A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
-jre-
in its name (FragPipe-jre-21.1.zip) contains a Java runtime for Windows only./bin
subdirectory you will find a shell script for Linux
, bat file for Windows
, and an exe file for Windows
v21.1:
,
as the decimal points in some regions-jre-
in its name (FragPipe-jre-21.0.zip) contains a Java runtime for Windows only./bin
subdirectory you will find a shell script for Linux
, bat file for Windows
, and an exe file for Windows
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.
v21.0:
DDA+
(Workflow tab). MSFragger will perform full isolation window search, identifying multiple co-fragmented peptides from chimeric DDA spectra. This mode significantly boosts the number of IDs compared to conventional DDA search. DDA+ mode is compatible with close search-based DDA workflows (e.g., Default, LFQ-MBR, etc.).DIA_SpecLib_Quant_Phospho
. This workflow includes site localization analysis via PTMProphet. The site localization information is then propagated to the precursor-level quantification tables (additional columns with site localization added to the DIA-NN generated report.pr_matrix.tsv file).MT16-ubiquitination-K_tmt_or_ubiq
and TMT16-ubiquitination-K_tmt_plus_ubiq
workflowsdiann-output
to report
)add top N complementary
option (MSFragger tab)The zip (FragPipe-20.0.zip) doesn't contain Java, you will need Java 9+ to run.
The other zip with -jre-
in its name (FragPipe-jre-20.0.zip) contains a Java runtime for Windows only.
/bin
subdirectory you will find a shell script for Linux
, bat file for Windows
, and an exe file for Windows
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.
v20.0:
PSM.tsv
file, removed. This option also saves Percolator model files from the first search to be used in the second search, as well as the "second pass" workflow file to be loaded and used for the second search.Require precursor
option for MSFragger-DIA (MSFragger tab)Reuse DIA fragment peaks
option for MSFragger-DIA (MSFragger tab)spectral processing
panel (MSFragger tab)TMT10-acetyl
and TMT16-acetyl
workflows as TMT10-acetyl-noloc
and TMT16-acetyl-noloc
. Revise TMT10-acetyl
and TMT16-acetyl
workflows to enable PTM-Prophet site localization.TMT10-ubiquitination-K_tmt_or_ubiq
, and TMT10-ubiquitination-K_tmt_plus_ubiq
workflows that use PTM-Prophet for localizationOpen-quickscan
workflow for faster (but less sensitive and less accurate) Open searchMSstatsTMT_annotation.csv
file for MSstatsTMTexperiment_annotation.tsv
file for FragPipe-AnalystThe zip (FragPipe-19.1.zip) doesn't contain Java, you will need Java 9+ to run.
The other zip with -jre-
in its name (FragPipe-jre-19.1.zip) contains a Java runtime for Windows only.
/bin
subdirectory you will find a shell script for Linux
, bat file for Windows
, and an exe file for Windows
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.
v19.1:
experiment_annotation.tsv
The zip (FragPipe-19.0.zip) doesn't contain Java, you will need Java 9+ to run.
The other zip with -jre-
in its name (FragPipe-jre-19.0.zip) contains a Java runtime for Windows only.
/bin
subdirectory you will find a shell script for Linux
, bat file for Windows
, and an exe file for Windows
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.
v19.0:
The zip (FragPipe-18.0.zip) doesn't contain Java, you will need Java 9+ to run.
The other zip with -jre-
in its name (FragPipe-jre-18.0.zip) contains a Java runtime for Windows only.
/bin
subdirectory you will find a shell script for Linux
, bat file for Windows
and an exe file for Windows
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.
v18.0:
The zip (FragPipe-17.1.zip) doesn't contain Java, you will need Java 1.8+ to run.
The other zip with -jre-
in its name (FragPipe-jre-17.1.zip) contains a Java runtime for Windows only.
/bin
subdirectory you will find a shell script for Linux
, bat file for Windows
and an exe file for Windows
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.
v17.1:
contam_
prefix to contaminants in the downloaded databaseThe zip (FragPipe-17.0.zip) doesn't contain Java, you will need Java 1.8+ to run.
The other zip with -jre-
in its name (FragPipe-jre-17.0.zip) contains a Java runtime for Windows only.
/bin
subdirectory you will find a shell script for Linux
, bat file for Windows
and an exe file for Windows
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.
v17.0:
The zip (FragPipe-16.0.zip) doesn't contain Java, you will need Java 1.8+ to run.
The other zip with -jre-
in its name (FragPipe-jre-16.0.zip) contains a Java runtime for Windows only.
/bin
subdirectory you will find a shell script for Linux
, bat file for Windows
and an exe file for Windows
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.
v16.0:
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.
/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.v15.0: