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Harald Barsnes edited this page Aug 6, 2015 · 2 revisions

Release Notes

Changes in PRIDE Converter v2.5.7:

  • LIBRARY UPDATE: Updated the omssa parser to version 1.6.3, fixing a problem with parsing omx files with intensity scale was a floating value.
  • LIBRARY UPDATE: Updated X!Tandem parser to version 1.7.7.
  • LIBRARY UPDATE: Updated ols-dialog to version 3.4.2.

Changes in PRIDE Converter v2.5.6 - (August 22. 2013):

  • BUG FIX: Fixed an issue with the wrapper on the newer Java versions.
  • BUG FIX: Fixed an issue with missing icons in the data source selection dialog.
  • BUG FIX: Fixed an issue with a possible null pointer in MS_LimsConverter related to strange PTMs.
  • BUG FIX: Replaced paths to CvMappingRules.xsl as the file had moved.
  • LIBRARY UPDATE: Updated cv-rule-reader to version 2.0.3.

Changes in PRIDE Converter v2.5.5 - (January 11. 2012):

  • BUG FIX: Updated to support new fragment ion types reported by Mascot dat file parser

Download count: 933

Changes in PRIDE Converter v2.5.4 - (October 18. 2011):

  • BUG FIX: use latest MascotDatFile version 3.2.6 fixing some issues when MascotDat header had been modified

Download count: 244

Changes in PRIDE Converter v2.5.3 - (August 11. 2011):

  • FEATURE IMPROVEMENT: removed support for DTASelect files, never properly implemented

Download count: 176

Changes in PRIDE Converter v2.5.2 - (June 21. 2011):

  • BUG FIX: Added 2 new FragmentIon accessions (PRIDE:0000280 and PRIDE:0000281)

Download count: 128

Changes in PRIDE Converter v2.5.1 - (April 19. 2011):

  • FEATURE IMPROVEMENT: Improved the GUI of the SpectraSelection panels by reducing the size of the "Load Spectra" button (and moving it), as this was pressed by some users even when not doing manual selection, thus slowing down the process.

Download count: 222

Changes in PRIDE Converter v2.5.0 - (March 14. 2011):

  • FEATURE IMPROVEMENT: Replacement of PSI with MS ontology.
  • BUG FIX: fixed unhandled case in modification mapping when mass was not specified.

Download count: 92

Changes in PRIDE Converter v2.4.9 - (Dec. 16. 2010):

  • BUG FIX: Removed 'percent_coverage' value parsing from TPP protXML files (since we don't know how these percentage values are encoded).
  • BUG FIX: Update JRAP library (external dependency) to latest version jrap_StAX_v5.2.

Download count: 174

Changes in PRIDE Converter v2.4.8 - (Dec. 6. 2010):

  • BUG FIX: Mascot Generic files (MascotGenericConverter.java): Change in the Retention Time management: two retention times are now allowed.
  • BUG FIX: For ms_lims the modification mass is now also added as a ModMonoDelta tag. Fixed an issue with the user name being set incorrectly in the default ms_lims login dialog.
  • BUG FIX: Fixed some minor GUI details in the Output Details panel related to the OMSSA settings.
  • LIBRARY UPDATE: ols-dialog from version 3.2.3 to 3.2.4.
  • LIBRARY UPDATE: omssa-parser to version 1.4.2, that fixes a bug in parsing some special case omx files.

Download count: 41

Changes in PRIDE Converter v2.4.7 - (Nov. 27. 2010):

  • NEW FEATURE / BUG FIX: Using Peptide Score Threshold has now been implemented for Mascot dat files.

Download count: 30

Changes in PRIDE Converter v2.4.6 - (Nov. 23. 2010):

  • FEATURE IMPROVEMENT: Fixed an issue with a remaining reference to the old ms_lims Spectrumfile table.

Download count: 17

Changes in PRIDE Converter v2.4.5 - (Nov. 17. 2010):

  • FEATURE IMPROVEMENT: Improved parsing for SwissProt database in OMSSA module
  • FEATURE IMPROVEMENT: Re-definition of STY Phosphorylation in UserProperties.prop

Download count: 23

Changes in PRIDE Converter v2.4.4 - (Oct. 29. 2010):

  • FEATURE IMPROVEMENT: The charge state in OMSSA is captured now from the highest scored result, not from the spectrum.
  • FEATURE IMPROVEMENT: Enhanced parsing for Swissprot and Trembl protein entries in OMSSA.
  • BUG FIX: Fixed a bug in the GUI: ModificationMapping.java

Download count: 52

Changes in PRIDE Converter v2.4.3 - (Oct. 12. 2010):

  • BUG FIX: Fixed a bug in the method for outputting the residues affected by a modification as defined by OMSSA.

Download Count: 28

Changes in PRIDE Converter v2.4.2 - (Aug. 23. 2010):

  • FEATURE IMPROVEMENT: Sequest parsing improved (PTM description). SEQUEST updated to v.28.

Download Count: 99

Changes in PRIDE Converter v2.4.1 - (Aug. 13. 2010):

  • FEATURE IMPROVEMENT: Project tag is now mandatory.
  • LIBRARY UPDATE: ms-lims updated to version 7.4.1.

