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FragPipe v22.0

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@fcyu fcyu released this 30 May 01:18
· 142 commits to develop since this release
22.0
a187705

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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:

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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