FragPipe Versions Save

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data

14.0

3 years ago

Downloading

Running

  • Unzip the file
  • In /bin subdirectory you will find a shell script for Linux, bat file for Windows and an exe file for Windows

Note to Windows users

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.

Changelog:

v14.0:

  • Add PTMProphet.
  • Upgrade Crystal-C to 1.3.2.
  • Upgrade IonQuant to 1.4.4.
  • Upgrade TMT-Integrator to 2.1.4.
  • Upgrade PTM-Shepherd to 0.4.0.
  • Require MSFragger 3.1+.
  • Retire MsAdjuster. Using MSFragger's built-in isotope error correction module.
  • New button to add contaminants and decoys to a fasta.
  • Correct the path in interact-*.pep.xml file.
  • Print related references after the job.

13.0

4 years ago

Downloading

Running

  • Unzip the file
  • In /bin subdirectory you will find a shell script for Linux, bat file for Windows and an exe file for Windows

Note to Windows users

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.

Changelog:

v13.0:

  • Brand new fragpipe, rebuilt almost from ground up
  • TMT-Integrator, PTM-Shepherd, IonQuant included
  • Spectral library generation with EasyPQP
  • Workflows for easier quick-start and sharing

v12.2:

  • Check FASTA file for presence of decoys before running PeptideProphet or Report
  • Fix some Philosopher workspace related bugs
  • Spectral library generation update
  • IMQuant is now IonQuant

12.2

4 years ago

Windows users

  • Download FragPipe.exe 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 FragPipe-12.2.zip.
    • Zip contains FragPipe.bat file, which can be started by either clicking or running it from the command line.
  • Or download the FragPipe-12.2.jar.
    • You can start the jar file with java -jar FragPipe-12.2.jar or start javaw -jar FragPipe-12.2.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

  • Either download FragPipe-12.2.zip, which contains FragPipe shell script to start the program
  • Or download the FragPipe-12.2.jar and run with java -jar FragPipe-12.2.jar.

Changelog:

v12.2:

  • Check FASTA file for presence of decoys before running PeptideProphet or Report
  • Fix some Philosopher workspace related bugs
  • Spectral library generation update
  • IMQuant is now IonQuant

v12.1:

  • IMQuant fixes after initial release.

12.1

4 years ago

Windows users

  • Download FragPipe.exe 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 FragPipe-12.1.zip.
    • Zip contains FragPipe.bat file, which can be started by either clicking or running it from the command line.
  • Or download the FragPipe-12.1.jar.
    • You can start the jar file with java -jar FragPipe-12.1.jar or start javaw -jar FragPipe-12.1.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

  • Either download FragPipe-12.1.zip, which contains FragPipe shell script to start the program
  • Or download the FragPipe-12.1.jar and run with java -jar FragPipe-12.1.jar.

Changelog:

v12.1:

  • IMQuant fixes after initial release.

v12.0:

  • Add IMQuant - quantitation for timsTOF.
  • PTMShepherd updates - in-depth PTM analysis and reporting.
  • Fix running FragPipe without an internet connection.
  • Choice of default enzyme specifications in MSFragger config.

v11.0:

  • Parallel execution engine. Used only for PeptideProphet now, utilizing all CPU cores.
  • DIA-Umpire requires MSConvert from ProteoWizard on Linux.

12.0

4 years ago

FragPipe v12.0

Windows users

  • Download FragPipe.exe 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 FragPipe-12.0.zip.
    • Zip contains FragPipe.bat file, which can be started by either clicking or running it from the command line.
  • Or download the FragPipe-12.0.jar.
    • You can start the jar file with java -jar FragPipe-12.0.jar or start javaw -jar FragPipe-12.0.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

  • Either download FragPipe-12.0.zip, which contains FragPipe shell script to start the program
  • Or download the FragPipe-12.0.jar and run with java -jar FragPipe-12.0.jar.

Changelog:

v12.0:

  • Add IMQuant - quantitation for timsTOF.
  • PTMShepherd updates - in-depth PTM analysis and reporting.
  • Fix running FragPipe without an internet connection.
  • Choice of default enzyme specifications in MSFragger config.

v11.0:

  • Parallel execution engine. Used only for PeptideProphet now, utilizing all CPU cores.
  • DIA-Umpire requires MSConvert from ProteoWizard on Linux.

v10.0:

  • Add PTMShepherd with UI.
  • Thermo RAW files and Bruker TimsTOF .d directories are supported. They do require new MSFragger with 'ext' directory for libraries and additional binaries.
  • Fix for changes to modification tables not always being propagated to config files if the user didn't leave the editing field.
  • Saving all the FragPipe options before run + buttons to Save/Load configurations.
  • Fix iProphet command threads and how it's invoked when multi-experiment is enabled.