Download Count: 18

Changes in PRIDE Converter v2.4 - (July 5. 2010):

  • FEATURE IMPROVEMENT: Major revision of the graphical user interface making it look better on Windows 7 and on high resolution screens.
  • FEATURE IMPROVEMENT: Addition of retention time parsing for mgf files.
  • LIBRARY UPDATE: omssa-parser updated to version 1.3.7.
  • LIBRARY UPDATE: old-dialog updated to version 3.2.3

Download Count: 68

Changes in PRIDE Converter v2.3.4 - (May 19. 2010):

  • NEW FEATURE: Added support for sf score in SEQUEST result file converter.
  • LIBRARY UPDATE: mascotdatfile update to 3.2.

Download Count: 84

Changes in PRIDE Converter v2.3.3 - (May 7. 2010):

  • NEW FEATURE: ms_lims version 7.3 is now supported.
  • LIBRARY UPDATE: ms_lims updated to 7.3.

Download Count: 10

Changes in PRIDE Converter v2.3.2 - (April 26. 2010):

  • BUG FIX: Turned the ErrorLog back on again.
  • BUG FIX: Converting Mascot Dat files is now working again.
  • LIBRARY UPDATE: omssa-parser library updated to version 1.3.6.

Download Count: 35

Changes in PRIDE Converter v2.3.1 - (April 22. 2010):

  • FEATURE IMPROVEMENT: Added species check to sample properties input frame and updated sample properties file.

Download Count: 8

Changes in PRIDE Converter v2.3 - (April 7. 2010):

  • FEATURE IMPROVEMENT: Change the way of capturing reference metadata.
  • FEATURE IMPROVEMENT: Minor change on the label of sample description.
  • LIBRARY UPDATE: Integrated the new release of Mascot dat library, version 3.0.2.

Download Count: 30

Changes in PRIDE Converter v2.2.1 - (Feb. 5. 2010):

  • FEATURE IMPROVEMENT: Added support for multiple charges in mgf files when the charge values are separated by "and".
  • FEATURE IMPROVEMENT: Added support for Terminal Modifications in PeptideProphet files.

Download Count: 114

Changes in PRIDE Converter v2.2 - (Dec. 22. 2009):

  • FEATURE IMPROVEMENT: Improved support for DTASelect.
  • BUG FIX: TPP Converter handling of modifications.
  • LIBRARY UPDATE: mascot_datfile updated from 2.2.2 to 2.2.3.

Download Count: 65

Changes in PRIDE Converter v2.1.2 - (Nov. 25. 2009):

  • FEATURE IMPROVEMENT: On Windows platforms PRIDE Converter can now be run from paths containing spaces.

Download Count: 34

Changes in PRIDE Converter v2.1.1 - (Oct. 09. 2009):

  • FEATURE IMPROVEMENT: Updated the default subject in the mailto links.
  • BUG FIX: When parsing decoy proteins from PeptideProphet XML files the total number of proteins can now be 0.
  • LIBRARY UPDATE: OMSSA Parser updated to version 1.3.4.
  • LIBRARY UPDATE: OLS Dialog updated to version 3.2.2, which includes new search options and additional features.

Download Count: 98

Changes in PRIDE Converter v2.1 - (Sept. 24. 2009):

  • FEATURE IMPROVEMENT: The RequestFtpAccess dialog now includes a mailto link with a default e-mail for requesting FTP access.
  • FEATURE IMPROVEMENT: The text in the JOptionPane dialogs has been by simplified and shortened. Some minor typos have also been fixed.
  • FEATURE IMPROVEMENT: Reduced the size of the PRIDE Converter zip file by removing unused libraries.
  • FEATURE IMPROVEMENT: Improved the radio button renderer.
  • FEATURE IMPROVEMENT: The default browser launcher now recognizes more browsers.
  • BUG FIX: Fixed a problem in the spectra selection frame where the selection in the table was not always updated correctly if sorting was turned on.
  • BUG FIX: The PSI-MOD modification mass check is now working again. (The DiffMono mass value had been moved back to the PSI-MOD metadata section after being in the xrefs section for a while.)
  • BUG FIX: Fixed a GUI bug in the peptide counter for DTASelect and TPP data sets. (Note: The bug did not affect the contents of the file.)
  • BUG FIX: Clicking cancel when mapping OMSSA modifications to PSI-MOD modifications now cancels the conversion process.
  • BUG FIX: Fixed two Mac and Linux GUI bugs where the content in the first and last frame was not shown correctly.
  • LIBRARY UPDATE: ols-dialog updated to v2.0.1 which includes modification mass search when mapping PSI-MOD modifications.

Download Count: 29

Changes in PRIDE Converter v2.0.3 - (Aug. 21. 2009):

  • BUG FIX: Fixed a serious bug for OMSSA conversion where integer division was used when scaling the mz and intensity peak values, and the precursor mz value.

Download Count: 55

Changes in PRIDE Converter v2.0.2 - (Aug. 19. 2009):

  • FEATURE IMPROVEMENT: The OLS Dialog has been redesigned (and made into a separate project (http://ols-dialog.googlecode.com)).
  • FEATURE IMPROVEMENT: Made sure that an ambiguous spectrum mapping (for mapping a peptide identification to a spectrum) cancels the conversion process.
  • BUG FIX: Updated the fragment ion CV term mappings to be able to handle H2O neutral losses using both 'O' (the letter) and '0' (the number) in the H2O tag.
  • LIBRARY UPDATE: ols-client-1.14 has been replaced/extended by ols-dialog-1.0.1.
  • LIBRARY UPDATE: Updated the utilities library to version 2.9.9.
  • LIBRARY UPDATE: Updated the mascot_datfile library to version 2.2.2.

