MSFragger-GUI v4.7 (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 v4.7 changelog:

v4.7:

• Support new packaging of MSFragger jar with onejar.
• Check for TSV output from MSFragger when other downstream tools are also requested.

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 v4.6 (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 v4.6 changelog:

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.

v4.4: MSFragger + 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 v4.4 changelog:

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.

v4.3: MSFragger + 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.

Release Notes

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.

v4.2: MSFragger + Prophets + Philosopher Reports

Windows users

• You may download the .zip file.
  • You can start the jar file with javaw -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.

Release Notes

• Fix bug with FraggerPanel throwing an exception in the constructor in some cases
• Support for newer versions of MSFragger
• Detection of some artifacts left over from older versions of Fragger and GUI
• Java 9 warning
• Notifications about new versions of GUI and MSFragger
• Notification about old incompatible MSFRagger versions
• Automatic update of decoy tag between PeptideProhpet and Philosopher Reports

v4.1: MSFragger + Prophets + Philosopher Reports

Windows users

Windows users may download the .exe file and just run that. 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.

Release Notes

• Support for newer versions of MSFragger
• Detection of some artifacts left over from older versions of Fragger and GUI
• Java 9 warning
• Notifications about new versions of GUI and MSFragger
• Notification about old incompatible MSFRagger versions
• Automatic update of decoy tag between PeptideProhpet and Philosopher Reports

v4.0: MSFragger + Prophets + Philosopher Reports

Windows users

Windows users may download the .exe file and just run that. 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.

Release Notes

• notifications about new versions of GUI and MSFragger
• notification about old incompatible MSFRagger versions
• automatic update of decoy tag between PeptideProhpet and Philosopher Reports

v3.0 GUI: MSFragger + Peptide/ProteinProphet + Reports

Windows users

Windows users may download the .exe file and just run that. 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_v3.0.jar.

Release Notes

• a one-time warning about poor MSFragger MGF file compatibility

• landing page for MSFragger download with academic/commercial licenses

• fix PeptideProphet default params

• fix default maxppmdiff param for ProteinProphet in open search defaults

• Dropdown selector for MSFragger output type: pepXML or tsv

• mapmods option was removed temporarily, while we're figuring out how to do it better

v2.9 GUI: MSFragger + Peptide/ProteinProphet + Reports

• a one-time warning about poor MSFragger MGF file compatibility

• landing page for MSFragger download with academic/commercial licenses

• fix PeptideProphet default params

• fix default maxppmdiff param for ProteinProphet in open search defaults

• Dropdown selector for MSFragger output type: pepXML or tsv

• mapmods option was removed temporarily, while we're figuring out how to do it better

v2.8.3 GUI: MSFragger + Peptide/ProteinProphet + Reports

• a one-time warning about poor MSFragger MGF file compatibility

• landing page for MSFragger download with academic/commercial licenses

• fix PeptideProphet default params

• Dropdown selector for MSFragger output type: pepXML or tsv

• mapmods option was removed temporarily, while we're figuring out how to do it better