FragPipe v9.0: large parts of UI rewritten, multi-experiment comparisons and much more

Windows users

• Download the .exe file and just run that. Windows 10 might show a UAC prompt, saying that this is not a trusted program, it's up to you whether to run it or not.
  • If you don't have a compatible Java version, you will be redirected to a website where you can download one.
• Or download the .jar file.
  • You can start the jar file with java -jar FragPipe-9.0.jar or start javaw -jar FragPipe-9.0.jar if you prefer to not have the console window open.
    If Java is configured to auto-run .jar files, double clicking might also work.

Linux/MacOS users

Download the .jar file and run with java -jar FragPipe-9.0.jar.

FragPipe v9.0 changelog:

v9.0:

• Downstream tab groups all downstream processing tools in one place.
• Simplified Config tab with more links and hint.
• Much improved saving and restoring of edited fields.
• Support MSFragger 20190222

v8.8:

• iProphet for peptide level reports.
• Moved all downstream tools (Peptide/Protein Prophet, Crystal-C) to a single tab.
• Simplified reports tab.
• Ask twice about loading defaults automatically.
• Removed decoy tag specification from command line fields. It's now always added implicitly.

FragPipe 8.7: Experiment groups, combined protein reports for groups, new MSFragger version, Philosopher 20181119

Windows users

• Download the .exe file and just run that. Windows 10 might show a UAC prompt, saying that this is not a trusted program, it's up to you whether to run it or not.
  • If you don't have a compatible Java version, you will be redirected to a website where you can download one.
• Or download the .jar file.
  • You can start the jar file with java -jar FragPipe-8.7.jar or start javaw -jar FragPipe-8.7.jar if you prefer to not have the console window open.
    If Java is configured to auto-run .jar files, double clicking might also work.

Linux/MacOS users

Download the .jar file and run with java -jar FragPipe-8.7.jar.

FragPipe v8.7 changelog:

v8.7:

• Support for new Philosopher 20181119, Report Abacus --protein flag.

v8.6:

• Updated nonspecific search default options.
• Colorized console output.
• Multiple UI fixes and updates.

v8.5:

• Updated spectral library generation. LCMS files are copied and deleted from the right locations.
• Multi-experiment protein level report.
• Multi-experiment quantitation
• Allow separate processing of input files one-by-one.

v8.4:

• Combined protein report for multiple file groups.

v8.3:

• LCMS files can be processed in separate groups.
• Python detection on Windows via registry.
• Python binary location can be specified manually.

v8.1:

• DIA-Umpire SE added as an optional component. Mark the checkbox on Config panel to enable.

v8.0:

• Added MSAdjuster, Crystal-C. Both packaged with the release, no extra downloads.

v7.2:

• Added database slicing via a python script (Requires Python 3, NumPy, Pandas).

v7.1:

• Added label free quantitation.

v7.0:

• MFFragger-GUI is now calledFragPipe.
• Clear out Fragger modification tables when loading new parameter files to avoid ghost entries.
• Update the github urls for checking new versions.

v6.0.1:

• Allow loading of empty-valued parameters from fragger *.properties files.
• Comments in fragger.properties won't overwrite non-commented properties anymore.

v6.0:

• Automatic updates for MSFragger
• mass_offsets parameter for MSFragger
• Lower default number of fragments required in Closed search to 4
• Improved tooltips in MSFragger tab
• Initial defaults are loaded for Closed search now instead of Open

v5.4:

• Restore last location of MSfragger params file save/load operation.
• Show errors from loading msfragger.params files

v5.3:

• Button for auto-detection of decoy prefixes
• When sequence DB changes, display the number of proteins.
• Auto-detect buggy cached --clevel option and change it to -2.

v5.2:

• Revert PeptideProphet --clevel option default to '-2' for Open Searching.

v5.1:

• Bug fixes for cross-tool decoy tag updates.

v5.0:

• Separate tab for sequence database.
• Display info about known compatibility of newer versions of Philosopher.

FragPipe 8.6: Experiment groups, combined protein reports for groups, new MSFragger version

Windows users

• Download the .exe file and just run that. Windows 10 might show a UAC prompt, saying that this is not a trusted program, it's up to you whether to run it or not.
  • If you don't have a compatible Java version, you will be redirected to a website where you can download one.
• Or download the .jar file.
  • You can start the jar file with java -jar FragPipe-8.6.jar or start javaw -jar FragPipe-8.6.jar if you prefer to not have the console window open.
    If Java is configured to auto-run .jar files, double clicking might also work.

