses could cancel the loading of the data.
  • LIBRARY UPDATE: Updated utilities to version 4.3.3.

New in PeptideShaker 1.2.2 (Dec 8, 2015)

  • LIBRARY UPDATE: Updated utilities to version 4.1.15.

New in PeptideShaker 1.2.1 (Dec 8, 2015)

  • FEATURE IMPROVEMENT: Added support for new enzyme: Trypsin + Glu-C.
  • BUG FIX: Added a temporary fix for importing c-terminal modifications for Comet.
  • BUG FIX: Fixed a null pointer that occurred if trying to open a new project from inside PeptideShaker.
  • LIBRARY UPDATE: Updated utilities to version 4.1.14.

New in PeptideShaker 1.2.0 (Dec 8, 2015)

  • FEATURE IMPROVEMENT: Added support for LysargiNase.
  • FEATURE IMPROVEMENT: Improved the Validation plots.
  • FEATURE IMPROVEMENT: Updated the parameters related classes to work with json files
  • FEATURE IMPROVEMENT: Added support for exporting the sequence coverage plot.
  • FEATURE IMPROVEMENT: Implemented speed ups in the protein groups handling.
  • FEATURE IMPROVEMENT: Re-added the CV term for the Andromeda result files to the mzid export.
  • FEATURE IMPROVEMENT: Added tooltips to all validation plots.
  • FEATURE IMPROVEMENT: The methods report now includes the occurrence of the species.
  • FEATURE IMPROVEMENT: Updated the Example Dataset.
  • BUG FIX: Fixed issues with the high resolution exports of the plots in the Spectrum IDs tab.
  • BUG FIX: Added a temporary fix to the Progenesis export.
  • BUG FIX: Fixed a rare bug in the Confidence plot that occurred if two consecutive x-values were identical, which messed up the color coding.
  • BUG FIX: Fixed a bug in the #Unique PSMs plot in the Spectrum IDs tab.
  • BUG FIX: Fixed a possible null pointer in the protein inference peptide level dialog.
  • LIBRARY UPDATE: Updated utilities to version 4.1.13.

New in PeptideShaker 1.1.3 (Nov 4, 2015)

  • BUG FIX: Made the tool work on Java 1.6 again.
  • LIBRARY UPDATE: Updated utilities to version 4.1.8.

New in PeptideShaker 1.1.2 (Oct 18, 2015)

  • FEATURE IMPROVEMENT: Updated Ensembl Genomes to version 29
  • BUG FIX: Fixed a typo in the Annotation tab
  • LIBRARY UPDATE: Updated utilities to version 4.1.1

New in PeptideShaker 1.1.1 (Oct 18, 2015)

  • FEATURE IMPROVEMENT: Extended the user selected file methods to support suggested/default file names
  • LIBRARY UPDATE: Updated utilities to version 4.0.15

New in PeptideShaker 1.1.0 (Oct 18, 2015)

  • FEATURE IMPROVEMENT: Sped up the peptide to protein mapping.
  • BUG FIX: Corrected a bug in the use of the temp folder in command line
  • BUG FIX: Cleaned up some of the saving code which would not work without a waiting handler.
  • LIBRARY UPDATE: Updated omssa-parser to version 1.7.1.
  • LIBRARY UPDATE: Updated xtandem-parser to version 1.8.1.
  • LIBRARY UPDATE: Updated mascotdatfile to version 3.4.32.
  • LIBRARY UPDATE: Updated utilities to version 4.0.14.

New in PeptideShaker 1.0.9 (Oct 18, 2015)

  • LIBRARY UPDATE: Updated utilities to version 4.0.13.

New in PeptideShaker 1.0.8 (Oct 18, 2015)

  • LIBRARY UPDATE: Updated utilities to version 4.0.12.

New in PeptideShaker 1.0.7 (Oct 18, 2015)

  • BUG FIX: Corrected references to the outdated cps file format (now cpsx) for some of the command lines.

New in PeptideShaker 1.0.6 (Oct 18, 2015)

  • FEATURE IMPROVEMENT: Updated Ensembl to version 82
  • LIBRARY UPDATE: Updated utilities to version 4.0.10

New in PeptideShaker 1.0.5 (Oct 18, 2015)

  • FEATURE IMPROVEMENT: Made sure that the default PTM scoring is the same for both the GUI and the command line.
  • FEATURE IMPROVEMENT: Cleaned up the GUI for handling the PTM score selection.
  • LIBRARY UPDATE: Updated utilities to version 4.0.9.

New in PeptideShaker 1.0.4 (Oct 18, 2015)

  • BUG FIX: Fixed a bug in the mzIdentML export required to be compatible with the next Skyline release.
  • BUG FIX: Fixed a bug in the mzIdentML export where the file format for MyriMatch was set to tab delimited instead if mzid.

New in PeptideShaker 1.0.3 (Oct 18, 2015)

  • FEATURE IMPROVEMENT: Extended the timeout when mapping peptides to proteins.
  • FEATURE IMPROVEMENT: Improved the handling of the advanced search engine settings in the search parameters.
  • FEATURE IMPROVEMENT: Added the version number to the Welcome and About dialogs.
  • FEATURE IMPROVEMENT: Started improving and extending the protein inference dialogs.
  • LIBRARY UPDATE: Updated utilities to version 4.0.8.

New in PeptideShaker 1.0.2 (Oct 18, 2015)

  • FEATURE IMPROVEMENT: The XYPlottingDialog can now be opened by right clicking the column headers as well, and now opens the given column as a density chart as a default.
  • BUG FIX: Corrected a bug in the validation of PSMs that could cancel the processing.
  • BUG FIX: Fixed a possible null pointer in the output exporter.
  • BUG FIX: Fixed a possible null pointer in the PTM tab.
  • BUG FIX: Fixed bugs in the spectrum annotation menu where the mz ion table and bubble plot bar options could not be turned on.
  • LIBRARY UPDATE: Updated jsparklines to version 1.0.6.
  • LIBRARY UPDATE: Updated utilities to version 4.0.5.

New in PeptideShaker 1.0.1 (Oct 18, 2015)

  • BUG FIX: Fixed an issue with the wrapper in handling memory warnings for 32 bit Java 8.
  • LIBRARY UPDATE: Updated utilities to version 4.0.4.

New in PeptideShaker 1.0.0 (Aug 29, 2015)

  • NEW FEATURE: PTM masses are now set via the atomic composition.
  • NEW FEATURE: Added a spectrum export.
  • NEW FEATURE: Added the normalized spectrum counting to the export.
  • NEW FEATURE: Renamed .cps to .cpsx and .parameters to .par.
  • FEATURE IMPROVEMENT: Updated Ensembl to version 81.
  • FEATURE IMPROVEMENT: Made sure that the content of CV and user parameters is escaped for non-supported characters when exporting to XML.
  • FEATURE IMPROVEMENT: Improved the naming of the peptide and PSM subgroups in the Validation tab.
  • BUG FIX: Fixed bugs in PathSettingsCLI where the paths could not be set.
  • BUG FIX: Corrected potential concurrency issues.
  • BUG FIX: Fixed a bug in the Find feature where the peptide matches were added to the protein map, which resulted in them not being batch loaded.
  • LIBRARY UPDATE: Updated mascotdatfile to version 3.4.31.
  • LIBRARY UPDATE: Updated xtandem-parser to version 1.8.0.
  • LIBRARY UPDATE: Updated omssa-parser to version 1.7.0.
  • LIBRARY UPDATE: Updated utilities to version 4.0.0.

New in PeptideShaker 0.41.1 (Jul 1, 2015)

  • BUG FIX: Added support for loading Comet .pep.xml and Tide .txt files via the command line.

New in PeptideShaker 0.41.0 (Jun 30, 2015)

  • NEW FEATURE: Added support for raw files as spectrum input in PRIDE Reshake.
  • FEATURE IMPROVEMENT: Added support for zip files in the PRIDE Reshake.
  • BUG FIX: Fixed a bug in the PRIDE Reshake were canceling the public/private dialog still downloaded the public data.
  • LIBRARY UPDATE: Updated utilities to version 3.49.21.

New in PeptideShaker 0.40.4 (Jun 29, 2015)

  • FEATURE IMPROVEMENT: Added a "Download All" option to the files table in PRIDE Reshake.
  • BUG FIX: Fixed a bug that results in the PRIDE XML export not working.

New in PeptideShaker 0.40.3 (Jun 24, 2015)

  • BUG FIX: Corrected a bug in the validation of datasets with few hits.

New in PeptideShaker 0.40.2 (Jun 23, 2015)

  • FEATURE IMPROVEMENT:
  • Updated the Example Dataset
  • BUG FIX:
  • Fixed bugs in accessing private data in PRIDE Reshake.
  • Fixed a problem with the modification parsing in the mzid parser.
  • Fixed a possible multi threading issue when loading PSMs.
  • Fixed a bug in the GO mappings that resulted from a change in the Ensembl BioMart.
  • Corrected a bug where the assumptions validation level was not set.
  • LIBRARY UPDATE:
  • Updated web-service-model to version 0.2.12
  • Updated utilities to version 3.49.19

New in PeptideShaker 0.40.1 (Jun 23, 2015)

  • BUG FIX:
  • Avoided restoring the database connection when active during saving
  • LIBRARY UPDATE:
  • Updated utilities to version 3.49.9

New in PeptideShaker 0.40.0 (Jun 23, 2015)

  • FEATURE IMPROVEMENT:
  • Made sure the search settings are only editable when they can actually be edited
  • Made the Group Selection table in the Validation tab resize with the size of the frame
  • BUG FIX:
  • Fixed a bug in the validation of matches with uncommon distributions of decoys
  • Avoiding the creation of empty distributions
  • LIBRARY UPDATE:
  • Updated utilities to version 3.49.7

New in PeptideShaker 0.39.1 (Jun 23, 2015)

  • BUG FIX:
  • Fixed a bug in the progress display when validating matches
  • LIBRARY UPDATE:
  • Updated utilities to version 3.49.4

New in PeptideShaker 0.39.0 (Jun 23, 2015)

  • FEATURE IMPROVEMENT:
  • Parsing big mzIdentML files is now a lot faster and uses less memory
  • The validation QC filters are available again (beta)
  • Updated the Ensembl mappings to Ensembl 80
  • Made sure that all fragment ions are annotated when exporting to mzIdentML and PRIDE XML
  • BUG FIX:
  • Removed an unnecessary white space in the Peptide tag in the mzIdentML export
  • The modification specificity rules are now annotated correctly
  • Corrected bugs in PTM scoring
  • Implemented PTM specific sequence matching preferences.
  • LIBRARY UPDATE:
  • Updated utilities to version 3.49.2.

New in PeptideShaker 0.38.5 (May 18, 2015)

  • FEATURE IMPROVEMENT: Added support for parsing UniRef headers.
  • FEATURE IMPROVEMENT: Sped up the simplification of the protein groups.
  • LIBRARY UPDATE: Updated utilities to version 3.48.5.

