FragPipe v15.0

Downloading

• The zip (FragPipe-15.0.zip) doesn't contain Java, you will need Java 1.8+ to run.

• The other zip with -jre- in its name (FragPipe-jre-15.0.zip) contains a Java runtime for Windows only.

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:

v15.0:

• Require MSFragger 3.2+.
• Upgrade IonQuant to 1.5.5.
• Upgrade TMT-Integrator to 2.4.0.
• Upgrade PTM-Shepherd to 1.0.0.
• Upgrade DIA-Umpire-SE to 2.2.1, which now supports mzML, mzXML, and raw formats natively.
• Automated MSFragger download.
• Add a button to install/upgrade EasyPQP.
• Automatically detect data types for .d and .raw.
• Additional options added for EasyPQP
• Cosmetic changes for DIA-Umpire, IonQuant, TMT-Integrator tabs
• Remove 'process each experiment separately' checkbox.
• Do not allow space in the path of MSFragger and Philosopher.
• Follow XDG specification for Unix.
• Upgrade the bundled JRE to 11.

FragPipe v14.0

Downloading

• The zip (FragPipe-14.0.zip) doesn't contain Java, you will need Java 1.8+ to run.

• The other zip with -jre- in its name (FragPipe-jre-14.0.zip) contains a Java runtime for Windows only.

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.

FragPipe v13.0

Downloading

• The zip (FragPipe-13.0.zip) doesn't contain Java, you will need Java 1.8+ to run.

• The other zip with -jre- in its name (FragPipe-jre-13.0.zip) contains a Java runtime for Windows only.

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

FragPipe v12.2

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.

FragPipe v12.1

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.

FragPipe v12.0

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.

FragPipe v11.0

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-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.

FragPipe v10.1

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.

FragPipe v9.4

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

FragPipe v9.1

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