11.0

4 years ago

Windows users

  • Download FragPipe.exe 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 FragPipe-11.0.zip.
    • Zip contains FragPipe.bat file, which can be started by either clicking or running it from the command line.
  • Or download the FragPipe-11.0.jar.
    • You can start the jar file with java -jar FragPipe-11.0.jar or start javaw -jar FragPipe-11.0.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

  • Either download FragPipe-11.0.zip, which contains FragPipe shell script to start the program
  • Or download the FragPipe-11.0.jar and run with java -jar FragPipe-11.0.jar.

Changelog:

v11.0:

  • Parallel execution engine. Used only for PeptideProphet now, utilizing all CPU cores.
  • DIA-Umpire requires MSConvert from ProteoWizard on Linux.

v10.0:

  • Add PTMShepherd with UI.
  • Thermo RAW files and Bruker TimsTOF .d directories are supported. They do require new MSFragger with 'ext' directory for libraries and additional binaries.
  • Fix for changes to modification tables not always being propagated to config files if the user didn't leave the editing field.
  • Saving all the FragPipe options before run + buttons to Save/Load configurations.
  • Fix iProphet command threads and how it's invoked when multi-experiment is enabled.

10.1

4 years ago

Windows users

  • Download .exe: FragPipe.exe 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 .zip: FragPipe-10.1.zip.
    • Zip contains FragPipe.bat file, which can be started by either clicking or running it from the command line.
  • Or download the FragPipe-10.1.jar.
    • You can start the jar file with java -jar FragPipe-10.1.jar or start javaw -jar FragPipe-10.1.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

Either download FragPipe-10.1.zip, which contains FragPipe shell script to start the program or download the FragPipe-10.1.jar and run with java -jar FragPipe-10.1.jar.

Changelog:

v10.0:

  • Add PTMShepherd with UI.
  • Thermo RAW files and Bruker TimsTOF .d directories are supported. They do require new MSFragger with 'ext' directory for libraries and additional binaries.
  • Fix for changes to modification tables not always being propagated to config files if the user didn't leave the editing field.
  • Saving all the FragPipe options before run + buttons to Save/Load configurations.
  • Fix iProphet command threads and how it's invoked when multi-experiment is enabled.

v9.4:

  • Fixes to MSFragger Split program for very large databases.

9.4

5 years ago

Windows users

  • Download .exe: FragPipe.exe 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 .zip: FragPipe-9.4.zip.
    • Zip contains FragPipe.bat file, which can be started by either clicking or running it from the command line.
  • Or download the FragPipe-9.4.jar.
    • You can start the jar file with java -jar FragPipe-9.4.jar or start javaw -jar FragPipe-9.4.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

Either download FragPipe-9.4.zip, which contains FragPipe shell script to start the program or download the FragPipe-9.4.jar and run with java -jar FragPipe-9.4.jar.

FragPipe v9.4 changelog:

v9.4:

  • Fixes to MSFragger Split program for very large databases.

v9.3:

  • Calibrate masses option in MSFragger
  • Custom ion series option in MSFragger
  • Turning off usage of protxml file in Filter command when Protein Prophet is not run
  • Query user if protxml files exist while Protein Prophet is not run
  • 'Print Decoys' option/checkbox for Report command
  • Update CrystalC-1.0.5
  • Checkbox for generating report in mzID format
  • UI for downloading protein databases via philosopher

v9.1:

  • Fix Abacus command bug with unrecognized options from Filter command being carried over.

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

9.1

5 years ago

Windows users

  • Download .exe: FragPipe.exe 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 .zip: FragPipe-9.1.zip.
    • Zip contains FragPipe.bat file, which can be started by either clicking or running it from the command line.
  • Or download the FragPipe-9.1.jar.
    • You can start the jar file with java -jar FragPipe-9.1.jar or start javaw -jar FragPipe-9.1.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

Either download FragPipe-9.1.zip, which contains FragPipe shell script to start the program or download the FragPipe-9.1.jar and run with java -jar FragPipe-9.1.jar.

FragPipe v9.1 changelog:

v9.1:

  • Fix Abacus command bug with unrecognized options from Filter command being carried over.

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

9.0

5 years ago

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.