New in PeptideShaker 0.38.4 (May 13, 2015)

  • NEW FEATURE: Added the option to start PeptideShaker with opening a zipped project from a URL.
  • NEW FEATURE: Made it possible to load zipped cps files via the PeptideShaker GUI command line.
  • FEATURE IMPROVEMENT: Leading and trailing white space is now removed before parsing FASTA headers.
  • LIBRARY UPDATE: Updated utilities to version 3.48.4.

New in PeptideShaker 0.38.3 (May 8, 2015)

  • BUG FIX: Fixed a bug in calculating the min/max mz value in a spectrum that occurred if the spectrum contained no peaks.
  • LIBRARY UPDATE: Updated utilities to version 3.48.2.

New in PeptideShaker 0.38.2 (May 4, 2015)

  • BUG FIX: Fixed a bug in the PTM scoring that occurred if using Java 7.
  • LIBRARY UPDATE: Updated utilities to version 3.48.1.

New in PeptideShaker 0.38.1 (Apr 27, 2015)

  • FEATURE IMPROVEMENT: Increased the precision of the PhosphoRS calculation.
  • BUG FIX: Fixed a bug in the spectrum annotation where the intensity limit was not set correctly.
  • BUG FIX: Fixed a bug in the CV term mapping for pyro-cmc.
  • BUG FIX: Fixed a bug in the saving that made it impossible to open saved projects.
  • BUG FIX: Fixed a backwards computability issue with the spectrum annotation.
  • BUG FIX: Fixed a bug in the spectrum annotation where the intensity limit was not set correctly.
  • BUG FIX: Corrected a bug in the setting of temporary folders.
  • LIBRARY UPDATE: Updated utilities to version 3.47.4.

New in PeptideShaker 0.38.0 (Apr 17, 2015)

  • FEATURE IMPROVEMENT: Multithreaded and thus sped up the validation, filtering and PTM scoring.
  • BUG FIX: Fixed issues in the PhosphoRS scoring.
  • BUG FIX: Corrected a threading issue in the validation of multiple mgf files.
  • BUG FIX: Corrected a memory leak, thus reducing the memory usage.
  • LIBRARY UPDATE: Updated utilities to version 3.47.1.

New in PeptideShaker 0.37.7 (Mar 27, 2015)

  • FEATURE IMPROVEMENT: Added a simpler way of resetting the spectrum annotation.
  • FEATURE IMPROVEMENT: Updated the Ensembl mappings to Ensembl 79.
  • BUG FIX: Fixed bugs in the peptide annotation where the location of the PTM site was incorrect.
  • BUG FIX: Fixed backwards compatibility issues in the TideParameters.
  • BUG FIX: Fixed a typo in the mass for the TMT130 reporter for 6plex TMT.
  • BUG FIX: Fixed bugs related to starting peptides and PSMs directly in the tables.
  • BUG FIX: The precursor m/z error filter is disabled if very few precursors are found.
  • LIBRARY UPDATE: Updated utilities to version 3.46.9.

New in PeptideShaker 0.37.6 (Mar 12, 2015)

  • FEATURE IMPROVEMENT: Added protein coverage for the main protein to the mzid export.
  • FEATURE IMPROVEMENT: Made it possible to cancel the batch loading in the table models.
  • FEATURE IMPROVEMENT: PSI-MS CV terms are now used for the fragment and precursor ions instead of PRIDE CV terms.
  • BUG FIX: Corrected a bug in the handling of default paths.
  • BUG FIX: Fixed a possible null pointer in the New Project dialog occurring if the search parameters did not have a FASTA file.
  • BUG FIX: Fixed a null pointer in the PTM tab that occurred if a variable PTM was not detected in any peptides.
  • BUG FIX: Fixed bugs in the equals methods for the Tide parameters.
  • BUG FIX: Removed the text from the precursor m/z field in the PSM tab in the FindDialog.
  • LIBRARY UPDATE: Updated utilities to version 3.45.44.

New in PeptideShaker 0.37.5 (Feb 18, 2015)

  • FEATURE IMPROVEMENT: Sped up the PSM exports.
  • FEATURE IMPROVEMENT: Improved the format selection when exporting.
  • BUG FIX: The progress bar is now displayed when unzipping PeptideShaker projects.
  • LIBRARY UPDATE: Updated utilities to version 3.45.35.

New in PeptideShaker 0.37.4 (Feb 17, 2015)

  • FEATURE IMPROVEMENT: It is now possible to open zipped PeptideShaker projects.
  • Follow-up, report, and mzidCLI also support zip file input.
  • FEATURE IMPROVEMENT: Improved the error handling for the command line mode.
  • FEATURE IMPROVEMENT: Made it possible to control the PSM sort order (score or retention time).
  • FEATURE IMPROVEMENT: Removed spaces from the name of the command line exports.
  • BUG FIX: Gene mapping files are now set when starting a command line.
  • BUG FIX: Fixed a bug where the project creation date was not set in the project details.
  • BUG FIX: Fixed a bug in the color coding of the PI column in the peptide table in the PTMs tab.
  • LIBRARY UPDATE: Updated utilities to version 3.45.33.

New in PeptideShaker 0.37.3 (Jan 30, 2015)

  • BUG FIX: Fixed a bug where neutral losses and reporter ions for user defined modifications disappeared.
  • LIBRARY UPDATE: Updated utilities to version 3.45.25.

New in PeptideShaker 0.37.2 (Jan 29, 2015)

  • BUG FIX: Fixed a bug in the pepxml reader where only the location of the first variable PTM in a peptide was correct.
  • BUG FIX: Fixed a bug in the parsing iTRAQ PTMs for X!Tandem data.
  • BUG FIX: Fixed bugs in the peptide PTM annotation and tooltips.
  • BUG FIX: Fixed a bug where score_neutral_losses had not been included in the list of supported parameters.
  • BUG FIX: Backward compatibility fixes.
  • LIBRARY UPDATE: Updated xtandem parser to version 1.7.18.
  • LIBRARY UPDATE: Updated utilities to version 3.45.24.

New in PeptideShaker 0.37.1 (Jan 24, 2015)

  • BUG FIX: The example dataset now works again.

New in PeptideShaker 0.37.0 (Jan 23, 2015)

  • NEW FEATURE: Added support for Tide. (beta)
  • FEATURE IMPROVEMENT: Added retention time to the mzid export.
  • FEATURE IMPROVEMENT: Updated Ensembl Genomes to version 25.
  • BUG FIX: In the New Project dialog loading a project without changing the search settings resulted in a missing FASTA file.
  • BUG FIX: In the Spectrum IDs tab the retention time conversion to minutes was not done for the minimum retention time value.
  • BUG FIX: In the mzid export a test CV term for the upcoming mzid 1.2 format changes was not removed.
  • BUG FIX: The accuracy slider in the spectrum panels had stopped working.
  • LIBRARY UPDATE: Updated utilities to version 3.45.19.

New in PeptideShaker 0.36.2 (Jan 17, 2015)

  • NEW FEATURE: Added the option to turn on/off the labels for the proteins and peptides in the protein inference graph.
  • NEW FEATURE: Added the option to select all proteins and peptides in the protein inference graph.
  • FEATURE IMPROVEMENT: Added the PeptideShaker PubMed ID to the methods export dialog.
  • BUG FIX: Fixed a bug in the PRIDE Reshake where the drop down menus in the project filtering dialog did not include all values.

New in PeptideShaker 0.36.1 (Jan 12, 2015)

  • FEATURE IMPROVEMENT: Updated the Example Dataset.

New in PeptideShaker 0.36.0 (Jan 10, 2015)

  • NEW FEATURE: Mirrored spectra support in the spectrum panels.
  • NEW FEATURE: Protein inference graphs in the protein inference dialogs.
  • NEW FEATURE: neXtProt FASTA headers can now be parsed.
  • FEATURE IMPROVEMENT: Multithreaded the scoring of PTMs.
  • FEATURE IMPROVEMENT: Iterating matches is now faster and requires less memory.
  • FEATURE IMPROVEMENT: Updated the gene and GO mappings to Ensembl version 78.
  • FEATURE IMPROVEMENT: Extended the file size columns in the PRIDE Reshake to "Size (MB)" and added sparklines.
  • FEATURE IMPROVEMENT: The downloading of the PRIDE projects in the Reshake is now done in batches and with a progress bar.
  • FEATURE IMPROVEMENT: Improved the way the selection of multiple PSMs are annotated in the spectrum panel border.
  • FEATURE IMPROVEMENT: Multiple selection in the PTM tables in the Search Settings Dialog no longer requires the use of the Ctrl key.
  • FEATURE IMPROVEMENT: Added the files reprocessed to the PRIDE Reshake report.
  • FEATURE IMPROVEMENT: Added the Enzymatic column to the ProteinInferencePeptideLevelDialog.
  • FEATURE IMPROVEMENT: Scientific notation is now used for the spectrum counting and intensity columns.
  • FEATURE IMPROVEMENT: Retention time is now given in minutes instead of seconds.
  • FEATURE IMPROVEMENT: The search parameters can now be extracted from the SearchGUI zip file.
  • FEATURE IMPROVEMENT: Minor improvements to the command line progress display.
  • FEATURE IMPROVEMENT: Made it possible to set the Java Home from the GUI.
  • FEATURE IMPROVEMENT: Added a shortcut to the PRIDE free text search in the Project filtering dialog in the PRIDE Reshake.
  • FEATURE IMPROVEMENT: Added CV term for the MyriMatch e-values to the mzid and PRIDE XML exports.
  • FEATURE IMPROVEMENT: Improved the selection of the search engine first hit.
  • FEATURE IMPROVEMENT: Added a dialog to edit the path preferences.
  • FEATURE IMPROVEMENT: Improved the handling of an exception at startup.
  • BUG FIX: Fixed a bug in the ExportGraphicsDialog where the last selected folder was not set.
  • BUG FIX: Fixed a bug where the tool failed to start if less than 1GB of memory was the maximum value allowed by the system.
  • BUG FIX: Fixed a bug in the Species Dialog where the text on the Update/Download button was not always correct.
  • BUG FIX: Fixed a minor GUI issue with the progress bar in the PRIDE Reshake.
  • BUG FIX: The sequence matching type is now set to amino acid when checking the fixed modifications.
  • BUG FIX: The PSM PTM mapping no longer ignores the user canceling the process in the waiting dialog.
  • BUG FIX: Fixed a bug with the renderer for the coverage column in the Fractions tab.
  • BUG FIX: Solved issues that resulted in the best match selection being different between Java 7 and 8.
  • LIBRARY UPDATE: Updated omssa-parser to version 1.6.12.
  • LIBRARY UPDATE: Updated xtandem-parser to version 1.7.17.
  • LIBRARY UPDATE: Updated mascotdatfile to version 3.4.28.
  • LIBRARY UPDATE: Updated utilities to version 3.45.18.

New in PeptideShaker 0.35.6 (Dec 2, 2014)

  • BUG FIX: Fixed an issue in the retrieval of public PRIDE projects.
  • BUG FIX: Fixed some possible issues in the Search Settings Dialog.
  • BUG FIX: Improved the handling of canceling the Search Settings and Processing Preferences dialogs.
  • LIBRARY UPDATE: Updated utilities to version 3.43.17.