Linux/MacOS users

Download the .jar file and run with java -jar FragPipe-8.6.jar.

FragPipe v8.6 changelog:

v8.6:

• Updated nonspecific search default options.
• Colorized console output.
• Multiple UI fixes and updates.

v8.5:

• Updated spectral library generation. LCMS files are copied and deleted from the right locations.
• Multi-experiment protein level report.
• Multi-experiment quantitation
• Allow separate processing of input files one-by-one.

v8.4:

• Combined protein report for multiple file groups.

v8.3:

• LCMS files can be processed in separate groups.
• Python detection on Windows via registry.
• Python binary location can be specified manually.

v8.1:

• DIA-Umpire SE added as an optional component. Mark the checkbox on Config panel to enable.

v8.0:

• Added MSAdjuster, Crystal-C. Both packaged with the release, no extra downloads.

v7.2:

• Added database slicing via a python script (Requires Python 3, NumPy, Pandas).

v7.1:

• Added label free quantitation.

v7.0:

• MFFragger-GUI is now calledFragPipe.
• Clear out Fragger modification tables when loading new parameter files to avoid ghost entries.
• Update the github urls for checking new versions.

v6.0.1:

• Allow loading of empty-valued parameters from fragger *.properties files.
• Comments in fragger.properties won't overwrite non-commented properties anymore.

v6.0:

• Automatic updates for MSFragger
• mass_offsets parameter for MSFragger
• Lower default number of fragments required in Closed search to 4
• Improved tooltips in MSFragger tab
• Initial defaults are loaded for Closed search now instead of Open

v5.4:

• Restore last location of MSfragger params file save/load operation.
• Show errors from loading msfragger.params files

v5.3:

• Button for auto-detection of decoy prefixes
• When sequence DB changes, display the number of proteins.
• Auto-detect buggy cached --clevel option and change it to -2.

v5.2:

• Revert PeptideProphet --clevel option default to '-2' for Open Searching.

v5.1:

• Bug fixes for cross-tool decoy tag updates.

v5.0:

• Separate tab for sequence database.
• Display info about known compatibility of newer versions of Philosopher.

v4.9:

• Stop execution of the pipeline if one of the processes returns non-zero exit code.
• Colorize console output a bit, red color for errors.
• Button that redirects to the issue tracker online for bug reporting.

v4.8:

• Introduce notifications about update contents
• User-message can now be shown without a newer version available
• Added export button and context menu item to the console to simplify bug reporting by users.

v4.7:

• Support new packaging of MSFragger jar with onejar.

v4.6:

• Fix mixed up order of philosopher calls.

v4.5:

• Show parsed versions of tools in the UI.
• Print detected versions of tools to console before each run.

v4.4:

• Only run Philosopher workspace --clean/--init once per analysis.

v4.3:

• Locale dependency fix for MSfragger parameters panel.
• Philosopher checks version comparing to GitHub at startup.

v4.2:

• Fix the issue that Fragger panel constructor could cause IOException and prevent the whole app from loading.

v4.1:

• Variable mod site definition warning text if cached from older versions.
• Java 9 warning for Fragger.
• Non-symmetric precursor mass tolerance and detection of "[*" for var mods.
• Cache fragger params after a dry-run or a real run.

v4.0:

• Added version check for MSFragger-GUI itself, comparing to GitHub.
• Two way sync of decoy/tag prefix used by Peptide Prophet and Philosopher Report.
• Fix how msfragger jar is auto-found.
• Added version to msfragger properties.
• MSFragger version check.

FragPipe v7.1 (previously MSFragger-GUI. Includes MSFragger, Peptide/Protein Prophets, Philosopher Reports

Windows users

• You may download the .zip file.
  • You can start the jar file with start javaw -jar FragPipe.jar or java -jar FragPipe.jar or using the provided .bat script in the zip archive. If Java is configured to auto-run .jar files, double clicking might also work.
• You may download the .exe file and just run that. Windows 10 might show a UAC prompt, saying that this is not a trusted program, it's up to you whether to run it or not.
  • If you don't have a compatible Java version, you will be redirected to a website where you can download one.

