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FragPipe v20.0
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@fcyu fcyu released this 31 May 22:17
· 622 commits to master since this release
20.0
6a21a48

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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:

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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