New in PeptideShaker 0.35.5 (Nov 28, 2014)

  • BUG FIX: Corrected possible null pointers in the PRIDE XML and mzIdentML exports when processing Mascot scores.
  • BUG FIX: Fixed a bug in the conversion of mgf files for use in Comet where scan numbers resulted in it being impossible to map back to the original mgf file.
  • LIBRARY UPDATE: Updated utilities to version 3.43.16.

New in PeptideShaker 0.35.4 (Nov 19, 2014)

  • BUG FIX: Fixed a bug in adding decoy sequences to FASTA files containing headers without descriptions.

New in PeptideShaker 0.35.3 (Nov 18, 2014)

  • FEATURE IMPROVEMENT: Updated Ensembl Genomes to version 24, adding Zootermopsis nevadensis.
  • FEATURE IMPROVEMENT: Added a check for if SearchGUI is started from within a zip file.
  • FEATURE IMPROVEMENT: Added project tags to the project table in PRIDE Reshake.
  • FEATURE IMPROVEMENT: PRIDE Reshake: added sparkline for the file size column.
  • BUG FIX: Fixed a bug that resulted in all keys released when the PSM table had focus resulted in the spectrum annotation disappearing.
  • BUG FIX: Fixed a bug in the download of gene mappings for non-vertebrate species.
  • BUG FIX: Fixed some special case Derby shutdown and restart issues.
  • LIBRARY UPDATE: Added Jung2 dependencies.
  • LIBRARY UPDATE: Updated web-service-model to version 0.2.7.
  • LIBRARY UPDATE: Updated utilities to version 3.43.13.

New in PeptideShaker 0.35.2 (Nov 14, 2014)

  • FEATURE IMPROVEMENT: Multithreaded the import of PSMs.
  • FEATURE IMPROVEMENT: Minor speed improvements to the tag and peptide mapping.
  • FEATURE IMPROVEMENT: Disabled the batch peptide mapping on low memory setups.
  • BUG FIX: Fixed a bug in the appending of decoy sequence which in some cases altered the FASTA headers.
  • BUG FIX: Corrected a bug when working with very small databases.
  • LIBRARY UPDATE: Updated utilities to version 3.43.10.

New in PeptideShaker 0.35.1 (Oct 27, 2014)

  • BUG FIX: Fixed a bug in the auto update feature.
  • BUG FIX: Fixed some backward compatibility issues.
  • BUG FIX: Corrected a bug in the tag mapping.
  • LIBRARY UPDATE: Updated utilities to version 3.41.1.

New in PeptideShaker 0.35.0 (Oct 24, 2014)

  • NEW FEATURE: Comet (or more generally pep.xml) is now supported.
  • NEW FEATURE: Export features as Excel files.
  • NEW FEATURE: Added progress bar when zipping.
  • FEATURE IMPROVEMENT: Updated Ensembl Genomes to version 77, adding Vervet-AGM (Chlorocebus sabaeus).
  • FEATURE IMPROVEMENT: Improved the PTM annotation in tables and tooltips.
  • FEATURE IMPROVEMENT: Improved the handling of ambiguously localized PTMs.
  • FEATURE IMPROVEMENT: Improved the handling of complex PTM combinations.
  • FEATURE IMPROVEMENT: Improved the mapping of PTM scores at the peptide and protein level.
  • FEATURE IMPROVEMENT: Sped up the unzipping of projects in the New Project dialog.
  • FEATURE IMPROVEMENT: Sped up the PTM scoring.
  • FEATURE IMPROVEMENT: Sped up the peptide to protein mapping using multithreading.
  • FEATURE IMPROVEMENT: Added an OK/Cancel option to the save dialog appearing when exporting as zipping and the project is not saved.
  • FEATURE IMPROVEMENT: The list of database types and their occurrences is now included in the FASTA index.
  • FEATURE IMPROVEMENT: The "not a UniProt database" warning is now only shown if the main database type is not UniProt (hence adding custom headers from other databases is no longer an issue.)
  • FEATURE IMPROVEMENT: Renamed "no enzyme" to the more understandable "unspecific".
  • FEATURE IMPROVEMENT: Added support for unspecific cleavage for X!Tandem.
  • FEATURE IMPROVEMENT: Added a button for selecting search settings files in the New Project dialog.
  • BUG FIX: Fixed a bug in the use of the Ensembl gene mappings where a field had been renamed in the Ensembl web service.
  • BUG FIX: Corrected a bug impairing the import of results without decoys sequences.
  • BUG FIX: Fixed a bug in the New Project Dialog where canceling the unzipping still loaded the files.
  • BUG FIX: Fixed a bug in the Spectrum IDs tab where the fixed PTMs where always shown in the Spectrum Identification Results table.
  • BUG FIX: Fixed a bug that resulted in asking if the user wanted to save projects even though nothing had actually changed.
  • BUG FIX: Made sure that the correct sequence matching preferences are set when loading PeptideShaker projects.
  • BUG FIX: The PeptideShaker table in the Spectrum IDs tab now has the correct color for the links even when the row is selected.
  • BUG FIX: Fixed a minor bug in the table to file export for the PSM tables.
  • BUG FIX: The table to file exports now work again for the 3D Structures tab.
  • BUG FIX: Fixed a bug in writing of user parameters with values in the mzid export.
  • BUG FIX: Fixed a bug in the protein coverage panel where the whole protein and top down enzymes were not supported correctly.
  • LIBRARY UPDATE: Updated utilities to version 3.40.0.

New in PeptideShaker 0.34.0 (Sep 19, 2014)

  • FEATURE IMPROVEMENT: Improved the memory handling when loading data.
  • FEATURE IMPROVEMENT: Tried to speed up the loading of the data.
  • FEATURE IMPROVEMENT: Improved the handling of poorly localized PTMs.
  • FEATURE IMPROVEMENT: Tried to escape regular expressions in protein accession numbers.
  • FEATURE IMPROVEMENT: The waiting handler is now used when unzipping SearchGUI results in PeptideShaker.
  • FEATURE IMPROVEMENT: Fixed an issue with indexing mgf files with empty charge tags.
  • BUG FIX: Fixed a command line bug where the neutral losses were not set, resulting in slightly different results compared to the GUI.
  • BUG FIX: The sequence matching preferences now change according to the search parameters in the New Project Dialog.
  • BUG FIX: Fixed a bug where the show/hide of the fixed PTMs was not working as it should in all tabs.
  • BUG FIX: Corrected a bug where the cleaning of the obsolete protein trees was deleting all files in the folder.
  • LIBRARY UPDATE: Updated jsparklines to version 1.0.4.
  • LIBRARY UPDATE: Updated utilities to version 3.37.3.

New in PeptideShaker 0.33.6 (Sep 8, 2014)

  • FEATURE IMPROVEMENT: Updated to the new PRIDE web service model (needed for the PRIDE Reshake).
  • FEATURE IMPROVEMENT: Improved the parsing of headers of type genome translated to protein sequence.
  • LIBRARY UPDATE: Updated utilities to version 3.35.7.

New in PeptideShaker 0.33.5 (Sep 1, 2014)

  • FEATURE IMPROVEMENT: Improved the mapping to the protein 3D structure, resulting in a lot more mapped peptides.

New in PeptideShaker 0.33.4 (Sep 1, 2014)

  • FEATURE IMPROVEMENT: Changed the default PTM localization score to A-score.
  • FEATURE IMPROVEMENT: Added a special fix to the file import to escape Mascot mapping multiple fixed PTMs to the same residue.
  • FEATURE IMPROVEMENT: Updated the example dataset.
  • BUG FIX: Added a missing line break in the display of the extracted search parameters in PRIDE Reshake.
  • LIBRARY UPDATE: Updated utilities to version 3.35.6.

New in PeptideShaker 0.33.3 (Aug 30, 2014)

  • FEATURE IMPROVEMENT: Updated the getting started slides.
  • FEATURE IMPROVEMENT: Changed the default PRIDE export to mzIdentML.
  • FEATURE IMPROVEMENT: Made the progress bar when unzipping in the New Project dialog indeterminate.
  • FEATURE IMPROVEMENT: Hid the PRIDE generated mgf and mzTab files from the Reshake as the file links for these do not yet work.
  • BUG FIX: Fixed a bug in the setting of the species in the PRIDE Reshake.
  • BUG FIX: Fixed a bug with the use of custom PTM patterns.
  • BUG FIX: Fixed a bug with the tooltips for the PTMs in the Search Settings dialog.
  • BUG FIX: Fixed a bug in the default peptide export where additional empty columns where added messing.
  • LIBRARY UPDATE: Updated utilities to version 3.35.5.

New in PeptideShaker 0.33.1 (Aug 25, 2014)

  • FEATURE IMPROVEMENT: Updated Ensembl genomes to release 23.
  • BUG FIX: Fixed an issue in the auto update feature that could occur on specific client machine setups.
  • LIBRARY UPDATE: Updated utilities to version 3.35.3.

New in PeptideShaker 0.33.0 (Aug 25, 2014)

  • FEATURE IMPROVEMENT: Improvements in the peptide to protein inference.
  • FEATURE IMPROVEMENT: Peptides are now sorted before remapped to proteins, which should be quicker.
  • FEATURE IMPROVEMENT: Peptides with too many Xs are now filtered out.
  • FEATURE IMPROVEMENT: Several fixes related to running PeptideShaker from SearchGUI.
  • BUG FIX: Fixed a bug in the import in the New Project dialog where the listing the mgf files use) was not used if inside a zip file.
  • BUG FIX: Settings files from MS Amanda are no longer selected as identification files.
  • LIBRARY UPDATE: Updated mascotdatfile parser to version 3.4.25.
  • LIBRARY UPDATE: Updated omssa parser to version 1.6.9.
  • LIBRARY UPDATE: Updated xtandem parser to version 1.7.13.
  • LIBRARY UPDATE: Updated utilities to version 3.35.2.

New in PeptideShaker 0.32.3 (Aug 7, 2014)

  • NEW FEATURE: Added PTM tooltips in the tables in the SearchSettings dialog.
  • FEATURE IMPROVEMENT: Updated the Ensembl mappings to Ensembl 76 and added seven new species: duck, cave fish, flycatcher, cod, spotted gar, sheep and amazon molly.
  • FEATURE IMPROVEMENT: Improved the species names listed for vertebrates.
  • FEATURE IMPROVEMENT: Minor formatting improvement in the PeptideShakerMethods export.
  • BUG FIX: Fixed a bug where the search engine version numbers had gone missing when loading from mzid files.
  • LIBRARY UPDATE: Updated utilities to version 3.31.2

New in PeptideShaker 0.32.2 (Aug 2, 2014)

  • FEATURE IMPROVEMENT: Improved the MyriMatch support for terminal PTMs.
  • FEATURE IMPROVEMENT: Improved handling of end of file exceptions occurring when opening a corrupt project.
  • BUG FIX: Corrected a bug where the id filters were not always used.
  • LIBRARY UPDATE: Updated utilities to version 3.30.3.

New in PeptideShaker 0.32.1 (Aug 1, 2014)

  • NEW FEATURE: Added a new command line parameter called species_update to the PeptideShakerCLI to control the update of species and GO mappings.
  • FEATURE IMPROVEMENT: Updated the included human gene and GO mappings to Ensembl version 75.
  • FEATURE IMPROVEMENT: Improved the tag to protein mapping.
  • FEATURE IMPROVEMENT: Changed the order of the columns in the PSM export.
  • FEATURE IMPROVEMENT: Fixed issues with automatic update of gene and GO mappings when PeptideShaker was started from SearchGUI.
  • LIBRARY UPDATE: Updated utilities to version 3.30.1.

New in PeptideShaker 0.32.0 (Jul 30, 2014)

  • NEW FEATURE: Added support for MyriMatch.
  • NEW FEATURE: Support of zip export from the command line.
  • NEW FEATURE: Possible to import zipped SearchGUI projects.
  • NEW FEATURE: Added export functionality for search engine results.
  • FEATURE IMPROVEMENT: Made sure that the column in the exports are always in the same order.
  • FEATURE IMPROVEMENT: Made sure that the PeptideShaker log is saved even if the processing fails when run from SearchGUI.
  • BUG FIX: Fixed a bug in the PRIDE Reshake to support zipped mgf files.
  • BUG FIX: X!Tandem modifications are now added only if X!Tandem results are found.
  • BUG FIX: Corrected the output of the discarded protein mappings.
  • BUG FIX: Corrected minor HTML formatting issues in the help texts.
  • LIBRARY UPDATE: Updated jsparklines to version 0.8.0.
  • LIBRARY UPDATE: Updated utilities to version 3.29.7.

New in PeptideShaker 0.31.5 (Jun 26, 2014)

  • FEATURE IMPROVEMENT: Improved the way multiple species are supported in the UniProt link in the Reshake Settings dialog.
  • FEATURE IMPROVEMENT: The order of the search engines in the Spectrum IDs tab overview plots is now always the same.
  • FEATURE IMPROVEMENT: Added a remove all filters option in the main PRIDE Reshake window.
  • FEATURE IMPROVEMENT: Made sure that closing a dialog is always considered the same as clicking the cancel button.
  • FEATURE IMPROVEMENT: Extended the PRIDE Reshake help texts.

New in PeptideShaker 0.31.4 (Jun 25, 2014)

  • FEATURE IMPROVEMENT: Improved the Waiting Dialog to work better for big projects.
  • FEATURE IMPROVEMENT: Cleaned up the closing of the internal database connection.
  • FEATURE IMPROVEMENT: Improved the end of process messages in command lines.
  • BUG FIX: Fixed bugs in the mzid export, which now passes the PRIDE validation.
  • BUG FIX: Fixed a bug in the PRIDE XML export that resulted in the exported files not validating.
  • BUG FIX: Fixed a bug in the e-value parsing in the mzid reader.
  • LIBRARY UPDATE: Updated utilities to version 3.28.30.

New in PeptideShaker 0.31.3 (Jun 19, 2014)

  • FEATURE IMPROVEMENT: Improved the selections in the PRIDE Reshake Setup Dialog.
  • BUG FIX: Fixed a bug with case sensitivity in the PRIDE PTM mapping.
  • BUG FIX: Improved the PTM mapping during file import.
  • LIBRARY UPDATE: Updated utilities to version 3.28.22.

New in PeptideShaker 0.31.2 (Jun 19, 2014)

  • BUG FIX: Improved the PTM mapping during file import.
  • BUG FIX: Fixed bugs in the PRIDE Reshake.
  • LIBRARY UPDATE: Updated utilities to version 3.28.20.

New in PeptideShaker 0.31.1 (Jun 19, 2014)

  • BUG FIX: Fixed bugs in the PRIDE Reshake.

New in PeptideShaker 0.31.0 (Jun 18, 2014)

  • NEW FEATURE: Redesigned PRIDE Reshake.
  • BUG FIX: Fixed various bugs in the mzid export.
  • LIBRARY UPDATE: Updated utilities to version 3.28.18.

New in PeptideShaker 0.30.2 (Jun 14, 2014)

  • FEATURE IMPROVEMENT: Made it possible to extract the version number for MS Amanda csv files.
  • FEATURE IMPROVEMENT: Extended the PRIDE PTM mapping.
  • BUG FIX: Fixed a bug where PTM masses in MS Amanda files could not be processed if comma was used as the decimal symbol.
  • BUG FIX: Fixed typos in the spectrum panel help text.
  • LIBRARY UPDATE: Updated utilities to version 3.28.16.

New in PeptideShaker 0.30.1 (Jun 6, 2014)

  • BUG FIX: Fixed a bug in the parsing of terminal modifications for MS Amanda.
  • BUG FIX: Fixed a bug where MS Amanda results files where not recognized if PeptideShaker was started from SearchGUI.
  • LIBRARY UPDATE: Updated utilities to version 3.28.11.

New in PeptideShaker 0.30.0 (Jun 5, 2014)

  • NEW FEATURE: mzIdentML export.
  • NEW FEATURE: Import of mzid files from other algorithms than MS-GF+. (beta)
  • FEATURE IMPROVEMENT: Sped up the indexing of mgf files.
  • FEATURE IMPROVEMENT: Improved and extended the Methods Section export.
  • FEATURE IMPROVEMENT: Better formatting of long lines in the waiting handler.
  • FEATURE IMPROVEMENT: Removed the Venn diagram from the Spectrum IDs tab, as they only supported max three search engines.
  • BUG FIX: Fixed issues with opening cps files created on other platforms.
  • BUG FIX: Tried to make the table models more robust against database connection dropped issues.
  • LIBRARY UPDATE: Removed charts4j as a dependency.
  • LIBRARY UPDATE: Removed jdas as a dependency.
  • LIBRARY UPDATE: Updated utilities to version 3.28.10.

New in PeptideShaker 0.29.1 (May 21, 2014)

  • BUG FIX: Fixed a bug with the gene/GO downloads for non-vertebrate species.
  • LIBRARY UPDATE: Updated utilities to version 3.26.41.

New in PeptideShaker 0.29.0 (May 21, 2014)

  • FEATURE IMPROVEMENT: Improved the handling of terminal PTMs.
  • FEATURE IMPROVEMENT: Improved the canceling of the species and GO downloads.
  • FEATURE IMPROVEMENT: Changed the message given if the FASTA file is not found from an error message to a warning message.
  • FEATURE IMPROVEMENT: Updated the Java Settings dialogs.
  • FEATURE IMPROVEMENT: Added a longer time out for some of the IO intensive methods, which could result in issues on slower systems.
  • BUG FIX: Corrected a bug where the PSM precursor errors were sometime added twice.
  • BUG FIX: Corrected an error in the PRIDE XML export.
  • BUG FIX: Fixed a bug in the handling of protein keys that are too long for the database.
  • BUG FIX: Fixed a bug in the peptide filters where the modifications where not set correctly.
  • BUG FIX: Fixed a bug in the sorting in the coverage column.
  • BUG FIX: Fixed a bug in the progress display when downloading gene/GO details.
  • LIBRARY UPDATE: Updated jsparklines to version 0.6.7.
  • LIBRARY UPDATE: Updated utilities to version 3.26.39.

New in PeptideShaker 0.28.3 (May 7, 2014)

  • BUG FIX: Fixed a bug in the sequence coverage panel when using semi specific enzymes.
  • BUG FIX: Fixed a case sensitivity bug in the Find feature in the Spectrum IDs tab.

New in PeptideShaker 0.28.2 (May 7, 2014)

  • FEATURE IMPROVEMENT: Simplified the way SearchGUI can be downloaded and updated from within PeptideShaker.
  • FEATURE IMPROVEMENT: Made it possible to rely on spectrum indexes if an mzid file does not contain the spectrum titles.
  • FEATURE IMPROVEMENT: Updated the example dataset.
  • BUG FIX: Fixed a bug in the updating of the sequence coverage panel where the protein accession was used instead of the protein group key.
  • BUG FIX: Added a print out of the stack trace if the estimateSpectrumCounting method finds a non-existing protein key.
  • LIBRARY UPDATE: Updated utilities to version 3.26.33.

New in PeptideShaker 0.28.1 (Apr 30, 2014)

  • NEW FEATURE: Added new command line options for path configuration.
  • NEW FEATURE: Added a first draft of a methods section writing dialog. (beta)
  • NEW FEATURE: Made the species download available from the command line.
  • NEW FEATURE: Added a reset thresholds button in the Validation tab.
  • FEATURE IMPROVEMENT: The sequence coverage now also shows the doubtful and not validated matches.
  • FEATURE IMPROVEMENT: Added a check and warning if using Java 1.5 or 1.6.
  • FEATURE IMPROVEMENT: Renamed the Reshake button in the WelcomeDialog to PRIDE Reshake.
  • FEATURE IMPROVEMENT: Added the algorithm scores in the export.
  • FEATURE IMPROVEMENT: The validation thresholds are now displayed in the match validation dialog.
  • FEATURE IMPROVEMENT: Made it possible to use the escape button to close the New Project and Getting Started dialogs.
  • FEATURE IMPROVEMENT: Made it possible to cancel the PDB mapping downloads.
  • FEATURE IMPROVEMENT: Added the possibility for the user to turn on and off the auto update.
  • BUG FIX: Fixed a bug in the PtmSiteInferenceDialog where the PTM localization in the two tables were not the same.
  • BUG FIX: Fixed a bug in the PTM panel where the orange icon got stuck.
  • BUG FIX: Added .mzid and .cvs to PeptideShaker command line option description.
  • BUG FIX: Fixed a bug in the MzIdentML Export Dialog where the convert button could be clicked before an output file was selected.
  • BUG FIX: Fixed some issues with incorrect table references in the Overview and 3D Structures tab.
  • BUG FIX: Fixed problems with turning the sparklines on/off.
  • LIBRARY UPDATE: Updated jsparklines to version 0.6.6.
  • LIBRARY UPDATE: Updated utilities to version 3.26.28.

New in PeptideShaker 0.28.0 (Apr 12, 2014)

  • NEW FEATURE: Added support for MS Amanda (beta).
  • FEATURE IMPROVEMENT: The PSM scoring now adapts to the different fractions when possible.
  • BUG FIX: Fixed problems with creating terminal PTMs with empty modification patterns.
  • BUG FIX: Fixed a bug in the table model in the Modifications tab.
  • LIBRARY UPDATE: Updated utilities to version 3.26.14.

New in PeptideShaker 0.27.4 (Apr 2, 2014)

  • BUG FIX: Fixed a bug in the PRIDE export where the PRIDE XML validation failed.
  • BUG FIX: Fixed a bug in the export of accession numbers in the Annotation panel where also the validation status was included.

New in PeptideShaker 0.27.3 (Apr 1, 2014)

  • BUG FIX: Fixed a bug in the PRIDE export where the PRIDE XML validation failed.
  • BUG FIX: Fixed a bug in the export of accession numbers in the Annotation panel where also the validation status was included.