Linux/MacOS users

Download the .zip file and either run the included launcher shell script or just with java -jar FragPipe.jar.

FragPipe v7.1 changelog:

v7.1:

• Added label free quantitation.

v7.0:

• MFFragger-GUI is now calledFragPipe.
• Clear out Fragger modification tables when loading new parameter files to avoid ghost entries.
• Update the github urls for checking new versions.

v6.0.1:

• Allow loading of empty-valued parameters from fragger *.properties files.
• Comments in fragger.properties won't overwrite non-commented properties anymore.

v6.0:

• Automatic updates for MSFragger
• mass_offsets parameter for MSFragger
• Lower default number of fragments required in Closed search to 4
• Improved tooltips in MSFragger tab
• Initial defaults are loaded for Closed search now instead of Open

v5.4:

• Restore last location of MSfragger params file save/load operation.
• Show errors from loading msfragger.params files

v5.3:

• Button for auto-detection of decoy prefixes
• When sequence DB changes, display the number of proteins.
• Auto-detect buggy cached --clevel option and change it to -2.

v5.2:

• Revert PeptideProphet --clevel option default to '-2' for Open Searching.

v5.1:

• Bug fixes for cross-tool decoy tag updates.

v5.0:

• Separate tab for sequence database.
• Display info about known compatibility of newer versions of Philosopher.

v4.9:

• Stop execution of the pipeline if one of the processes returns non-zero exit code.
• Colorize console output a bit, red color for errors.
• Button that redirects to the issue tracker online for bug reporting.

v4.8:

• Introduce notifications about update contents
• User-message can now be shown without a newer version available
• Added export button and context menu item to the console to simplify bug reporting by users.

v4.7:

• Support new packaging of MSFragger jar with onejar.

v4.6:

• Fix mixed up order of philosopher calls.

v4.5:

• Show parsed versions of tools in the UI.
• Print detected versions of tools to console before each run.

v4.4:

• Only run Philosopher workspace --clean/--init once per analysis.

v4.3:

• Locale dependency fix for MSfragger parameters panel.
• Philosopher checks version comparing to GitHub at startup.

v4.2:

• Fix the issue that Fragger panel constructor could cause IOException and prevent the whole app from loading.

v4.1:

• Variable mod site definition warning text if cached from older versions.
• Java 9 warning for Fragger.
• Non-symmetric precursor mass tolerance and detection of "[*" for var mods.
• Cache fragger params after a dry-run or a real run.

v4.0:

• Added version check for MSFragger-GUI itself, comparing to GitHub.
• Two way sync of decoy/tag prefix used by Peptide Prophet and Philosopher Report.
• Fix how msfragger jar is auto-found.
• Added version to msfragger properties.
• MSFragger version check.

MSFragger-GUI v6.0 (MSFragger, Peptide/Protein Prophets, Philosopher Reports)

Windows users

• You may download the .zip file.
  • You can start the jar file with start javaw -jar MSFragger-GUI.jar or java -jar MSFragger-GUI.jar or using the provided .bat script in the zip archive. If Java is configured to auto-run .jar files, double clicking might also work.
• You may download the .exe file and just run that. Windows 10 might show a UAC prompt, saying that this is not a trusted program, it's up to you whether to run it or not.
  • If you don't have a compatible Java version, you will be redirected to a website where you can download one.

Linux/MacOS users

Download the .zip file and either run the included launcher shell script or just with java -jar MSFragger-GUI.jar.

MSFragger-GUI v6.0 changelog:

v6.0:

• Automatic updates for MSFragger
• mass_offsets parameter for MSFragger
• Lower default number of fragments required in Closed search to 4
• Improved tooltips in MSFragger tab
• Initial defaults are loaded for Closed search now instead of Open

v5.4:

• Restore last location of MSfragger params file save/load operation.
• Show errors from loading msfragger.params files

v5.3:

• Button for auto-detection of decoy prefixes
• When sequence DB changes, display the number of proteins.
• Auto-detect buggy cached --clevel option and change it to -2.

v5.2:

• Revert PeptideProphet --clevel option default to '-2' for Open Searching.

v5.1:

• Bug fixes for cross-tool decoy tag updates.

v5.0:

• Separate tab for sequence database.
• Display info about known compatibility of newer versions of Philosopher.

v4.9:

• Stop execution of the pipeline if one of the processes returns non-zero exit code.
• Colorize console output a bit, red color for errors.
• Button that redirects to the issue tracker online for bug reporting.

v4.8:

• Introduce notifications about update contents
• User-message can now be shown without a newer version available
• Added export button and context menu item to the console to simplify bug reporting by users.

v4.7:

• Support new packaging of MSFragger jar with onejar.

v4.6:

• Fix mixed up order of philosopher calls.

v4.5:

• Show parsed versions of tools in the UI.
• Print detected versions of tools to console before each run.

v4.4:

• Only run Philosopher workspace --clean/--init once per analysis.

v4.3:

• Locale dependency fix for MSfragger parameters panel.
• Philosopher checks version comparing to GitHub at startup.

v4.2:

• Fix the issue that Fragger panel constructor could cause IOException and prevent the whole app from loading.

v4.1:

• Variable mod site definition warning text if cached from older versions.
• Java 9 warning for Fragger.
• Non-symmetric precursor mass tolerance and detection of "[*" for var mods.
• Cache fragger params after a dry-run or a real run.

v4.0:

• Added version check for MSFragger-GUI itself, comparing to GitHub.
• Two way sync of decoy/tag prefix used by Peptide Prophet and Philosopher Report.
• Fix how msfragger jar is auto-found.
• Added version to msfragger properties.
• MSFragger version check.

MSFragger-GUI v5.4 (MSFragger, Peptide/Protein Prophets, Philosopher Reports)

Windows users

• You may download the .zip file.
  • You can start the jar file with start javaw -jar MSFragger-GUI.jar or java -jar MSFragger-GUI.jar or using the provided .bat script in the zip archive. If Java is configured to auto-run .jar files, double clicking might also work.
• You may download the .exe file and just run that. Windows 10 might show a UAC prompt, saying that this is not a trusted program, it's up to you whether to run it or not.
  • If you don't have a compatible Java version, you will be redirected to a website where you can download one.

Linux/MacOS users

Download the .zip file and either run the included launcher shell script or just with java -jar MSFragger-GUI.jar.

MSFragger-GUI v5.4 changelog:

v5.4:

• Restore last location of MSfragger params file save/load operation.
• Show errors from loading msfragger.params files

v5.3:

• Button for auto-detection of decoy prefixes
• When sequence DB changes, display the number of proteins.
• Auto-detect buggy cached --clevel option and change it to -2.

v5.2:

• Revert PeptideProphet --clevel option default to '-2' for Open Searching.

v5.1:

• Bug fixes for cross-tool decoy tag updates.

v5.0:

• Separate tab for sequence database.
• Display info about known compatibility of newer versions of Philosopher.

v4.9:

• Stop execution of the pipeline if one of the processes returns non-zero exit code.
• Colorize console output a bit, red color for errors.
• Button that redirects to the issue tracker online for bug reporting.

v4.8:

• Introduce notifications about update contents
• User-message can now be shown without a newer version available
• Added export button and context menu item to the console to simplify bug reporting by users.

v4.7:

• Support new packaging of MSFragger jar with onejar.

v4.6:

• Fix mixed up order of philosopher calls.

v4.5:

• Show parsed versions of tools in the UI.
• Print detected versions of tools to console before each run.

v4.4:

• Only run Philosopher workspace --clean/--init once per analysis.

v4.3:

• Locale dependency fix for MSfragger parameters panel.
• Philosopher checks version comparing to GitHub at startup.

v4.2:

• Fix the issue that Fragger panel constructor could cause IOException and prevent the whole app from loading.

v4.1:

• Variable mod site definition warning text if cached from older versions.
• Java 9 warning for Fragger.
• Non-symmetric precursor mass tolerance and detection of "[*" for var mods.
• Cache fragger params after a dry-run or a real run.

v4.0:

• Added version check for MSFragger-GUI itself, comparing to GitHub.
• Two way sync of decoy/tag prefix used by Peptide Prophet and Philosopher Report.
• Fix how msfragger jar is auto-found.
• Added version to msfragger properties.
• MSFragger version check.

MSFragger-GUI v5.3 (MSFragger, Peptide/Protein Prophets, Philosopher Reports)

Windows users

• You may download the .zip file.
  • You can start the jar file with start javaw -jar MSFragger-GUI.jar or java -jar MSFragger-GUI.jar or using the provided .bat script in the zip archive. If Java is configured to auto-run .jar files, double clicking might also work.
• You may download the .exe file and just run that. Windows 10 might show a UAC prompt, saying that this is not a trusted program, it's up to you whether to run it or not.
  • If you don't have a compatible Java version, you will be redirected to a website where you can download one.