Download Count: 3

Changes in PRIDE Converter v2.0.1 - (July. 28. 2009):

  • BUG FIX: identical "title" annotations in mascot .dat files could mess up the spectrum mapping.

Download Count: 44

Changes in PRIDE Converter v2.0 - (July. 22. 2009):

  • NEW FEATURE: Fragment Ion Annotations are now included for: ms_lims, Mascot Data Files and OMSSA.
  • NEW FEATURE: PRIDE XML files are now gzipped after conversion to reduce the upload time to the PRIDE data repository.
  • NEW FEATURE: A dialog telling you to request access to the PRIDE FTP server now appears if the (unzipped) PRIDE XML files size is larger than 15 MB.
  • FEATURE IMPROVEMENT: The contents of comboboxes are now centrally aligned.
  • BUG FIX: Fixed two minor GUI bugs in the DataBase Details frame.
  • LIBRARY UPDATE: Updated utilities to version 2.9.2.
  • LIBRARY UPDATE: Updated pride-core to version 2.7.0.

Download Count: 18

Changes in PRIDE Converter v1.18.2 - (Jun. 16. 2009):

  • BUG FIX: When converting Peptide-/ProteinProphet projects the search_result tags can now be empty.

Download Count: 62

Changes in PRIDE Converter v1.18.1 - (Jun. 11. 2009):

  • FEATURE IMPROVEMENT: Added more default PSI-MOD modification mappings.
  • BUG FIX: Fixed a bug resulting in the conversion sometimes failing (with no error message) during the conversion when using the converter on Linux or Mac OS.
  • LIBRARY UPDATE: Updated the MascotDatFile library to version 2.1.4.
  • LIBRARY UPDATE: Updated the pride-core library to version 2.6.1.

Download Count: 11

Changes in PRIDE Converter v1.18 - (Jun. 03. 2009):

  • NEW FEATURE: PRIDE Converter now supports ms_lims 7 (ms_lims 6 is no longer supported).
  • NEW FEATURE: When converting MH+ values to m/z values the original MH+ value is now also included as a CV term.
  • FEATURE IMPROVEMENT: X!Tandem conversion is no longer limited to one file per conversion.
  • FEATURE IMPROVEMENT: Improved the error message given when failing to contact OLS.
  • FEATURE IMPROVEMENT: Individual spectrum comments are now added as spectrum description comments.
  • FEATURE IMPROVEMENT: Tried to add some memory clean ups to keep the converter from running out of memory when converting multiple files in a row. (Focused especially on Mascot Dat Files.)
  • FEATURE IMPROVEMENT: Added a reference to the release notes in the dialog informing about new version.
  • FEATURE IMPROVEMENT: Turned off schema validation for OMSSA and X!Tandem parsing.
  • FEATURE IMPROVEMENT: Improved the OMSSA support by handling spectra with no filenames, given that filenames does not seem to be mandatory.
  • BUG FIX: When converting MH+ values to m/z values the mass of a hydrogen is now used instead of the mass of a proton.
  • BUG FIX: Fixed a bug in the select all and invert selection features in the spectra selection tables.
  • BUG FIX: Fixed a bug so that individual spectrum comments now can be added for Mascot Dat Files (again).
  • BUG FIX: Fixed a bug in parsing of PeptideProphet files where empty msms runs resulted in problems.
  • LIBRARY UPDATE: Update the omssa-parser version to 1.3.2.

Download Count: 8

Changes in PRIDE Converter v1.17.1 - (May 15. 2009):

  • Added an experiment description text field.
  • Added a CV term for the original MS data file format. (Automatically added by the converter.)
  • Improved the information about the supported ms_lims version.
  • Fixed a minor GUI bug in the New Contact dialog. (Not all the buttons had the same horizontal position.)
  • Fixed a minor GUI bug in the Experiment Properties frame. (The two tables did not have the same height.)

Download Count: 21

Changes in PRIDE Converter v1.17 - (May 02. 2009):

  • PRIDE Converter now only requires Java 1.5 (previously 1.6).
  • Fixed a bug resulting in the precursor mass for the DTA files being set to the MH+ value and not the m/z value (affected DTA and Sequest result file conversions).
  • X!Tandem conversion now requires you to input the spectra files (pkl, dta, mgf, mzXML or mzData). This is due to the spectra given in the X!Tandem file may not include all peaks from the original spectra.
  • The omssaparser version has been upgraded to version 1.3.0.
  • Java stack size options has been added to the Java options file.
  • Added a help file for the spectrum user parameter input dialog.
  • Added two new dependencies (swingx-0.9.1 (for JXTable) and swing-layout-1.0.3 (for Java 1.6 GUI stuff)).
  • The icon images has been removed for the non-resizable dialogs due to this not being supported in Java 1.5.
  • Empty Sequest out files are now ignored (previuosly stopped the conversion).
  • Fixed a bug in the parsing of Sequest accession numbers containing more than one '|'.
  • Removed the option of converting more than one mzData file at once, due to this having the possibility of corrupting the precursor spectrum references.
  • The location of the modification mono mass in PSI-MOD appears to have moved. And is now extracted from the new location.
  • Improved the test to check if the mass of the selected PSI-MOD is too far from the mass given in the data file.
  • Removed a dependency exclusion (org.apache.axis) that seems to be needed in Java 1.5 (but not in Java 1.6) when accessing the OLS.
  • Fixed a minor GUI bug in the protein isoforms selection dialog.
  • Made the progress and help dialogs slightly wider.
  • Fixed a bug in the table sorting where autosorting had to be turned off before using select all etc. The fix speeds up the selection/sorting.
  • Fixed a bug where the select all spectra could be deselected automatically.

