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FragPipe v23.0

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@fcyu fcyu released this 03 May 23:04
· 439 commits to develop since this release
23.0
23a3691

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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
Assets 4
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