Linux/MacOS users

Download the .zip file and either run the included launcher shell script or just with java -jar MSFragger-GUI.jar.

MSFragger-GUI v5.3 changelog:

v5.3:

• Button for auto-detection of decoy prefixes
• When sequence DB changes, display the number of proteins.
• Auto-detect buggy cached --clevel option and change it to -2.

v5.2:

• Revert PeptideProphet --clevel option default to '-2' for Open Searching.

v5.1:

• Bug fixes for cross-tool decoy tag updates.

v5.0:

• Separate tab for sequence database.
• Display info about known compatibility of newer versions of Philosopher.

v4.9:

• Stop execution of the pipeline if one of the processes returns non-zero exit code.
• Colorize console output a bit, red color for errors.
• Button that redirects to the issue tracker online for bug reporting.

v4.8:

• Introduce notifications about update contents
• User-message can now be shown without a newer version available
• Added export button and context menu item to the console to simplify bug reporting by users.

v4.7:

• Support new packaging of MSFragger jar with onejar.

v4.6:

• Fix mixed up order of philosopher calls.

v4.5:

• Show parsed versions of tools in the UI.
• Print detected versions of tools to console before each run.

v4.4:

• Only run Philosopher workspace --clean/--init once per analysis.

v4.3:

• Locale dependency fix for MSfragger parameters panel.
• Philosopher checks version comparing to GitHub at startup.

v4.2:

• Fix the issue that Fragger panel constructor could cause IOException and prevent the whole app from loading.

v4.1:

• Variable mod site definition warning text if cached from older versions.
• Java 9 warning for Fragger.
• Non-symmetric precursor mass tolerance and detection of "[*" for var mods.
• Cache fragger params after a dry-run or a real run.

v4.0:

• Added version check for MSFragger-GUI itself, comparing to GitHub.
• Two way sync of decoy/tag prefix used by Peptide Prophet and Philosopher Report.
• Fix how msfragger jar is auto-found.
• Added version to msfragger properties.
• MSFragger version check.

MSFragger-GUI v5.0 (MSFragger, Peptide/Protein Prophets, Philosopher Reports)

Windows users

• You may download the .zip file.
  • You can start the jar file with start javaw -jar MSFragger-GUI.jar or java -jar MSFragger-GUI.jar or using the provided .bat script in the zip archive. If Java is configured to auto-run .jar files, double clicking might also work.
• You may download the .exe file and just run that. Windows 10 might show a UAC prompt, saying that this is not a trusted program, it's up to you whether to run it or not.
  • If you don't have a compatible Java version, you will be redirected to a website where you can download one.

Linux/MacOS users

Download the .zip file and either run the included launcher shell script or just with java -jar MSFragger-GUI.jar.

MSFragger-GUI v5.0 changelog:

v5.0:

• Separate tab for sequence database.
• Display info about known compatibility of newer versions of Philosopher.

v4.9:

• Stop execution of the pipeline if one of the processes returns non-zero exit code.
• Colorize console output a bit, red color for errors.
• Button that redirects to the issue tracker online for bug reporting.

v4.8:

• Introduce notifications about update contents
• User-message can now be shown without a newer version available
• Added export button and context menu item to the console to simplify bug reporting by users.

v4.7:

• Support new packaging of MSFragger jar with onejar.

v4.6:

• Fix mixed up order of philosopher calls.

v4.5:

• Show parsed versions of tools in the UI.
• Print detected versions of tools to console before each run.

v4.4:

• Only run Philosopher workspace --clean/--init once per analysis.

v4.3:

• Locale dependency fix for MSfragger parameters panel.
• Philosopher checks version comparing to GitHub at startup.

v4.2:

• Fix the issue that Fragger panel constructor could cause IOException and prevent the whole app from loading.

v4.1:

• Variable mod site definition warning text if cached from older versions.
• Java 9 warning for Fragger.
• Non-symmetric precursor mass tolerance and detection of "[*" for var mods.
• Cache fragger params after a dry-run or a real run.

v4.0:

• Added version check for MSFragger-GUI itself, comparing to GitHub.
• Two way sync of decoy/tag prefix used by Peptide Prophet and Philosopher Report.
• Fix how msfragger jar is auto-found.
• Added version to msfragger properties.
• MSFragger version check.