Download Count: 19

Changes in PRIDE Converter v1.16.2 - (Mar. 26. 2009):

  • Extended the advanced spectra selection support for Mascot dat files. The ID column is now filled with 'filename_queryNumber', e.g. 'F004071.dat_1'.
  • Updated the check for new versions, due to a minor change in the way google code annotated deprecated downloads.
  • Added some additional default PSI-MOD modification mappings.

Download Count: 36

Changes in PRIDE Converter v1.16.1 - (Mar. 20. 2009):

  • The conversion of PeptideProphet/ProteinProphet data sets now supports multiple analysis tags in both the pepxml and protxml files.
  • The PeptideProphet and ProteinProphet thresholds are now in the range 0.01 - 1.0 (previously 0-100), to better fit the thresholds used in the pepxml and protxml files.
  • Removed the #Terms column in the Protocol Properties table and the Instrument Properties - Analyzers table.

Download Count: 4

Changes in PRIDE Converter v1.16 - (Mar. 13. 2009):

  • DTASelect is now supported (beta).
  • A lot of minor bugs in the graphical user interface when run on Mac has been fixed.
  • Some minor bugs in the graphical user interface when run on Linux have been fixed.
  • Some platform independent minor bugs in the graphical user interface have been fixed.
  • Fixed a bug in the handling of sample CV terms, where the long ontology name was incorrectly used instead of the short ontology name. (This resulted in problems when trying to automatically map the terms in PRIDE.)
  • The Mascot confidence level can now be any number between 0 and 100, including non-integer values, e.g., 99.5.
  • Delete Rows and Add Empty Row has been added to the table popup menu when adding a list of peptide to protein mappings.
  • Fixed a bug in the Spectra Selection of Mascot Dat files that resulted in the Select identified spectra not being used correctly.
  • Added comments on how to increase the memory size in the JavaOptions file.
  • Fixed a bug in the OLS dialog. When selecting terms in the table using the keyboard, the term details was not updated correctly.

Download Count: 12

Changes in PRIDE Converter v1.15.3 - (Mar. 09. 2009):

  • Fixed a bug that made it difficult to a create new single sample. (The Next button did not become enabled when adding CV terms.)
  • Updated the data format descriptions.
  • Updated the data source selection help file.

Download Count: 1

Changes in PRIDE Converter v1.15.2 - (Feb. 06. 2009):

  • The Sample Details frame has been simplified, and it is now possible to add values to the added cv terms.
  • Fixed a minor bug in the File Selection frame for two data types, e.g., Sequest DTA and OUT files. The bug occurred if a folder and not individual files was selected, and resulted in not being able to load the spectra in the Spectra Selection frame.

Download Count: 27

Changes in PRIDE Converter v1.15.1 - (Feb. 04. 2009):

  • Adding spectrum cv and user parameters is now also supported for data formats with identifications.
  • Fixed a bug in the advanced spectra selection that resulted in the selection not being correct unless the spectra had been loaded into the table first.
  • The spectra count shown for ms_lims data sets in the dialog appearing after the conversion was incorrect. Has now been fixed.

Download Count: 2

Changes in PRIDE Converter v1.15 - (Feb. 02. 2009):

  • Added the possibility of converting more than one mzData file at the time.
  • Made it possible to add cv and user terms to given spectra (currently only for data formats without identifications).
  • Added a decoy protein identification accession number filter.
  • Fixed a bug that resulted in all spectra referring to itself as its precursor spectrum when no precursor spectrum was given. Is now replaced by "Precursor spectrum not submitted."
  • Removed unused dependencies: 49 dep -> 39 dep. Zip file size: 15.7 mb -> 13.2 mb.
  • Added a reference to changing the firewall settings if connecting to OLS fails.
  • Added dialogs whenever an exception can be thrown and a message is written to the ErrorLog.
  • pep xml and prot xml files can now be just xml files (no pep.xml or pepxml requirements).
  • Peptide-/ProteinProphet support extended: if the "spectrum, path" tag is missing, use the <msms_run_summary ... raw_data=".mzXML"> tag instead.
  • The JavaOptions file (the memory settings) is now included when importing old user settings.
  • Fixed a bug that could occur when importing instrument details from mzData and mzXML files.
  • Made it possible to add MS level for given spectra. (Added an MS Level column to Spectra Selection without identifications table (MS level is otherwise assumed to be MS2).)
  • Fixed a bug that made it impossible to convert mzData files without at least one sample description cv term.
  • Fixed a bug that resulted in problems if the instrument name in mzData files was "N/A".
  • Made the spectrum selection for PKL files more robust by adding charge to the key.
  • Replaced the splitting of data lines on tab by splitting on tab and white space.