New in PeptideShaker 0.27.2 (Mar 31, 2014)

  • FEATURE IMPROVEMENT: Updated the example dataset.
  • FEATURE IMPROVEMENT: The first number in the Spectrum IDs tab border title is now the number of validated PSMs.
  • FEATURE IMPROVEMENT: Updated the getting started slides to include MS-GF+.
  • BUG FIX: Fixed a bug in the protein filters that resulted in all protein filters returning false.
  • BUG FIX: The Spectrum IDs tab is now updated if the validation changes in the Validation tab.
  • BUG FIX: Fixed a bug in the SpectrumIDs tab where the spectrum panel border was not reset when selecting a spectrum without a PSM.
  • BUG FIX: Tried to fix a possible null pointer in the peptide border title.
  • LIBRARY UPDATE: Updated utilities to version 3.25.15.

New in PeptideShaker 0.27.1 (Mar 28, 2014)

  • BUG FIX: Fixed a bug in the method for getting all non fixed modifications.
  • LIBRARY UPDATE: Updated utilities to version 3.25.14.

New in PeptideShaker 0.27.0 (Mar 26, 2014)

  • NEW FEATURE: Added support for MS-GF+.
  • NEW FEATURE: Added PSM quality filters.
  • FEATURE IMPROVEMENT: Added an ID software color legend below the Spectrum Identification Results table in the Spectrum IDs tab.
  • FEATURE IMPROVEMENT: Added search engine specific file filters to the New Project dialog.
  • FEATURE IMPROVEMENT: Minor GUI fixes to the protein inference dialogs, also added the number of rows to the table border titles.
  • FEATURE IMPROVEMENT: Improved the display of non confident PTM sites.
  • FEATURE IMPROVEMENT: Improved the display of the protein table when scrolling.
  • FEATURE IMPROVEMENT: Added the protein description in the peptide output.
  • BUG FIX: Fixed a problem with parsing FASTA files containing headers with empty sequences.
  • BUG FIX: Fixed a bug in the settings dialog that closed the dialog if the user canceled the save as dialog.
  • LIBRARY UPDATE: Updated utilities to version 3.25.12.

New in PeptideShaker 0.26.2 (Mar 7, 2014)

  • BUG FIX: Fixed a icon image bug that occurred if one used the New Project option in the main frame.

New in PeptideShaker 0.26.1 (Mar 6, 2014)

  • FEATURE IMPROVEMENT: Added a high resolution option for the spectrum annotation.
  • FEATURE IMPROVEMENT: Added more advanced scrolling support for the tables.
  • BUG FIX: Fixed a bug in the parsing of FASTA files with unknown headers.
  • BUG FIX: Fixed errors with the TMT 10-plex reporter ion masses.
  • LIBRARY UPDATE: Updated utilities to version 3.23.18.

New in PeptideShaker 0.26.0 (Mar 4, 2014)

  • FEATURE IMPROVEMENT: The loading of search results is now a lot quicker!
  • FEATURE IMPROVEMENT: Reformatted the Spectrum IDs tab.
  • FEATURE IMPROVEMENT: Mass errors are no longer in absolute values.
  • FEATURE IMPROVEMENT: Updated the TMT modifications to support the new TMT 10-plex.
  • FEATURE IMPROVEMENT: Tried to improve the x-axis for the MS2 Quant QC plot.
  • FEATURE IMPROVEMENT: Improved the robustness of the FDR estimation.
  • FEATURE IMPROVEMENT: Replaced PSI-MOD modification mappings with Unimod.
  • FEATURE IMPROVEMENT: Added table column header tooltips for the MatchValidationDialog.
  • BUG FIX: Corrected a bug in the import of the quick pyro and acetyl options of X!Tandem.
  • BUG FIX: Separated the PTM mass tolerance from the fragment mass tolerance in the PTM mapping of Mascot and X!Tandem, that could result in protein inference issues.
  • BUG FIX: Fixed a bug in the psm validation code that resulted in the loading being canceled if an mgf file contained no validated psms.
  • BUG FIX: Fixed a bug in the progress bar when loading spectrum files when loading a project.
  • BUG FIX: Fixed a bug where using the Save option in the Save Dialog resulted in a null pointer if the project was not previously saved.
  • BUG FIX: Fixed some issues with the hiding of the jsparklines.
  • BUG FIX: Corrected a bug in the custom PSM and peptide exports.
  • BUG FIX: Unified the separators in peptide exports.
  • BUG FIX: Improved the handling of protein tree creation crashes.
  • BUG FIX: Fixed a bug where the orange waiting icon was not used in the New Project dialog when updating the species.
  • BUG FIX: If the protein mapping is not present when calling the isDecoy method of a peptide, the peptide will be mapped.
  • BUG FIX: Fixed a minor GUI bugs in the Peptide tab in the Export dialog.
  • BUG FIX: Corrected minor bugs in the exports.
  • BUG FIX: Fixed a bug in the table column header tooltips for the ProteinInferencePeptideLevelDialog.
  • BUG FIX: Fixed is a problem with unmapped search engine advocates.
  • LIBRARY UPDATE: Updated utilities to version 3.23.13.

New in PeptideShaker 0.25.2 (Feb 11, 2014)

  • BUG FIX: Fixed a bug in the report command line export, where two options with the same name (-out) could get confused

New in PeptideShaker 0.25.1 (Feb 11, 2014)

  • BUG FIX: Fixed a memory issue occurring during the protein database loading for Mac and Linux.
  • BUG FIX: Added a test for no enzyme set, as old search parameter files could result in a null pointer exception.
  • BUG FIX: Tried to get rid of one of the reasons for the "please contact the developers" message when moving around in the Overview tab.
  • LIBRARY UPDATE: Updated utilities to version 3.21.30.

New in PeptideShaker 0.25.0 (Feb 5, 2014)

  • NEW FEATURE: The versions of the search engines are now stored in the project details and showed in the project report.
  • NEW FEATURE: The PeptideShaker report is now saved together with the cps file.
  • NEW FEATURE: Added the possibility to create identification parameters files from the command line.
  • NEW FEATURE: Added a simple swath export.
  • NEW FEATURE: New auto updater feature for PeptideShaker and SearchGUI.
  • NEW FEATURE: Added an "Open Example Dataset" option to the file menu.
  • FEATURE IMPROVEMENT: Improved the memory handling.
  • FEATURE IMPROVEMENT: The number of confident/doubtful proteins/peptides/PSMs can now be changed by the user.
  • BUG FIX: Fixed a bug in the SpectrumFactory where one ended up with partial index files if the process was canceled by the user.
  • BUG FIX: Fixed a bug in the sorting of the #Peptides and #Spectra columns, causing the sorting to be fairly random.
  • BUG FIX: Corrected a bug resulting in a null pointer when the A-score was used and only multiply modified peptides are found at a given charge.
  • BUG FIX: Corrected a bug where modifications were disappearing from the GUI.
  • BUG FIX: Fixed a backwards compatibility issues with the precursor accuracy in the search parameters.
  • BUG FIX: Fixed a bug in the peptide keys used in the spectrum and Progenesis exports.
  • LIBRARY UPDATE: Updated xtandem parser to version 1.7.7.
  • LIBRARY UPDATE: Updated omssa parser to version 1.6.3.
  • LIBRARY UPDATE: Updated mascotdatfile to version 3.4.19.
  • LIBRARY UPDATE: Updated utilities to version 3.21.26.
  • LIBRARY UPDATE: Updated jsparklines to version 0.6.5.

New in PeptideShaker 0.24.3 (Jan 31, 2014)

  • BUG FIX: Corrected the peptide key used in the spectrum and Progenesis exports.

New in PeptideShaker 0.24.2 (Jan 31, 2014)

  • LIBRARY UPDATE: Updated ols-dialog to version 3.4.2, fixing a bug in the View Term Hierarchy Graph.

New in PeptideShaker 0.24.1 (Jan 31, 2014)

  • BUG FIX: Fixed an issue with the fragment ion annotation in the PRIDE export.
  • LIBRARY UPDATE: Updated utilities to version 3.20.3.

New in PeptideShaker 0.24.0 (Jan 9, 2014)

  • NEW FEATURE: Validated protein, peptide and PSM matches are now also filtered for quality and marked if doubtful, e.g., less than 2 peptides detected for a given protein.
  • NEW FEATURE: The user can now click the id and spectrum files text field in the New Project dialog to see and edit the list of selected files.
  • FEATURE IMPROVEMENT: The peptide and spectrum count columns plus the QC plots now include the new "doubtful" category.
  • FEATURE IMPROVEMENT: PeptideShaker now corrects for input where the same ptm is found multiple times.
  • FEATURE IMPROVEMENT: PeptideShaker projects zipped on Windows can now also be opened on Mac and Linux.
  • FEATURE IMPROVEMENT: Improved the way export to zip is performed if the project is not already saved.
  • BUG FIX: Fixed an issue where the height if the spectrum sub plots ended up as too small if hidden and then re-displayed.
  • BUG FIX: Corrected bugs in the sparklines for the protein table in the GO and Fractions tabs.
  • BUG FIX: Fixed bugs in the hide/show of the Score/Confidence column.
  • BUG FIX: Fixed a bug in the jump to feature where strings that could not be converted to amino acid characters broke the search.
  • BUG FIX: Corrected a typo impairing the calculation of NSAF indexes.
  • LIBRARY UPDATE: Updated jsparklines to version 0.6.4.
  • LIBRARY UPDATE: Updated xtandem parser to version 1.7.5.
  • LIBRARY UPDATE: Updated utilities to version 3.20.2.

New in PeptideShaker 0.23.0 (Dec 10, 2013)

  • NEW FEATURE: Improved protein inference handling, i.e., peptide to protein mapping.
  • NEW FEATURE: Added a first version of a basic graph database export for Cytoscape, Gephi and Neo4j to the follow up export dialog.
  • NEW FEATURE: A low memory and Java version check is now performed when starting the tool and a warning is shown in the waiting dialog.
  • NEW FEATURE: The species can now be provided as input to SearchGUI (for use when reprocessing in PRIDE).
  • FEATURE IMPROVEMENT: Extended the list of PRIDE project available in the reshaking.
  • FEATURE IMPROVEMENT: Improved the Search Settings dialog, which is now identical to the one in SearchGUI and also displays the fixed PTMs.
  • FEATURE IMPROVEMENT: Reshake now supports a default enzyme mapping, and user selection of enzyme if the mapping fails. Also now supports multiple enzymes.
  • FEATURE IMPROVEMENT: Added MD Score localization to the to the export.
  • FEATURE IMPROVEMENT: Better support for semi-specific enzymes.
  • FEATURE IMPROVEMENT: Updated the tips of the day.
  • FEATURE IMPROVEMENT: Updated the getting started slides.
  • FEATURE IMPROVEMENT: Added some options to the fragment ion export.
  • FEATURE IMPROVEMENT: The intensity, mass error and bubble plots now include all currently selected ions, and not only the default a-c and x-z ions.
  • FEATURE IMPROVEMENT: Mgf validation is now performed in SearchGUI, and the information is saved so that is does not have to be done more than once.
  • FEATURE IMPROVEMENT: Added the possibility to score PTMs with phosphoRS.
  • FEATURE IMPROVEMENT: Added the number of missed cleavages in the peptide and PSM exports.
  • FEATURE IMPROVEMENT: If the id file parsers run out of memory this is now picked up, the search canceled and a message shown to the user.
  • FEATURE IMPROVEMENT: Slightly reduced the height needed for the content in the Annotation tab.
  • FEATURE IMPROVEMENT: Got rid of the derby.log file.
  • FEATURE IMPROVEMENT: Improved the default name of the search results folder for reshake results.
  • FEATURE IMPROVEMENT: Implemented memory usage reduction during PSM processing.
  • FEATURE IMPROVEMENT: Closing the Reshake dialog before starting the reshaking now takes the user back to the Welcome dialog.
  • FEATURE IMPROVEMENT: Sequence coverage is now estimated/displayed using indistinguishable amino acids.
  • FEATURE IMPROVEMENT: Replaced the FTP file downloaded with a version that is faster on the EBI wireless.
  • FEATURE IMPROVEMENT: Added a check if the PRIDE XML file exists locally before downloading the file from the FTP server.
  • BUG FIX: Fixed various minor bugs in the PRIDE export dialogs.
  • BUG FIX: Fixed a bug in the mass error type tooltip in the PSM table.
  • BUG FIX: Enzymes without a value (i.e., an enzyme name) in the PRIDE XML file no longer breaks the reshake feature.
  • BUG FIX: Semicolons are no longer supported in project and sample name (as these result in issues with Derby).
  • BUG FIX: Fixed a bug where the FDR corrected p-values of the hypergeometric test in the GO tab could become bigger than 1.
  • BUG FIX: Fixed a bug in the protein QC plots where the numbers didn't add up.
  • BUG FIX: Corrected bugs in the Follow Up command line for the accession and inclusion list export options.
  • BUG FIX: Fixed various bugs in the command line reports and follow up analysis exports.
  • BUG FIX: Fixed a bug where empty decoy tags were not handled correctly.
  • BUG FIX: Fixed an issue for the peptide export where shared peptides did not list all parent proteins.
  • BUG FIX: Fixed a bug where TMT reporter ions were not displayed again if hidden as these had no variable modifications with reporter ions, unlike iTRAQ.
  • BUG FIX: Fixed a bug with changing the reporter and neutral ions in the PtmDialog.
  • BUG FIX: Fixed various minor GUI issues in the Fractions tab.
  • BUG FIX: Fixed a bug where the project could not be saved after loading results in the Fractions tab.
  • BUG FIX: Fixed a bug with the handling of corrupt PRIDE PTM mapping files.
  • LIBRARY UPDATE: Removed sqlite as a transitive dependency.
  • LIBRARY UPDATE: Removed twitter4j-core as a dependency.
  • LIBRARY UPDATE: Updated ols-dialog to version 3.4.1.
  • LIBRARY UPDATE: Updated omssa parser to version 1.6.1.
  • LIBRARY UPDATE: Updated xtandem parser to version 1.7.3.
  • LIBRARY UPDATE: Updated utilities to version 3.19.5.

New in PeptideShaker 0.22.6 (Aug 13, 2013)

  • FEATURE IMPROVEMENT:
  • Added an edit modifications option to the SearchPreferencesDialog.
  • Removed spectrum file renaming for Mascot Distiller files.
  • BUG FIX:
  • Fixed a bug in the handling of missing mgf files.
  • LIBRARY UPDATE:
  • Updated omssa parser to version 1.5.13.
  • Updated mascotdatfile parser to version 3.4.15.
  • Updated utilities to version 3.14.19.

New in PeptideShaker 0.22.5 (Jul 15, 2013)

  • FEATURE IMPROVEMENT: Improved the progress display in the Progenesis export.
  • BUG FIX: Fixed an issue with the sorting order indicator icons.
  • BUG FIX: Made the tool Java 6 compatible again.
  • LIBRARY UPDATE: Updated omssa parser to version 1.5.12.
  • LIBRARY UPDATE: Updated xtandem parser to version 1.6.2.
  • LIBRARY UPDATE: Updated mascotdatfile parser to version 3.4.14.
  • LIBRARY UPDATE: Updated utilities to version 3.14.16.

New in PeptideShaker 0.22.4 (Jul 5, 2013)

  • NEW FEATURE: Extended the species support.
  • FEATURE IMPROVEMENT: Added fragment ion annotation in the exports as well as modified sequence.
  • FEATURE IMPROVEMENT: Renamed the Validation plot from Benefit/Cost to Cost/Benefit.
  • BUG FIX: Fixed a bug in the PSM table where the row selection was not cleared before the table was updated.
  • LIBRARY UPDATE: Updated utilities to version 3.14.1.

New in PeptideShaker 0.22.3 (Jun 27, 2013)

  • FEATURE IMPROVEMENT:
  • Added gene name and chromosome number to the default protein report.
  • Gene name and chromosome is no longer exported for decoy sequences.
  • Improved the way the progress bar is canceled when the Progenesis export is done.
  • The Validation settings not applied warning is now only shown when leaving the Validation tab.
  • BUG FIX:
  • Fixed a bug in the Progenesis export where a method was called recursively without stop.
  • Fixed bugs in the custom exports for gene name and chromosome where column separators where missing.
  • The simple protein description now include the "-reverse" tag for decoy sequences.
  • Tried to fix the reason for the table model number conversion exception being thrown.
  • LIBRARY UPDATE:
  • Updated utilities to version 3.13.56.

New in PeptideShaker 0.22.2 (Jun 27, 2013)

  • NEW FEATURE:
  • The tool now checks if 64 bit Java is used the first time PeptideShaker is started.
  • FEATURE IMPROVEMENT:
  • Added gene details in the default custom exports.
  • BUG FIX:
  • Corrected a bug in the Progenesis export.
  • Fixed a bug where the coverage panel had gone missing.
  • Fixed a bug in the gene name comparison as part of the protein inference grouping where gene names of length 1-2 resulted in issues.
  • Corrected bugs in the custom exports.
  • LIBRARY UPDATE:
  • Updated utilities to version 3.13.55.

New in PeptideShaker 0.22.1 (Jun 27, 2013)

  • FEATURE IMPROVEMENT:
  • Cleaned up the use of the New Project dialog when called from the Welcome dialog.
  • BUG FIX:
  • Fixed a bug where missing mgf files that had to be relocated where not indexed.
  • Fixed a bug in the code for locating a FASTA file if it was not in the location given in the cps file.
  • Fixed a bug that made is impossible to set the species if no species was selected when loading the project.
  • Handled a possible null pointer in the Overview tab.

New in PeptideShaker 0.22.0 (Jun 25, 2013)

  • NEW FEATURE:
  • The tool now checks if 64 bit Java is used the first time PeptideShaker is started.
  • FEATURE IMPROVEMENT:
  • Added gene details in the default custom exports.
  • BUG FIX:
  • Corrected a bug in the Progenesis export.
  • Fixed a bug where the coverage panel had gone missing.
  • Fixed a bug in the gene name comparison as part of the protein inference grouping where gene names of length 1-2 resulted in issues.
  • Corrected bugs in the custom exports.
  • LIBRARY UPDATE:
  • Updated utilities to version 3.13.55.

New in PeptideShaker 0.21.0 (Jun 6, 2013)

  • NEW FEATURE:
  • Species is now selected when creating a project.
  • Added a species tag to the command line for setting the species.
  • The protein evidence level is now used when selecting the "main match" in a protein group. (UniProt databases only.)
  • FEATURE IMPROVEMENT:
  • The species selection is now stored in the project.
  • Removed the species selection section in the GO tab.
  • Updated the Ensembl species list.
  • Added a check for duplicate spectrum titles when selecting mgf files.
  • Replace protein evidence level number with text in the protein inference dialogs.
  • Added chromosome mapping to the protein inference dialogs.
  • The gene name is now used when comparing the proteins in a protein group, if different or missing the description is still used. (UniProt databases only.)
  • Added a more visible "add new report type" option to the custom export dialog.
  • BUG FIX:
  • Fixed a bug with the hiding and reshowing of the spectrum panel in the Overview tab.
  • Fixed a bug with updating in the gene and GO mappings where a file could not be deleted.
  • Fixed some resizing issues in the PRIDE annotation dialogs.
  • Improved the handling of errors occurring when establishing a database connection when importing a PeptideShaker project.
  • Fixed the background color for the ProjectDetailsDialog.
  • Fixed a bug in the peptide selection when changing the protein selection where the selected row was not made visible.
  • Tried to fix issues related to maintaining the sorting in the tables.
  • Fixed a problem that could occur with the size of the Venn diagrams in the Spectrum IDs tab.
  • Fixed a bug in the setting of the OMSSA indexes for older search parameter files.
  • Fixed a bug with the icon not turning gray again after selecting a peptide in the Overview tab.
  • LIBRARY UPDATE:
  • Updated mascot dat file to version 3.4.11.
  • Updated utilities to version 3.13.30.

New in PeptideShaker 0.20.1 (May 21, 2013)

  • BUG FIX:
  • Fixed a bug where white space was not allowed in the installation path.
  • LIBRARY UPDATE:
  • Updated utilities to version 3.13.18.

New in PeptideShaker 0.20.0 (May 21, 2013)

  • NEW FEATURE:
  • New self updating tables with better support for bigger datasets.
  • Added a chromosome mapping column to the protein table.
  • FEATURE IMPROVEMENT:
  • Improved the peptide inference method for miscleaved peptides.
  • Sped up the PTM inference processing.
  • Improved the way extracted PRIDE search parameters are displayed.
  • The waiting dialog now has "close when complete" turned on as the default.
  • If a bubble plot displays more that 20 spectra the plot legend is now hidden as to not cover too much of the plotting area.
  • Re-added the PRIDE and project zip exports to the Export menu.
  • Improve the way selections are handled across the tabs.
  • BUG FIX:
  • Fixed a problem with starting the tool on the latest Java release.
  • Fixed a bug where the tooltips and popup menus in the sequence coverage plot included all peptides even when a subset (enzymatic/non-enzymatic) was selected.
  • Added a check that the matches folder exists before deleting or listing it's files.
  • Fixed an issue with locating SearchGUI via the PrideSearchParametersDialog if the provided SearchGUI folder could not be found.
  • Removed a GUI references in the FileImporter class, improving the command line support.
  • LIBRARY UPDATE:
  • Updated jsparklines to version 0.6.0.
  • Updated utilities to version 3.13.16.

New in PeptideShaker 0.19.3 (Apr 3, 2013)

  • FEATURE IMPROVEMENT: Further developed the Progenesis export with more options.
  • LIBRARY UPDATE: Updated xtandem-parser to version 1.5.14, fixing a problem with the parsing of spectrum titles with retention time in them.
  • LIBRARY UPDATE: Updated utilities to version 3.11.29.