MSFragger-GUI v4.9 (MSFragger, Peptide/Protein Prophets, Philosopher Reports)

Windows users

• You may download the .zip file.
  • You can start the jar file with start javaw -jar MSFragger-GUI.jar or java -jar MSFragger-GUI.jar or using the provided .bat script in the zip archive. If Java is configured to auto-run .jar files, double clicking might also work.
• You may download the .exe file and just run that. Windows 10 might show a UAC prompt, saying that this is not a trusted program, it's up to you whether to run it or not.
  • If you don't have a compatible Java version, you will be redirected to a website where you can download one.

Linux/MacOS users

Download the .zip file and either run the included launcher shell script or just with java -jar MSFragger-GUI.jar.

MSFragger-GUI v4.9 changelog:

v4.9:

• Stop execution of the pipeline if one of the processes returns non-zero exit code.
• Colorize console output a bit, red color for errors.
• Button that redirects to the issue tracker online for bug reporting.

v4.8:

• Introduce notifications about update contents
• User-message can now be shown without a newer version available
• Added export button and context menu item to the console to simplify bug reporting by users.

v4.7:

• Support new packaging of MSFragger jar with onejar.

v4.6:

• Fix mixed up order of philosopher calls.

v4.5:

• Show parsed versions of tools in the UI.
• Print detected versions of tools to console before each run.

v4.4:

• Only run Philosopher workspace --clean/--init once per analysis.

v4.3:

• Locale dependency fix for MSfragger parameters panel.
• Philosopher checks version comparing to GitHub at startup.

v4.2:

• Fix the issue that Fragger panel constructor could cause IOException and prevent the whole app from loading.

v4.1:

• Variable mod site definition warning text if cached from older versions.
• Java 9 warning for Fragger.
• Non-symmetric precursor mass tolerance and detection of "[*" for var mods.
• Cache fragger params after a dry-run or a real run.

v4.0:

• Added version check for MSFragger-GUI itself, comparing to GitHub.
• Two way sync of decoy/tag prefix used by Peptide Prophet and Philosopher Report.
• Fix how msfragger jar is auto-found.
• Added version to msfragger properties.
• MSFragger version check.

MSFragger-GUI v4.8 (MSFragger, Peptide/Protein Prophets, Philosopher Reports)

Windows users

• You may download the .zip file.
  • You can start the jar file with start javaw -jar MSFragger-GUI.jar or java -jar MSFragger-GUI.jar or using the provided .bat script in the zip archive. If Java is configured to auto-run .jar files, double clicking might also work.
• You may download the .exe file and just run that. Windows 10 might show a UAC prompt, saying that this is not a trusted program, it's up to you whether to run it or not.
  • If you don't have a compatible Java version, you will be redirected to a website where you can download one.

Linux/MacOS users

Download the .zip file and either run the included launcher shell script or just with java -jar MSFragger-GUI.jar.

MSFragger-GUI v4.8 changelog:

v4.8:

• Introduce notifications about update contents
• User-message can now be shown without a newer version available
• Added export button and context menu item to the console to simplify bug reporting by users.

v4.7:

• Support new packaging of MSFragger jar with onejar.

v4.6:

• Fix mixed up order of philosopher calls.

v4.5:

• Show parsed versions of tools in the UI.
• Print detected versions of tools to console before each run.

v4.4:

• Only run Philosopher workspace --clean/--init once per analysis.

v4.3:

• Locale dependency fix for MSfragger parameters panel.
• Philosopher checks version comparing to GitHub at startup.

v4.2:

• Fix the issue that Fragger panel constructor could cause IOException and prevent the whole app from loading.

v4.1:

• Variable mod site definition warning text if cached from older versions.
• Java 9 warning for Fragger.
• Non-symmetric precursor mass tolerance and detection of "[*" for var mods.
• Cache fragger params after a dry-run or a real run.

v4.0:

• Added version check for MSFragger-GUI itself, comparing to GitHub.
• Two way sync of decoy/tag prefix used by Peptide Prophet and Philosopher Report.
• Fix how msfragger jar is auto-found.
• Added version to msfragger properties.
• MSFragger version check.