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Releases: Nesvilab/FragPipe

FragPipe v23.1

30 Jun 17:40
@fcyu fcyu
23.1
d8bf745

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FragPipe v23.1 Latest
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  • In Windows, install FragPipe using the installer. Then double-click the FragPipe-23.1.exe file.
  • In Linux, unzip the file. In bin subdirectory you will find a shell script for Linux

Changelog:

v23.1:

  • FragPipe GUI:
    • New metaproteomics database generation module (beta)
    • Add Prosit MultiFrag model to the MSBosoter's dropdown menu
    • Do not run Abacus when IonQuant is used in the TMT intensity extraction
    • Add intensity mode to IonQuant panel
    • Add the 'export log' back
    • Optimize the memory footprint
  • MSFragger version 4.3 full changelog can be found in https://msfragger.nesvilab.org/CHANGELOG.html
  • IonQuant version 1.11.11 full changelog can be found in https://ionquant.nesvilab.org/CHANGELOG.html
  • diaTracer version 1.3.3 changelog can be found in https://diatracer.nesvilab.org/CHANGELOG.html
  • Various bug fixes and performance improvements
  • Miscellaneous:
    • Require Java 11+
    • Require MSFragger 4.3+
    • Require IonQuant 1.11.11+
    • Require diaTracer 1.3.3+
    • Require Python 3.9, 3.10, or 3.11
    • Require EasyPQP 0.1.52+
    • Upgrade Crystal-C to 1.5.9
    • Upgrade MSBooster to 1.3.17
    • Upgrade Philosopher to 5.1.2
    • Upgrade PTM-Shepherd to 3.0.2
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FragPipe v23.0

03 May 23:04
@fcyu fcyu
23.0
23a3691

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FragPipe v23.0

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Running

  • In Windows, install FragPipe using the installer. Then double-click the FragPipe-23.0.exe file.
  • In Linux, unzip the file. In bin subdirectory you will find a shell script for Linux

Changelog:

v23.0:

  • FragPipe GUI:
    • Create an installer for the Windows version
    • Bundle Python and Python packages. In Windows, they will be installed automatically during the installation process
    • Add Batch tab with ability to run a series of FragPipe runs ('jobs') in a batch and save/load job files
    • Add GUI table editor for MSFragger detailed mass offsets
    • Add workflow for TMT-based quantification using Bruker timsTOF (ddaPASEF) platform
    • Add workflow for TMT data on Thermo Fisher Scientific Astral platform
    • Add workflow for TMT35-plex quantification
    • New tool for generating summary reports ('Generate Summary Report' option in the 'Run' tab). It will generate a summary report for the result in the 'output dir'
    • Add 'export matched fragments' option to the 'Run' tab
    • Automatically load the workflow when it is selected in the dropdown menu on the 'Workflow' tab. There is no 'Load' button anymore.
    • Adjust the 'Download' window according to the changes of the tools downloading
    • Use '@' to replace '-' for nonspecific and nocleavage enzymes
    • Ignore the _uncalibrated and _calibrated files when loading the LC-MS files
    • Print tools' versions to the log and workflow files
    • Print each task's runtime to the end of the log
    • Allow terminal characters in mass offset sites
  • MSFragger version 4.2 full changelog can be found in https://msfragger.nesvilab.org/CHANGELOG.html. Major changes:
    • Write MS1 to the calibrated and uncalibrated mzML files
    • Write MS2 after calibration, deisotoping, and neutral loss removal to calibrated.mzML file
    • Optimize the order of search and post-processing to significantly reduce the memory usage, especially in Astral DIA data
    • Support for low resolution MS1/MS2 DIA and GPF-DIA data (Stellar)
  • IonQuant version 1.11.9 full changelog can be found in https://ionquant.nesvilab.org/CHANGELOG.html. Major changes:
    • Support the timsTOF ddaPASEF isobaric-labeling quant
    • Add the chemical formula support to the isotopic label quant with the '--formula' parameter
    • Significantly improve the quantification accuracy and precision
    • Significantly optimize the memory footprint and speed
  • diaTracer version 1.2.5 changelog can be found in https://diatracer.nesvilab.org/CHANGELOG.html. Major changes:
    • Improved isotope grouping and filtering during diaPASEF data processing, resulting in smaller extracted psedo-MS/MS (diatracer.mzML) files and cleaner data, noticably benefiting open/mass-offset PTM searches
  • MSBooster:
    • Add IM model to the MSBooster panel
    • Add a panel to take spectral library file in the MSBooster panel
    • More robust HTTP requests for Koina model requests
    • Reimplemented ion mobility features and ion mobility best model search
    • AlphaPeptDeep recognizes more UniMod PTM entries
    • New Koina models: AlphaPeptDeep CCS, UniSpec, MS2PIP timsTOF, MS2PIP TTOF5600, MS2PIP Immuno HCD, Prosit citrullination models
    • Updated figures for mass offset RT/IM calibration
    • Reduced memory requirements for mzML initialization
    • Better support for C-terminal PTMs
    • Added new spectral similarity features weighted spectral entropy, hypergeometric probability, and intersection
  • Philosopher:
    • Add group FDR filtering support for peptide- and ion-level
    • Add 'Intensity', 'Resolution', and 'SNR' columns to psm.tsv for isobaric labeling data
    • Propagate various columns to psm/ion/peptide/protein reports, including 'IMScore', 'Class', 'Is Decoy', 'Is Contaminant' and 'Qvalue'
    • Fix the issue with peptide I/L substitution after razor assignment, thanks to David Hollenstein @hollenstein
    • Fix bugs in peptide-to-protein mapping when locating peptides within proteins
    • Fix a bug with PTM localization
    • Fix bugs with PTM group-FDR filtering
  • PTM-Shepherd:
    • Support results with delta mass reported as a variable mod from MSFragger
    • Add option to read MSFragger localization instead of re-localizing
    • Overhaul internal PSM handling
    • Improve internal spectrum handling
    • Add glyco-only run mode option
  • Isobaric quantification:
    • Support the timsTOF isobaric-labeling quant
    • Support TMT 35-plex
    • Add 'min resolution' and 'min SNR' options
    • Remove the 'top 3 ions' option
    • Automatically generate TMT annotation files if they are not provided
    • Reimplemented core functionality for improved efficiency and maintainability
    • Redesigned report generation pipeline: eliminates temporary files and improves speed by over 50%
    • Extended 'allow_overlabel' to support for user-defined labels
    • Added new columns to output reports to provide more comprehensive information such as mapped proteins and genes
  • Spectral library generation:
    • Stop using the old UniMod for EasyPQP. Upgrade pyOpenMS to 3.3.0
    • Not include amino acid masses in the modification mass string of the spectral library
  • DIA Quantification:
    • Bring the GPF-DIA data type code back
    • Support DIA-NN 1.9 to 2.1.0. Convert the report.parquet to report.tsv.
    • Rename the 'diann-output' folder to 'dia-quant-output'
    • Generate site reports for the DIA data analysis
  • Skyline:
    • Overhaul the input and logic for Skyline document generation to make it more robust and user-friendly
    • Rename the Skyline dir name, and move mod.xml to the Skyline dir
    • Add precursor and fragment tolerance options to Skyline tab
  • Various bug fixes and improvements
  • Miscellaneous:
    • Require Java 11+
    • Require MSFragger 4.2+
    • Require IonQuant 1.11.9+
    • Require diaTracer 1.2.5+
    • Require Python 3.9, 3.10, or 3.11
    • Require EasyPQP 0.1.52+
    • Upgrade Crystal-C to 1.5.8
    • Upgrade MSBooster to 1.3.9
    • Upgrade Percolator to 3.7.1
    • Upgrade Philosopher to 5.1.1
    • Upgrade PTM-Shepherd to 3.0.1
    • Upgrade TMT-Integrator to 6.1.1
    • Upgrade FragPipe-PDV to 1.4.4

Contributors

hollenstein
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FragPipe v22.0

30 May 01:18
@fcyu fcyu
22.0
a187705

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FragPipe v22.0

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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

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
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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
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FragPipe v21.0

19 Dec 21:11
@fcyu fcyu
21.0
0a5641c

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FragPipe v21.0

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:

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
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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
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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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  • 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
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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
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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
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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
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