New in PeptideShaker 0.19.2 (Apr 3, 2013)

  • BUG FIX: Fixed a bug that made it impossible to change the memory settings.
  • BUG FIX: Fixed a typo in the PRIDE Reshake dialog, PumMed > PubMed.
  • LIBRARY UPDATE: Updated utilities to version 3.11.27.

New in PeptideShaker 0.19.1 (Apr 3, 2013)

  • NEW FEATURE: PRIDE Reshake feature added for re-analyzing data in PRIDE. (beta)
  • NEW FEATURE: Created PRIDE XML files are now schema validated with user feedback if the validation fails.
  • NEW FEATURE: Added a new Save & Export dialog.
  • NEW FEATURE: Added simple data filters for the Plotting Dialog.
  • NEW FEATURE: Added a new total peptide count per fraction plot to the fraction tab.
  • NEW FEATURE: Added an option for exporting the extended spectrum panel (the spectrum and the corresponding plots) in the Overview tab as a single figure.
  • NEW FEATURE: A new custom report export option (beta).
  • FEATURE IMPROVEMENT: Search engines assumptions are now compared without accounting for PTM localization.
  • FEATURE IMPROVEMENT: The observed molecular weights are now recalculated if the user hides proteins via the FiltersDialog.
  • FEATURE IMPROVEMENT: Improved backward compatibility for older projects.
  • FEATURE IMPROVEMENT: Updated the Getting Started slides.
  • FEATURE IMPROVEMENT: Added a warning in case too many hits are kicked out by the filter.
  • FEATURE IMPROVEMENT: Cleaned up the error given if a protein cannot be found in the FASTA file.
  • FEATURE IMPROVEMENT: Added complete protein group (in alphabetical order) as an export option.
  • FEATURE IMPROVEMENT: The parsing of mgf (and mzml) files now support both upper and lower case file extensions.
  • FEATURE IMPROVEMENT: Added retention time to the PRIDE export.
  • BUG FIX: Removed some incorrect tooltips in the new project dialog.
  • BUG FIX: Fixed an inconsistency in the protein inference class descriptions used.
  • BUG FIX: Fixed a bug in the remapping of PTMs.
  • BUG FIX: Fixed a minor bug in the project export option where extra tabs were added at the end of each line for the PSMs.
  • BUG FIX: Fixed issues detected by FindBugs.
  • LIBRARY UPDATE: Updated MascotDatFile to version 3.4.10.
  • LIBRARY UPDATE: Updated pride-jaxb to version 1.0.9.
  • LIBRARY UPDATE: Updated utilities to version 3.11.25.

New in PeptideShaker 0.19.0 (Feb 7, 2013)

  • New features:
  • Added a new ID Rate column, and added a separate row for the total PeptideShaker results in the Spectrum IDs tab.
  • Made it possible to show/hide the fixed modifications in most tabs.
  • Added a new Plotting dialog, opened by right clicking in most tables.
  • Reimplemented the PeptideShaker command line support from scratch. (http://code.google.com/p/peptide-shaker/wiki/PeptideShakerCLI)
  • Added an open example dataset option to the WelcomeDialog.
  • Added a settings pop up menu to the WelcomeDialog.
  • Implemented False LocationRate (FLR) for modifications.
  • Modification patterns defined as part of a SearchGUI search are now supported.
  • Added precursor intensity to the spectrum table in the Spectrum IDs tab.
  • Added neXtProt and PDB links to the Annotation tab.
  • Added an option for exporting the maximal protein set (the accession numbers) to a file.
  • The precursor mass error now takes into account wrong isotope selection.
  • Feature improvements:
  • Simplified the way the user selected parameters are applied when moving away from the Validation tab.
  • Changed the precursor intensity shown in the Fractions tab from average to sum.
  • Added lower and upper ranges for the fraction molecular weights in the FractionDetailsDialog.
  • Made it possible to cancel the progress bars in the Validation tab.
  • Improved the search engine PTM recognition.
  • Improved the default PTM selection for X!Tandem.
  • Removed the use of UniProt to get the basic protein information. Now taken from the FASTA files instead.
  • Gene name and protein evidence level are now shown in the protein inference dialogs for UniProt data.
  • Improved the progress dialog in the Spectrum IDs tab.
  • PeptideShaker can now be run from paths containing special characters.
  • Mgf files with spectrum titles encoded in unicode are now supported.
  • The modal progress dialog is now closed if an error occurs during the saving of a project.
  • Added protein inference type, star property, tagged peptide sequence, is enzymatic, the surrounding peptide information for shared peptides and fixed modification details to the peptide exports.
  • Added total number of peptides and spectra, overall sequence coverage, has non-enzymatic peptides, MW and peptide and spectrum spread to the fractions export.
  • The filters in the FindDialog are now previewed in the tables only after the user stops typing. And the previewing of the filters in the FindDialog can now be turned on or off by the user.
  • Improved the tooltips in the molecular weight box plot in the Fractions tab.
  • Sped up the PRIDE export.
  • Generalized the "show tryptic/non tryptic peptides" to "show enzymatic/non enzymatic peptides".
  • Added a check for duplicate entries when loading a FASTA file.
  • Bug Fixes:
  • Fixed a bug in the mass of the glutamic acid amino acid.
  • Fixed a bug where the masses of user defined PTMs in the PRIDE export where set to null if a CV term mapping was added.
  • Fixed a bug that occurred if the user clicked the SE column for a PSM in the Overview tab before loading the Spectrum IDs tab.
  • Fixed a bug with multiple fixed modifications on the same peptide, e.g., when using iTRAQ or TMT labeling.
  • Fixed a bug that made the saving of bigger projects very very slow.
  • Fixed a bug in the export spectrum as mgf feature that made it impossible to export as mgf.
  • Fixed a bug in the average precursor intensity calculation for the proteins.
  • Fixed the progress bars in the Validation and PTM tabs to show actual progress.
  • Fixed an issues in the Spectrum IDs tab where the number of unassigned spectra was incorrect.
  • Fixed a bug with the maximum sparkline values in the Fractions tab.
  • Fixed a bug so that the icon doesn't stay orange when finished exporting/zipping a PeptideShaker project.
  • Fixed a bug in the possible sequence coverage displayed in the coverage panel, where the first residue and the last non-enzymatic peptide was not included.
  • Fixed an inconsistency in the sequence coverage output in the exports, as both 0-100 and 0-1 was used for percent values.
  • Fixed a bug i the restart after changing the memory setting, it crashed if a project was currently open.
  • Made a minor change to the pom file to handle a recursive issues that can occur when opening the project in NetBeans 7.2.
  • Fixed a bug resulting in the filters having to be applied twice. Also added the option of deleting filters.
  • Fixed a bug in the protein export where two columns had gotten mixed up.
  • Fixed a bug in the New Project dialog where opening the FASTA file didn't display the last selected folder.
  • Fixed a bug where the enzyme was reset when manually loading a FASTA file in the New Project dialog.
  • Fixed a bug where the progress bar was not closed in the New Project dialog if an error occurred when checking the FASTA file.
  • Fixed a bug with the use of "whole protein" as the enzyme.
  • Library Updates:
  • Removed unitprotjapi as a dependency.
  • Added twitter4j as a dependency.
  • Added mzdata-parser 1.2.1 as a dependency.
  • Updated the default Ensembl human to version 69.
  • Updated jsparklines to version 0.5.44.
  • Updated omssa parser to version 1.5.8.
  • Updated xtandem parser to version 1.5.12.
  • Updated mascot dat file parser to version 3.4.7.
  • Updated utilities to version 3.11.2.

New in PeptideShaker 0.18.3 (Sep 15, 2012)

  • FEATURE IMPROVEMENT: Improved the PRIDE export dialog.
  • FEATURE IMPROVEMENT: It is now possible to add more than one contact in the PRIDE export.
  • FEATURE IMPROVEMENT: The PRIDE settings are now stored in the PeptideShaker Project.
  • FEATURE IMPROVEMENT: Re-enabled the improved (but slower) ptm location code.
  • LIBRARY UPDATE: Updated ols-dialog to version 3.4.0, containing many GUI improvements.
  • LIBRARY UPDATE: Updated utilities to version 3.8.12.

New in PeptideShaker 0.18.2 (Sep 12, 2012)

  • BUG FIX: Had to (temporarily) disabled the new improved PTM location code as could result in null pointers.
  • LIBRARY UPDATE: Updated mascotdatfile to version 3.4.2, such that the Mascot search results can be loaded again.
  • LIBRARY UPDATE: Updated utilities to version 3.8.9, fixing an issues with the EBI proxy settings.

New in PeptideShaker 0.18.1 (Sep 12, 2012)

  • FEATURE IMPROVEMENT: Better support for spectrum titles in OMSSA files with special characters in them, e.g., \ or ".
  • FEEATURE IMPROVEMENT: The code now supports Maven 3.
  • LIBRARY UPDATE: Added the OMSSA, X!Tandem and Mascot parsers as dependencies.
  • LIBRARY UPDATE: Updated utilities to version 3.8.8.
  • LIBRARY UPDATE: Updated jmzml to version 1.6.8.

New in PeptideShaker 0.18.0 (Sep 8, 2012)

