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@fcyu fcyu released this Jul 22, 2021

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:

v16.0:

  • Require MSFragger 3.3+
  • Require Philosopher 4.0.0+
  • Upgrade Crystal-C to 1.4.2
  • Upgrade IonQuant to 1.7.5
  • Upgrade TMT-Integrator to 3.0.0
  • Upgrade PTMShepherd to 1.1.0
  • Upgrade batmass-io to 1.23.4
  • Add Percolator as an alternative to PeptideProphet
  • Change how files are passed to ProteinProphet, IonQuant, and EasyPQP to bypass the Windows command length limitation
  • Various minor bug fixes and improvements
Assets 4

@fcyu fcyu released this Mar 10, 2021

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:

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.
Assets 4

@fcyu fcyu released this Sep 30, 2020

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.
Assets 4

@chhh chhh released this Jun 5, 2020

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
Assets 4

@chhh chhh released this Jan 30, 2020

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.
Assets 5

@chhh chhh released this Nov 13, 2019

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.
Assets 5

@chhh chhh released this Nov 9, 2019

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.
Assets 5

@chhh chhh released this Sep 20, 2019

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.
Assets 5

@chhh chhh released this Sep 7, 2019

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.
Assets 5
Sep 4, 2019

10.0

Preparing 10.0 release