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Releases: Nesvilab/FragPipe

FragPipe v22.0

30 May 01:18
@fcyu fcyu
22.0
a187705
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FragPipe v22.0 Latest
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  • In /bin subdirectory you will find a shell script for Linux, bat file for Windows, and an exe file for Windows

Changelog:

v22.0:

  • diaTracer tool for generating pseudo-MS/MS spectra from diaPASEF data, enabling spectrum-centric, direct DIA analysis (including nonspecific and PTM searches).
  • Integration of Skyline in FragPipe (supporting DIA, DDA, and DDA glycoproteomics workflows).
  • Support for MSFragger DDA+ (full isolation window search) analysis of ddaPASEF data.
  • Support in MSBooster for using the Koina server for deep-learning predictions. Requires specifying the Koina URL.
  • Support user-specified glycans and glycan modifications for glycoproteomics searches.
  • Implement DIA glycoproteomics workflows.
  • Significantly faster loading of Thermo raw files in MSFragger and IonQuant.
  • Calculate and report more information useful for localizing the sites of modifications identified in open and mass-offset searches.
  • Add photo-affinity labeling (PAL) chemoproteomics workflow.
  • For DIA analysis, propagate the site localization, protein start, and protein end information to msstats.csv file.
  • For DIA analysis, propagate the site localization to the DIA-NN's reports.
  • For DIA analysis, propagate Proteotypic, AllMappedProteins, and AllMappedGenes columns to the DIA-NN reports.
  • Generate MSstatsPTM input files.
  • Add nocleavage option to the enzyme panel in the MSFragger tab.
  • Add analyze filter dropdown to the MSFragger tab to only search MS/MS scans of the specified type (ITMS or FTMS).
  • Change the default value of the IonQuant's minions to 1 (MaxLFQ normalization).
  • Overhaul MSFragger and IonQuant config panels. MSFragger, IonQuant, and diaTracer need to be in the same folder. Specify the folder in the Config tab.
  • Update the tool download panel
  • Bundle Philosopher
  • Upgrade the bundled JRE to version 17
  • Require Java 11+
  • Require MSFragger 4.1+
  • Require IonQuant 1.10.27+
  • Require Python 3.9, 3.10, or 3.11
  • Require EasyPQP 0.1.44+
  • Upgrade Crystal-C to 1.5.6
  • Upgrade MSBooster to 1.2.31
  • Upgrade Percolator to 3.6.5
  • Upgrade TMT-Integrator to 5.0.9
  • Various bug fixes and improvements
Assets 4
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FragPipe v21.1

21 Dec 01:26
@fcyu fcyu
21.1
3cf0e2a
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FragPipe v21.1

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

Changelog:

v21.1:

  • Fix a bug in TMT-Integrator that in the single/multi-site reports, the site, protein start, and protein end are off by 1
  • Fix a bug in MSBooster that using , as the decimal points in some regions
  • Require MSFragger 4.0+
  • Require Philosopher 5.1.0+
  • Require IonQuant 1.10.12+
  • Require Python 3.9
  • Require EasyPQP 0.1.41+
  • Upgrade MSBooster to 1.1.28
  • Upgrade TMT-Integrator to 5.0.7
Assets 4
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FragPipe v21.0

19 Dec 21:11
@fcyu fcyu
21.0
0a5641c
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FragPipe v21.0

Downloading

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  • 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:

v21.0:

  • Add support for the new MSFragger-DDA+ search mode (introduced in MSFragger 4.0). Data acquired in DDA mode (including wide-window DDA data) can now be annotated as 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.).
  • Add support for the detailed mass offset search mode (introduced in MSFragger 4.0). Each specified mass offset can have their own modification sites, neutral losses, and diagnostic ions. The detailed mass offsets are loaded from an external file (MSFragger tab). A sample mass offset file (mass_offset_template.tsv file) is available in the FragPipe/tools folder.
  • Add new workflow for DIA-based phosphoproteomics: 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).
  • In isobaric quantification workflows, switch to IonQuant for extraction of reporter ion intensities, MS1 intensities, and precursor purity calculation (Quant(Isobaric) tab). These steps were previously done using Philosopher LabelQuant and FreeQuant modules (now available as an option). As an additional benefit of using IonQuant, isobaric quantification workflows can now be used with Thermo's RAW files (i.e., without first converting to mzML).
  • Significantly improve the speed of spectral library building
  • Significantly improve the timsTOF ddaPASEF .d folder loading speed
  • Add new module for downstream analysis of FPOP data (Downstream tab)
  • Add MT16-ubiquitination-K_tmt_or_ubiq and TMT16-ubiquitination-K_tmt_plus_ubiq workflows
  • Adjust parameters in DIA workflows for improved analysis of Thermo Fisher's Astral narrow-window DIA data
  • Enable MSBooster and Percolator in the analysis of endogenous peptidome data (nonspecific_peptidome workflow).
  • Add the DIA-NN executable file box (Config tab) to support custom (user-downloaded) DIA-NN versions. If the path is left empty, FragPipe uses the default DIA-NN version 1.8.2_beta_8 included in the FragPipe.
  • Generate MSstats formatted output files in DIA workflows
  • Generate MSstatsPTM formatted files in DDA label-free-quantification workflows
  • Rename DIA-NN output files (diann-output to report)
  • Add support for DIA-NN's QuantUMS quantification option (DIA-NN tab)
  • Add support for TMT-0 and TMT-2 isobaric labelling (Quant(Isobaric) tab)
  • The isobaric quant annotation files can be in different folders
  • Add SDRF table writer
  • Add a button to load variable modifications specified in MSFragger to PTMProphet command box (Validation tab)
  • Add a docker image: https://hub.docker.com/r/fcyucn/fragpipe
  • Improve generation of the annotation files for FragPipe-Analyst: http://fragpipe-analyst.nesvilab.org/
  • Remove add top N complementary option (MSFragger tab)
  • Mark Philosopher FreeQuant as deprecated
  • Require MSFragger 4.0+
  • Require Philosopher 5.1.0+
  • Require IonQuant 1.10.12+
  • Require Python 3.9
  • Require EasyPQP 0.1.41+
  • Upgrade MSBooster to 1.1.27
  • Upgrade Percolator to 3.6.4
  • Upgrade PTMShepherd to 2.0.6
  • Upgrade FragPipe-PDV to 1.1.5
  • Upgrade O-Pair to 1.1.0
  • Upgrade TMT-Integrator to 5.0.6
  • Various bug fixes and improvements
Assets 4
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FragPipe v20.0

31 May 22:17
@fcyu fcyu
20.0
6a21a48
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FragPipe v20.0

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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:

v20.0:

  • Require MSFragger 3.8+
  • Require Philosopher 5.0.0+
  • Require IonQuant 1.9.8+
  • Require Python 3.9
  • Require EasyPQP 0.1.34+
  • Add MBR support for MS1-based label quantification (IonQuant in Quant(MS1) tab)
  • Add support for fractionated data in MS1-based label quantification (IonQuant in Quant(MS1) tab)
  • Add two-pass search support (checkbox in Run tab). Generate new calibrated mzML files with identified scans, i.e. those reported in the 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.
  • Add group FDR support based on the group label defined in the MSFragger tab. This complements the existing group FDR options in Philosopher for modification-based group FDR filtering in Philosopher (--mod and --delta command line options, Validation tab).
  • Add plexDIA support (DIA-NN tab).
  • Add Require precursor option for MSFragger-DIA (MSFragger tab)
  • Add Reuse DIA fragment peaks option for MSFragger-DIA (MSFragger tab)
  • Add report top-N options for DDA, DIA, and GPF-DIA, respectively (MSFragger tab)
  • Adjust the the spectral processing panel (MSFragger tab)
  • Add Oxonium ion filter (Glyco tab)
  • Add an option to choose one of the built-in Glycan databases or load a custom list (Glyco tab)
  • Add mass filtering option for Glycan database load when not using combinations (Glyco tab)
  • Support parsing glycan databases in alternate ("kind") MetaMorpheus format (Glyco tab)
  • Rename the old 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.
  • Add new TMT10-ubiquitination-K_tmt_or_ubiq, and TMT10-ubiquitination-K_tmt_plus_ubiq workflows that use PTM-Prophet for localization
  • Add new Open-quickscan workflow for faster (but less sensitive and less accurate) Open search
  • Tuned parameters in some built-in workflows
  • Faster processing speed and reduced memory usage due to major improvements in IO operations and database reading in Philosopher
  • Generate a single combined msstats.csv file for the TMT workflows
  • Generate MSstatsTMT_annotation.csv file for MSstatsTMT
  • Improved parsing of samples/conditions when preparing experiment_annotation.tsv file for FragPipe-Analyst
  • Upgrade Crystal-C to 1.5.2
  • Upgrade Percolator Windows version to 3.06
  • Upgrade PTMProphet to 6.3.2
  • Upgrade PTMShepherd to 2.0.5
  • Upgrade FragPipe-PDV to 1.1.1
  • Upgrade O-Pair to 1.1-rc2
  • Upgrade TMT-Integrator to 4.0.5
  • Various bug fixes and improvements
Assets 4
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FragPipe v19.1

13 Jan 20:57
@fcyu fcyu
19.1
70f2bb2
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FragPipe v19.1

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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:

v19.1:

  • Require MSFragger 3.7+
  • Require Philosopher 4.8.0+
  • Require IonQuant 1.8.10+
  • Require EasyPQP 0.1.34+
  • Add 'write uncalibrated mgf' checkbox
  • Add Add iTRAQ4-phospho workflow
  • Update iTRAQ4 workflow
  • Rename 'combined_annotation.tsv' to 'experiment_annotation.tsv'
  • Update the format of experiment_annotation.tsv
  • Allow MSBooster for mass-offset search
  • In GUI mode, do not load the tools' config paths from the workflow file
  • Upgrade Crystal-C to 1.5.1
  • Upgrade MSBooster to 1.1.11
  • Upgrade DIA-Umpire to 2.3.2
  • Various minor bug fixes and improvements
Assets 4
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FragPipe v19.0

03 Dec 17:47
@fcyu fcyu
19.0
3e0189e
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FragPipe v19.0

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:

v19.0:

  • Require Java 9+
  • Require MSFragger 3.6+
  • Require Philosopher 4.6.0+
  • Require IonQuant 1.8.9+
  • Require EasyPQP 0.1.34+
  • Add O-Pair for O-Glycan localization
  • Add downstream analysis tool SAINT
  • Support PTM localization using PTMProphet for timsTOF .d and Thermo .raw formats
  • Add --config-ionquant flag in headless mode
  • Add "delete calibrated mzML" and "delete temp files" checkboxes
  • Add "open FragPipe-Analyst" button
  • Add "remove contaminants" checkbox to the "FDR filter and report" panel
  • Add "neutral loss" checkbox to the speclib tab
  • Add glycan database loader to Glyco tab
  • Add mass-offset list loader to MSFragger tab
  • Put DIA-NN's output fies to "diann-output" folder
  • Put EasyPQP output files to "eaasypqp_files" directory
  • Rename "Open visualization window" button to "Open FragPipe-PDV viewer"
  • Remove "Close visualization window" button
  • Write all TMT annotations to a single combined_annotation.txt file
  • Upgrade DIA-NN to 1.8.2 beta 8
  • Upgrade PTM-Shepherd to 2.0.3
  • Upgrade TMT-Integrator to 4.0.4
  • Upgrade DIA-Umpire to 2.3.1
  • Upgrade MSBooster to 1.1.10
  • Upgrade FP-PDV to 1.0.5
  • Add more workflows
  • Various minor bug fixes and improvements
Assets 4
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FragPipe v18.0

27 May 16:07
@fcyu fcyu
18.0
7e42070
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FragPipe v18.0

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:

v18.0:

  • Require Java 9+
  • Require MSFragger 3.5+
  • Require Philosopher 4.2.2+
  • Require IonQuant 1.7.30+
  • Add new FragPipe-PDV visualization module
  • Add the IonQuant configuration panel
  • Add more workflows
  • Upgrade DIA-NN to 1.8.1
  • Upgrade PTM-Shepherd to 2.0.0
  • Upgrade TMT-Integrator to 3.3.3
  • Upgrade DIA-Umpire to 2.2.8
  • Upgrade MSBooster to 1.1.4
  • Upgrade Crystal-C to 1.4.4
  • Various minor bug fixes and improvements
Assets 4
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FragPipe v17.1

17 Nov 19:07
@fcyu fcyu
17.1
7b8eeb3
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FragPipe v17.1

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:

v17.1:

  • Require MSFragger 3.4+
  • Require Philosopher 4.1.0+
  • Add Pierce iRT file
  • Add contam_ prefix to contaminants in the downloaded database
  • Add more workflows
  • Upgrade PTM-Shepherd to 1.2.6
  • Upgrade IonQuant to 1.7.17
  • Upgrade TMT-Integrator to 3.2.1
  • Upgrade MSBooster
  • Various minor bug fixes and improvements
Assets 4
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FragPipe v17.0

31 Oct 15:28
@fcyu fcyu
17.0
f4f342f
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FragPipe v17.0

FragPipe v17.0

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:

v17.0:

  • Require MSFragger 3.4+
  • Require Philosopher 4.1.0+
  • Add MSBooster 1.0 for deep learning based rescoring (Validation)
  • Add glycan assignment with FDR control (PTM)
  • Add DIA quantification with DIA-NN 1.8 (DIA Quant tab)
  • Support two enzymes and N-terminal cutting enzyme (MSFragger tab)
  • Support DDA, DIA, GPF-DIA, and DIA-Quant data types
  • Upgrade PTM-Shepherd to 1.2.5
  • Upgrade DIA-Umpire to 2.2.3
  • Upgrade IonQuant to 1.7.16
  • Upgrade TMT-Integrator to 3.2.0
  • Various minor bug fixes and improvements
Assets 4
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FragPipe v16.0

22 Jul 23:54
@fcyu fcyu
16.0
f26eff4
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FragPipe v16.0

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
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