  • NEW FEATURE: A brand new database based backend.
  • NEW FEATURE: New improved and simplified Fractions tab.
  • NEW FEATURE: Automatic de novo sequencing can now be done using one or two charges for the fragment ions.
  • NEW FEATURE: Spaces are now allowed in protein accession numbers.
  • NEW FEATURE: The report created when loading a project in the waiting dialog is now automatically saved as part of the project details.
  • NEW FEATURE: Automated the delta thresholding.
  • NEW FEATURE: Added support for Mascot Server 2.4.
  • NEW FEATURE: Added a contextual options icon to the coverage tables, making is possible for the users to decide which peptides to show.
  • NEW FEATURE: The FragmentIonTable now supports multiple PSMs in the traditional theoretical m/z values setup as well.
  • FEATURE IMPROVEMENT: Replaced uses of "\n" with System.getProperty("line.separator"), making the export less system dependent.
  • FEATURE IMPROVEMENT: Minor GUI improvement to the Search Parameters dialog.
  • FEATURE IMPROVEMENT: Minor GUI improvement to the New Project dialog.
  • FEATURE IMPROVEMENT: Minor GUI fixes in the BugReport dialog.
  • FEATURE IMPROVEMENT: Added MW to the protein export options.
  • FEATURE IMPROVEMENT: Increased the length of the recent files displayed to 20.
  • FEATURE IMPROVEMENT: Updated human ENSEMBL to version 68.
  • FEATURE IMPROVEMENT: Better support for spectrum titles with "\\" in them.
  • FEATURE IMPROVEMENT: Changed the table export in the ptm tab so that it retrieves the same information as the overview table.
  • FEATURE IMPROVEMENT: Improved and extended the PRIDE Export, which now also includes PTM scores, spectrum file names and titles.
  • FEATURE IMPROVEMENT: A warning will now be displayed if the user tries to start the tool from within a zip file.
  • FEATURE IMPROVEMENT: GUI updates to make the tool look better on Java 7.
  • FEATURE IMPROVEMENT: Added the maximal coverage in the protein export.
  • BUG FIX: Fixed a bug that occurred if the user typed in the name of a file to load and the file was not found.
  • BUG FIX: Fixed a bug in the SearchPreferencesDialog where the the precursor accuracy was set incorrectly when loading a SearchGUI properties file.
  • BUG FIX: Fixed a bug in the BugReport dialog where it was impossible to export/save the log.
  • BUG FIX: Fixed a bug where the width of the accession columns were not set correctly.
  • BUG FIX: Fixed a couple of calls to convertRowIndexToModel that could be called on an incorrect row.
  • BUG FIX: Fixed a bug in the last selected folder feature that defaulted to the user home folder if the file did not have the correct file name (e.g., .txt).
  • BUG FIX: Fixed an issue in the ProgressDialog that resulted in threading issues and deadlock on Java 7.
  • BUG FIX: Fixed a bug in the spectrum annotation where the precursor charge interfered with the fragment ion charge.
  • BUG FIX: Fixed a null pointer that could occur if trying to close an empty/canceled project.
  • BUG FIX: Fixed a bug where the final y-ion was not annotated in the spectrum panel.
  • BUG FIX: Fixed the "Modification not found" error that occurred if opening two projects in a row without closing the tool.
  • BUG FIX: Fixed a bug where the list of spectrum files were not reset when opening a second project.
  • BUG FIX: Fixed a bug in the 3D tab where an error could occur if the user moved too fast in the pdb chains table.
  • BUG FIX: Fixed a bug in the ProteinInferenceDialog that could result in a null pointer as the wrong map was used.
  • BUG FIX: Made it possible to edit the user defined PTMs.
  • BUG FIX: Fixed various issues related to the canceling of progress dialogs.
  • BUG FIX: Fixed a bug in the FindDialog that resulted in protein filters that only filtered on protein confidence were considered as empty filters.
  • BUG FIX: Fixed a bug in the PRIDE export where it was impossible to select "Other" as the species and select your own CV term instead.
  • LIBRARY UPDATE: Updated uniprotapi to version 2012.06.
  • LIBRARY UPDATE: Updated jsparklines to version 0.5.40.
  • LIBRARY UPDATE: Updated utilities to version 3.8.6.

New in PeptideShaker 0.17.3 (Jul 3, 2012)

  • NEW FEATURE: Added automatic de novo sequencing.
  • FEATURE IMPROVEMENT: Re-enabled row sorting in the spectrum table in the Spectrum IDs tab.
  • FEATURE IMPROVEMENT: Sorting by clicking the table headers now results in the cursor changing into a waiting cursor and the PeptideShaker icon turning orange.
  • FEATURE IMPROVEMENT: The size of the accession column in the Fractions tab is now set to the same width as the other tabs.
  • FEATURE IMPROVEMENT: Updated the default human GO mappings to Ensembl version 67.
  • BUG FIX: Fixed a bug where the row selection in the Overview tab was not reset correctly after closing the SearchParameters dialog.
  • BUG FIX: Fixed some bugs with the contextual export options for the spectrum panel in the PTM tab.
  • BUG FIX: Fixed a bug in the GO tab that could result in issues if switching between rows in the GO table too fast.

New in PeptideShaker 0.17.2 (Jul 3, 2012)

  • NEW FEATURE: The amino acids Selenocysteine and Pyrrolysine are now supported.
  • FEATURE IMPROVEMENT: Improved the look and feel of the manual de novo sequencing.
  • FEATURE IMPROVEMENT: The Search Parameters dialog is now resizable.
  • FEATURE IMPROVEMENT: Missing GO conf files during startup no longer crash the tool.
  • BUG FIX: Fixed a bug in the wrapper where the upper memory limit was not automatically set when using Java 1.7.
  • LIBRARY UPDATE: Updated utilities to version 3.4.23.

New in PeptideShaker 0.17.1 (Jul 3, 2012)

  • NEW FEATURE: Added an initial Command Line Interface (CLI) functionality. (see wiki page for details)
  • FEATURE IMPROVEMENT: Allowed the user to tune the default FDR and disable A-score calculation.
  • FEATURE IMPROVEMENT: Improved the spectra recalibration method.
  • BUG FIX: Corrected bugs in the stats panel where thresholds were not remembered/saved.
  • BUG FIX: Fixed a bug where the BugReport could not locate the log file.
  • BUG FIX: Fixed a bug impairing the modification of the PTM list from the new dialog.
  • LIBRARY UPDATE: Updated utilities to version 3.4.22.

New in PeptideShaker 0.17.0 (Jul 3, 2012)

  • NEW FEATURE: Added a Protein Fractions tab.
  • NEW FEATURE: Added method for spectra recalibration.
  • FEATURE IMPROVEMENT: Simplified and sped up the setting of the width for the Accession columns.
  • FEATURE IMPROVEMENT: Spectra with out spectrum titles are now supported as input.
  • FEATURE IMPROVEMENT: Help files extended.
  • BUG FIX: Corrected a bug in mgf export output.
  • BUG FIX: Fixed a GUI resizing issue in the SearchPreferencesDialog.
  • LIBRARY UPDATE: Updated utilities to version 3.4.19.

New in PeptideShaker 0.16.3 (Jul 3, 2012)

  • NEW FEATURE: It is now possible to start SearchGUI directly from the Welcome dialog or from the File menu. (Requires SearchGUI v1.8.3 or newer.)
  • NEW FEATURE: Added a Getting Started tutorial to the Welcome Dialog.
  • NEW FEATURE: Added a gradient color coding panel below the A-score and Delta-score tables in the PTM tab displaying the PTM score certainty.
  • FEATURE IMPROVEMENT: Updated all the Welcome Dialog icons.
  • FEATURE IMPROVEMENT: Made it possible to close progress dialogs that track processes that previously could not be canceled. A warning is now instead showed and the user can decide if he/she still wants to cancel the process.
  • FEATURE IMPROVEMENT: Fixed the issue with the UniProt Java API needing its own proxy settings file.
  • FEATURE IMPROVEMENT: Updated the help files.
  • FEATURE IMPROVEMENT: Added protein description to the peptide, PSM and search engine feature export options.
  • FEATURE IMPROVEMENT: Improved the GUI of the Export Features dialog.
  • FEATURE IMPROVEMENT: Simplified the folder structure in the zip file.
  • BUG FIX: Fixed a bug in the selection of PSMs in the PTM tab, and for removing expected PTMs in the SearchPreferencesDialog.
  • BUG FIX: Fixed a bug that removed the dialog title for the Waiting Dialog.
  • LIBRARY UPDATE: Updated utilities to version 3.4.12.

New in PeptideShaker 0.16.2 (Jul 3, 2012)

  • BUG FIX: Fixed an issue with spaces in the splash screen graphics path on Windows.

New in PeptideShaker 0.16.1 (Jul 3, 2012)

  • NEW FEATURE: Added a PeptideShaker splash screen.
  • FEATURE IMPROVEMENT: Updated the Welcome dialog.
  • FEATURE IMPROVEMENT: Cleaned up the folder structure in the zip file.
  • BUG FIX: Fixed a bug in the method for setting the path for the icon and target in the desktop shortcut that occurred when running PeptideShaker from network drives.

New in PeptideShaker 0.16.0 (Jul 3, 2012)

  • NEW FEATURE: On Windows (on supported architectures) the user is now asked if a desktop shortcut should be added the first time he/she starts the tool.
  • NEW FEATURE: Added Request Validated to the Export Features dialog for the Search Engine export.
  • NEW FEATURE: The users can now change the spectrum annotation colors, plus the color and width of the peaks.
  • NEW FEATURE: Neutral losses and reporter ions are now ptm dependent and their selection is automated.
  • NEW FEATURE: Made it possible to add/edit PSI-MOD terms, neutral losses and reporter ions for the PTMs.
  • NEW FEATURE: Added a new tag to the search engine agreement columns. Orange is now used to indicate that one of the search engines failed to identify a spectrum that was identified by the other search engines used.
  • NEW FEATURE: Added a README file.
  • NEW FEATURE: The proteins for a given GO terms is now listed in a separate table in the GO tab.
  • FEATURE IMPROVEMENT: Tried to make the progress bar stay visible in the Overview tab until the data is finish loading.
  • FEATURE IMPROVEMENT: Redesigned the Export Features dialog.
  • FEATURE IMPROVEMENT: Improved the GUI for the SearchPreferencesDialog.
  • FEATURE IMPROVEMENT: Extended the protein outputGenerator to be able to export just the list of the main accession numbers. As needed for the Annotation tab.
  • FEATURE IMPROVEMENT: Refurbished the AnnotationPreferencesDialog.
  • FEATURE IMPROVEMENT: Updated the default human GO mappings to Ensembl version 66.
  • FEATURE IMPROVEMENT: Page up and page down will now result in selection updates in the tables (before only up and down was used).
  • FEATURE IMPROVEMENT: The sorting order in the tables are now kept when updating the table models.
  • FEATURE IMPROVEMENT: Replaced all the check boxes in tables with our own home made check mark.
  • FEATURE IMPROVEMENT: All progress dialogs can now be closed/canceled.
  • FEATURE IMPROVEMENT: Added progress dialogs to the Validation tab where missing.
  • FEATURE IMPROVEMENT: In the GO tab the number of GO mapped proteins for Ensembl and for the project is now shown.
  • FEATURE IMPROVEMENT: Updated the PeptideShaker icon.
  • FEATURE IMPROVEMENT: The precursor charge QC plot now uses the max charge detected in the project as the max value.
  • FEATURE IMPROVEMENT: Improved the GUI of the ImportSettingsDialog.
  • BUG FIX: Tried to fix the threading issues in the PtmPanel.
  • BUG FIX: Fixed a bug in the clearData method that resulted in issues when opening a second project.
  • BUG FIX: Fixed a threading issue that could result in a null pointer exception when closing the tool.
  • BUG FIX: Fixed a bug in the peptide export in the Export Features dialog where the order of the boolean variables had gotten mixed up.
  • BUG FIX: Fixed a serious bug in the GO tab: the max value used for the dataset was incorrect (and could result in an exception).
  • BUG FIX: Fixed a bug in the GO tab where the sorting of the table resulted in the wrong p-values being shown.
  • BUG FIX: Fixed a bug where the saving and closing of a project started at the same time.
  • BUG FIX: Fixed some bugs in the Modification tab related to selecting multiple PSMs.
  • BUG FIX: Corrected a bug in the new dialog which made it impossible to load data when not from SearchGUI.
  • BUG FIX: Corrected bugs concerning modifications and spectrum counting maximum.
  • LIBRARY UPDATE: Updated utilities to version 3.4.8.
  • LIBRARY UPDATE: Updated uniprotjapi to version 2012.03.
  • LIBRARY UPDATE: Added jshortcut as a dependency.
  • LIBRARY UPDATE: Removed swingx as a dependency.