Download Count: 3

Changes in PRIDE Converter v1.14.2 - (Dec. 15. 2008):

  • Fixed a bug where OMSSA data values was divided by 1000 to get the real value. Now the MSResponse_scale and the MSSpectrum_iscale values from the OMSSA file are used.
  • Upgraded to omssaparser-0.9.4.
  • Replaced Gel Free identifications by Other, to be able to support 1D Gel identifications.

Download Count: 74

Changes in PRIDE Converter v1.14.1 - (Dec. 08. 2008):

  • It is now possible to select if the identifications are 2D gel based or gel free.
  • The selected ProteinProphet threshold was not included in the PRIDE XML file, even though it was used for calculating the protein identifications to include. Instead a default threshold of 0.9 was used. This as now been fixed.

Download Count: 11

Changes in PRIDE Converter v1.14 - (Dec. 03. 2008):

  • The Peptide-/ProteinProphet conversion has been made more general and now also supports MGF files for the spectra.
  • Removed the extra space before "Emulates Mascot web results" in the OutputDetails frame.
  • For Sequest data the name of the database is now extracted from the files.
  • Reduced the size of the zip file by removing libraries that were not used.
  • Fixed a problem where fixed modifications in Sequest was added twice.
  • A set of default PSI-MOD mapping for the most common modifications has been added.
  • If CV term mapping is available when clicking an OLS button, information about the given term will be presented.
  • A third default instrument has been added: LTQ-Orbitrap.
  • Fixed a bug where the wrong default ontology was selected when adding editing sample CV terms.
  • Fixed a bug where the list of analyzers was not reset when importing instrument details from mzData files.

Download Count: 25

Changes in PRIDE Converter v1.13.2 - (Nov. 17. 2008):

  • The Peptide-/ProteinProphet conversion is no loner considered beta.
  • Changed the progress bar headings at the beginning of processing Peptide-/ProteinProphet data.
  • Updated the help text for the SampleProperties frame saying that iTRAQ is not currently supported for Peptide-/ProteinProphet data.
  • Made it possible to add default CV term mappings to the UserProperties file. And to keep them when upgrading.
  • PSI-MOD modifications are again labeled with MOD and not PSI-MOD. Using PSI-MOD made the searching against OLS difficult.
  • Fixed a bug that resulted in fixed modifications being handled incorrectly for Sequest data.
  • Fixed a bug that compared the mass of a PSI-MOD mapped modification to the wrong PSI-MOD modification mass.
  • The PSI-MOD modification mass (DiffMono) is now used as the modification mass, and not the mass provided (if any) in the data file.
  • The modification mass is now also included for fixed modifications in Sequest data sets.
  • Modification masses, extracted from PSI-MOD, are now included for Spectrum Mill data.
  • The modification masses for Mascot Dat files, X!Tandem, OMSSA and Peptide-/ProteinProphet are now extracted from PSI-MOD, and not from the file itself. Unless the modification mass is not found in PSI-MOD.

Download Count: 15

Changes in PRIDE Converter v1.13.1 - (Nov. 12. 2008):

  • Fixed a spectra reference bug in the Peptide-/ProteinProphet conversion.
  • The mzXML data folder is now also re-entered when you revisit the TPP FileSelection frame.
  • It is now possible for the user to change the Peptide and Protein thresholds when converting Peptide-/ProteinProphet data.
  • Fixed a typing error in the progress dialog when extracting identifications for TPP data.
  • The TPP properties file is no longer mandatory. The PSI-MOD mapping of the modifications is now done directly.
  • PSI-MOD modifications are now labeled with PSI-MOD and not just MOD as previously used.

Download Count: 4

Changes in PRIDE Converter v1.13 - (Nov. 11. 2008):

  • Peptide-/ProteinProphet is now supported. (beta)
  • Upgraded Mascot Dat File Parser to version 2.0.3.
  • Upgraded JGoodies - Looks version to 2.2.1.
  • Added a separate message to the progress dialog when the xml file is being validated. Previously this was included in Creating PRIDE XML File.
  • If an instrument or sample set already exists the program now asks if the exisiting protocol should be used. If not, it asks if the existing instrument/sample should be overwritten.
  • Changed the order of the dataformats in the DataSourceSelection frame.
  • The JDialog that appears if a sample already exists is now located relative to the SampleDetails frame, and not always in the center of screen.

Download Count: 2

Changes in PRIDE Converter v1.12 - (Oct. 31. 2008):

  • MS2 files are now supported.
  • mzData files are now supported.
  • Fixed a bug in the Spectra Selection frame for dataformats without identifications that made it impossible to go further if Select All had been deselected.
  • Fixed a bug that made it difficult (if not impossible) to delete Sample Sets.
  • Upgraded the ms_lims version to 6.1.1.

Download Count: 7

Changes in PRIDE Converter v1.11.4 - (Oct. 22. 2008):

  • The parsing of Mascot Dat Files has been re-implemented and is now up to 50% faster.
  • Fixed a bug that made it mandatory for dta and out, and pkl and pkl.spo files to be in the same folder.
  • Empty spectra (spectra with no peaks) are now disregarded and not included in the PRIDE xml file.

Download Count: 8

Changes in PRIDE Converter v1.11.3 - (Oct. 21. 2008):

  • Older Sequest files (files not containing the "Id#" column) are now supported.
  • Fixed a bug that resulted in the peptide and protein identifications being wrong for Sequest Result files.
  • If the Cancel button is clicked when mapping modifications to PSI-MOD for Sequest and Spectrum Mill, the conversion is now actually canceled.
  • Using comma as the decimal symbol is now also supported for pkl/pkx and dta files.
  • Fixed a possible bug that could occur if a CV term, instrument name etc., contained ": ".
  • Fixed a bug that made it impossible to import the old user settings if a file that was not a PRIDE Converter user properties file was chosen in the first selection.

Download Count: 2

Changes in PRIDE Converter v1.11.2 - (Oct. 20. 2008):

  • Empty peak lists (i.e., only the precursor details are given) no longer crashes the parsing of the given peak list.
  • In the Project Selection frame pressing space bar in the last column now results in the Next button being enabled or disabled.
  • Parsing of Mascot Generic Files no longer crashes when Spectra Selection is used and the charge is not given.

Download Count: 2

Changes in PRIDE Converter v1.11.1 - (Oct. 17. 2008):

  • The parsing of Mascot Generic Files have been re-implemented and is now up to 50% faster.
  • The parsing of Mascot Generic Files now also handles the use of "," has the decimal sign.
  • The parsing of Mascot Generic Files now also handles precursor charges without a + or - sign.

Download Count: 6

Changes in PRIDE Converter v1.11 - (Oct. 07. 2008):

  • VEMS pkx files are now supported.
  • Fixed a bug that made it difficult to add new users.
  • Made some changes to reduce the memory required when parsing files.
  • The name of the file currently being parsed has been added to the progress dialog.
  • When doing file selection for files to convert more than one file can be selected at the time.
  • The lower limit for indexing the Mascot Dat files has been moved from 100 MB to 40 MB. (Which seems to decrease the speed needed to parse big files.)
  • The message given if the program fails to start has been revised. The comment regarding java version has been removed and a comment regarding memory boundaries has been added.
  • Clicking Delete in most of the tables will now delete the selected rows.
  • Removed the limitation that pkl files could only include one spectra.
  • New version of the Mascot Dat file parser with some debug output removed.
  • Updated the welcome message and the data source information.
  • The bug that the converter sometimes (very rarely) halted after clicking the Convert! button in the last step has (hopefully) been fixed.
  • Fixed a bug that resulted in the "orginal accession number" field in the Output Properties fram remaining uneditable when returning to this frame even when the resubmission box was checked.

Download Count: 15

Changes in PRIDE Converter v1.10.1 - (Sep. 30. 2008):

  • Fixed a problem that occured when converting large Mascot Dat Files.

Download Count: 8

Changes in PRIDE Converter v1.10 - (Sep. 25. 2008):

  • Open Mass Spectrometry Search Algorithm (OMSSA) omx files are now supported.
  • The Java version checker now only requires Java 1.4. (Previously 1.5.)
  • Fixed a bug that made it possible to enter text into the E-mail and Institution fields in the New Contact dialog even when - Please select a contact - was selected.
  • Fixed a bug that made the Software Name and Software Version fields in the instrument frame appear editable even when - Please select an instrument - was selected.
  • The output frame now looks more symmetrical.
  • Extracting version numbers from IPI databases has been disabled because it was not general enough. Database version is now simply included in the database name.
  • Updated some of the help manuals.

Download Count: 6

Changes in PRIDE Converter v1.9.1 - (Sep. 22. 2008):

  • The Spectrum Mill protein scores are changed to the sum of the highest scores for each unique peptide (and not the average) to be consistent with Spectrum Mill.
  • Setting a lower threshold for the peptide identification scores is now possible for Spectrum Mill, X!Tandem and Sequest Result Files.
  • For Spectrum Mill the start and end indices are now included.

Download Count: 7

Changes in PRIDE Converter v1.9 - (Sep. 22. 2008):

  • Mac is now supported.
  • The mzXML support has been extended to also extract information about the instrument and processing.
  • Upgraded to Mascot Dat File Parser v2.0 and uses the new option of indexing large files to save memory.
  • The XML generation software cv-term was added once for each xml file generated after starting the converter. Resulting in two copies in the second file generated, three in the third etc.
  • The size of the PRIDE XML is now included in the summary of the conversion.
  • Fixed a bug that made the cancel button much smaller than the ok button in the option frame for providing instrument name etc.
  • A delete button has been added to the right of the instrument, contact, sample set and protcol comboboxes. (Previously deleting was done via a popup menu, but this for some reason is no longer working with the new look and feel.)
  • Fixed a bug in the tooltip text for comboboxes. No tooltip is now set to null and not an empty string.
  • The xml file details (number of spectra, number of identifications etc.) are now included in the Output Properties frame as well.
  • Added an automatic check for updates at startup.
  • Fixed a bug that made manual spectra selection impossible for sequest dta files.
  • Added updating of the spectra counters when loading spectra formats without identifications.
  • Added a java version test at start up. If java version 1.5 is used a message saying that you should upgrade to 1.6 is shown. Java versions older than 1.5 is not supported.
  • The java version used to start the program is now also used internally. Previously the default java version was used, which lead to problems is this version was older than 1.6.
  • Improved the error messages appearing if the converter fails to start. A log file is also created in the users home folder.
  • If the parsing of a file fails the error message shown is now extended with a reference to the ErrorLog where more details can be found.
  • The size of the two tables in the frame for selecting two data file types is now equal.
  • The Spectrum Mill parser has been rewritten. Should now support more versions of the pkl.spo files, and be more robust.
  • The Spectrum Mill parser now handles the situation where a peptide is modified with two different variable or fixed modification (for example an oxidation and a phosphorylation).
  • Made sure that the mouse pointer always changes into a wait icon when the program is working.
  • The correct file name is now given when parsing fails. Earlier the pkl file was given even if the problem was with the pkl.spo file etc.
  • The import old user settings as been made more robust. Now also tests if the Properties.prop file selected starts with the PRIDE Converter tag.
  • More than one ms_lims project can now be selected for inclusion in a PRIDE XML file.
  • Advanced spectra selection for ms_lims has been extended with selection based on identification ids.

Download Count: 4

Changes in PRIDE Converter v1.8:

  • Fixed a bug that resulted in the having to restart the program if a conversion got canceled by the user.
  • Fixed a bug that resulted in n- and c-terminal modifications being labeled on the first and last amino acid and not on the terminals.
  • Up- and downstream flanking sequences are ignored if empty for Spectrum Mill.
  • More than one modification (of the same type) on the same peptide is now detected for Spectrum Mill. (Previously only the first in the sequence was detected.)
  • Upgraded PRIDE_core to v2.5.5
  • Upgraded JGoodies looks to v2.2.0

Download Count: 45

Changes in PRIDE Converter v1.8_beta:

  • Basic mzXML support has been added (imports mz-values but not instrument details etc.)
  • Modifications are now detected, mapped to a PSI-MOD and included in the PRIDE XML file.
  • The Spectrum Mill support has been extended due to finding two slightly different file formats.
  • Settings from the previous version (when upgrading) can now be imported when starting the new version.
  • Fixed a bug that resulted in no spectra ending up in the xml file if manual spectra selection was used for Spectrum Mill and Sequest.
  • The user interface now supports the use of "large fonts" in windows xp without distorting the frame size.

Changes in PRIDE Converter v1.7:

  • Sequest Result Files are now supported.
  • New Folder and LoadSpectra icons.
  • Added CV terms for the upstream and downstream flanking peptide sequences (if detected).
  • Fixed a bug that resulted in all analyzer terms ending up as one analyzer when read from file.
  • Increased the width of all frames to improve the GUI on Linux.
  • Fixed a bug that resulted in an error when trying to add the same file to both of the data types in the DataSelection TwoFileTypes window. (Even though this error should never occur.)
  • Peptide sequences are now set to upper case before being submitted to PRIDE.
  • The program has now been tested on Linux and Windows Vista.
  • Reordering of the columns in the identification column in the FileSelection frame is now disabled.
  • The header for the help frame is updated to PRIDE Converter - Help.
  • All frame headers have been revised and the data source is no longer included.
  • Added a test that makes sure that only one set of spectrum data (the first) is retrieved from a pkl or dta file.
  • iTRAQ support has been added for ms_lims data.

Changes in PRIDE Converter v1.6:

  • Spectrum Mill is now supported.
  • Micromass PKL Files are now supported.
  • Added PRIDE Converter icons to the zip-file.
  • Simple MS/MS Data Format has been changed to Sequest DTA Files. The content has not been altered.
  • File name extentions can now be in both lower and upper case.
  • Non-identified spectra are now deselected when using the Select Identified popupmenu option.
  • Altered the text on the buttons to OK instead of Insert ... or Add ... in the NewContact etc. dialogs.
  • The Experiment Properties label has been added to the file name of the PRIDE xml file.
  • All properties of the iTRAQ calculation are now editable by the user.
  • iTRAQ is now supported for all formats except ms_lims.
  • Updated the GUI for it to become more platform independent.

Changes in PRIDE Converter v1.5:

  • Added support for xTandem data.
  • Added iTRAQ support for xTandem data.
  • Removed the hardcoded user parameters ScoreCalculation, ThresholdCalculation, PeptideIdentification, MascotConfidenceLevel. (MascotConfidenceLevel remains for Mascot Dat Files.)
  • Removed hardcoded cv parameters IntensityUnits=NumberOfCounts and activation method: Post-Source Decay.
  • New version of the Mascot Dat File parser.
  • The database is now set to "unknown" if it is not given.
  • If more than one protein accession number is given for an identification, e.g. HIT000030671.1|HIX0006375.1|BC001819.1|NO|NO|AA|cds, the first is now selected and used.
  • The individual peptide scores are now included.
  • The Mascot version taken from the Mascot Dat File was wrong. Has now been removed.
  • The database version taken from the Mascot Dat File was wrong. Has now been fixed.

Changes in PRIDE Converter v1.4:

  • Help text has been added for all the help icons.
  • Using line shift as file name separator now also works if you don't load the spectra first.
  • The text on the popup menus for deleting a sample set, protocol or instrument has been corrected (from not all saying "Delete Contact"...).
  • Reordering of the NewSample, NewProtocol and NewAnalyzer tables are now disabled also when editing an old instance.
  • Updated the help line at the bottom of the SampleDetails and ProtocolDetails frames.
  • Added Help and About icons to the two ProteinIsoforms dialogs.

Changes in PRIDE Converter v1.3:

  • In the Output Details frame the text in the Special Parameters border has been altered.
  • Added an experiment CV-term for the converter used to generate the xml file.
  • The name of PRIDE xml files created from ms_lims is now shown in the PRIDE XML Created message at the end.
  • Added project title to experiment frame.
  • Added tool tip for the Project field.
  • Fixed a bug that resulted in the converter not being able to start running on Linux.
  • Removed a debug output line that ended up in the ErrorLog.
  • Made some minor changes in the GUI. Mainly to make it look better on non-Windows platforms.
  • The groundwork for adding additional help texts/manual has been done, but the actual texts have not yet been added.

Changes in PRIDE Converter v1.2:

  • 'New Sample Step' was mistitled 'New Protocol Step'
  • Progress bars are now used when loading spectra in all spectra selection frames.
  • Fixed a bug that did not allow more than one analyzer.
  • Sometimes the Protocol and Sample name were empty in the xml file even though they were not empty in the converter.
  • The identifications in Mascot Dat files had to be loaded at the spectra selection stage in order to appear in the xml file.
  • The progress bar now no longer stays at 0% when getting IDs for Mascot Dat files.
  • Added an e-mail address to the otherwise still empty help pages.
  • When clicking the help icon in the dialogs the help page and not the about is now shown.
  • Added a link in the OLS Dialog that opens the browse ontology OLS web page.
  • Updated the About pages.
  • The external links in the help and about pages now opens in the default web browser.
  • Updated the information about the data sources and added external links. (But more changes are still needed.)
  • The last used data file folder is now remembered between each run.
  • Changes in the value column in the processing methods table are now detected and results in a question if the instrument should be saved.
  • Sample name is now mandatory.
  • When saving an instrument, protocol or sample set, the option of overwriting or saving as a new instance is given.
  • Previously only peptides with at least one peptide hit were included in the xml file. Now all are included.
  • Previously the references between the spectra and the identifications were wrong. Its now fixed.
  • Fixed a bug that resulted iTRAQ usage stopping the conversion.
  • Included the number of identifications (both peptides and proteins) in the PRIDE XML Created message at the end.
  • Three alternative ways of handling protein isoforms has been added to Mascot Dat File conversion.
  • Fixed a bug in the spectra selection frame for Mascot Dat files that resulted in the spectra list doubling when clicking on apply selection.
  • Fixed a bug in the spectra selection for ms_lims data that resulted in spectra never being deselected when applying advanced spectra selection.
  • Advanced spectra selection (selecting spectra based on file names) has been added to the Mascot Dat file spectra selection frame.
  • In the advanced spectra selection frames (selecting spectra based on file names) leaving the separator field empty now results in the use of the default separators (line shift, tab etc.).
  • Added an option to round the score and threshold down to the nearest integer before comparison. (To emulate the behaviour of the Mascot web results.)
  • Fixed a bug that made it impossible to delete instruments.
  • If an error occurs while parsing a data file the error is now caught and an error message is shown.
  • Example instruments, protocols and samples are now added to make it even easier to start using the converter.

Changes in PRIDE Converter v1.1:

  • The wrong main-class was used in the previous version. Is now fixed.

Changes in PRIDE Converter v1.0:

  • Name change: from ms_lims_to_PRIDE_converter to PRIDE Converter
  • Added a link to the home page in the about.
  • Removed the 'Preview XML' button in the output frame.
  • Removed the 'Select All Unidentified Spectra' from the Spectra Selection Frame.
  • Added a more advanced "Advanced Spectra Selection" where multiple (partial) file names can now be given.
  • Fixed a bug that made the 'Apply Selection' button stay enabled even if a loading of the spectra was cancelled. Or just when returning to the Spectra Selection frame when the file name criteria field was non-empty.
  • Added a new data source selection frame at the beginning of the wizard.
  • Moved the spectrum selection frame to after project selection.
  • Added longer name tags to each frame in the title ("Experiment Details - Step 3 of 8" etc.)
  • Mascot Dat File and Mascot Generic File support added.
  • Simple Data Format Files are now supported (simple MS/MS format).
  • Alpha version of iTRAQ support added.
  • More than one sample can now be added for one experiment. (Needed for iTRAQ, but can also be used without using iTRAQ.)
  • Multiple files can now be selected as the basis for the xml file.
  • Added a "welcome message" in the first frame.

Changes in ms_lims_converter_v1.10:

  • Added a Preview XML button in the output frame.
  • The Add Sample Details, Add Protocol Step and all the OLS buttons in the Instrument frame are now disabled when a sample, protocol or instrument is not selected, and only becomes enabled if a sample set, protocol or instrument is selected.

Changes in ms_lims_converter_v1.9:

  • Fixed a bug of a missing / at the end if the output folder setting, resulting in a wrong output folder being used.
  • Removed the error message saying that the user folder can not be found if this is the first time running the program. Now it just defaults to the user_home folder without the message.
  • Fixed a bug that resulted in the Project Selection frame sometimes being out of focus when finished loading all the projects.
  • Pressing Tab in the New Contact > Institution and New Reference > Reference text areas now moves the focus, while pressing Ctrl+Tab inserts a new Tab.

Changes in ms_lims_converter_1.8:

  • Updated the about.
  • Added a separate about for the OLS dialog.
  • In the experiment title field pressing Tab now moves the focus to the label field, while pressing Ctrl+Tab inserts a new Tab.
  • Re-added the step number in the Spectrum Selection frame title.
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