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FragPipe v24.0

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@fcyu fcyu released this 24 Dec 21:21
· 167 commits to develop since this release
24.0
c2f256c

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  • In Windows, install FragPipe using the installer. Then double-click the FragPipe-24.0.exe file.
  • In Linux, unzip the file. In bin subdirectory you will find a shell script for Linux

Changelog:

v24.0:

  • FragPipe GUI:

    • Add MSBooster transfer learning module for building in silico libraries. Requires setting up a GPU server or access to the server hosted by the Nesvizhskii lab (currently available to collaborators only)
    • Pass predicted library to DIA-NN automatically and adjust logic for enabling 'MBR' and 'Redo protein inference' options
    • Add Skyline quantification, export of quantification results, and report generation . As part of that process, Skyline trains an mProphet model and calculate q-values, which are then used as scores to calculate and apply precursor-level FDR by FragReporter.
    • Make Skyline train an mProphet model and calculate q-value
    • Add Astral Zoom TMT support
    • Use delta RT loess in real units for Percolator output to pepXML conversion
    • Fix passing invalid path to DIA-NN for .raw files with DIA-Quant data type
    • Increase maximum variable modification combinations limit for MSFragger
    • Add MBG and associated UI elements
    • Add 'ms2pip_CID_TMT', 'ms2pip_iTRAQphospho', and 'IM2Deep' models to MSBooster panel
    • Add 'auto' option to IonQuant's intensity mode and set it as the default value
    • Add labile ion series parameter for MSFragger
    • Fix bug where log file was not saved in headless mode
    • Save cache files to version-specific directories
    • Rename Site Reporter to FragReporter
    • Add FragAnnotator to replace PDV for annotating fragments in PSM.tsv file
    • Add batch table move up/down buttons
    • Move 'Load previous job' button from Workflow tab to Run tab
    • Add button to save glycan database to file on Glyco tab
    • Make 'sample_name' the same as 'sample' in the experiment_annotation.tsv file
    • Update workflows

  • MSFragger version 4.4 full changelog can be found at https://msfragger.nesvilab.org/CHANGELOG.html. Major changes:

    • Add 'digestion only' mode, enabled when there are no LC-MS files
    • Support any ion series being labile in labile modification search
    • For ddaPASEF data, use precursor ID as MS2 scan number

  • IonQuant version 1.11.18 full changelog can be found at https://ionquant.nesvilab.org/CHANGELOG.html. Major changes:

    • Add Astral Zoom TMT support
    • Add iodoTMT-6 label
    • Add 'auto' option to intensity mode

  • diaTracer version 2.2.1 changelog can be found at https://diatracer.nesvilab.org/CHANGELOG.html. Major changes:

    • Support Synchro-PASEF and Slice-PASEF formats

  • MSBooster:

    • Transfer learning workflow with server-based model training and prediction
    • IM2Deep support for ion mobility prediction
    • DeepLC UniMod modification reading support
    • THERMOTOF instrument support
    • ms2pip_CID_TMT model support
    • ms2pip_iTRAQphospho model support
    • z', a+1, x+1 fragment ion type support
    • NCE and instrument parameters for trainer
    • Cumulative QC plots for multiple mzML files
    • Delta RT loess scoring in real units

  • Philosopher:

    • Allow adding contaminants to a custom database
    • Add exit and error messages for failed peptide-protein matches when using an unmatched database
    • Fix bug in database-origin determination for the TAIR resource
    • Add check to avoid slice errors when extracting sequence window
    • Remove non-razor proteins not found in PSMs after protein FDR filtering
    • Fix bug in group FDR filtering that affects DDA+ search results

  • PTM-Shepherd:

    • Manually handle cys-disulfide -116 dual-site mod for mass-diff-to-varmod > 0
    • Add option to shuffle fragment intensities instead of random masses for second pass
    • Add Y and oxonium spectral similarity scores
    • Add filtering options for consensus glyco spectra
    • Support parsing multiple assigned mods on same site
    • Handle terminal delta masses in PSMs
    • Synchronize glyco names and remove duplicates from default glyco databases
    • Use both glyco and common mods for annotation when glyco is selected
    • Update common mods annotation to match UniMod
    • Handle C-terminal assigned mods
    • Remove glycoPSMs not passing FDR from psm.tsv; save unfiltered_psm.tsv to ptm-shepherd-output directory
    • Add LDA target proportion filtering and parameter
    • Add glycan frequency score
    • Remove deprecated yCount and yHyper scores
    • Add second pass mass and isotope scores with options
    • Refactor glyco results to store all scores in glycan candidates
    • Add KL and Y proportion scores with IonQuant API integration
    • Modularize and simplify glycan FDR computation
    • Glyco LDA scoring initial implementation
    • Fix critical glyco bug that gave decoys the wrong mass

  • Isobaric Quantification:

    • Generate modified peptide reports when Mod tag is set to 'none' and Min site probability is -1
    • Reformat index for modified peptide report
    • Fix glycan mod parsing when more than one glycan is on a peptide
    • Add check to prevent unsupported composition indexing for O-glyco
    • Prevent crash when user sets mod_tag and min_site_prob is -1

  • DIA Quantification:

    • Expose 'MBR' and 'Protein inference' options in the GUI
    • Generate additional reports using FragReporter

  • Skyline:

    • Add quantification and mProphet scoring
    • Generate additional reports using FragReporter

  • Various bug fixes and improvements

  • Miscellaneous:

    • Require Java 11+
    • Require MSFragger 4.4+
    • Require IonQuant 1.11.18+
    • Require diaTracer 2.2.1+
    • Require Python 3.9, 3.10, or 3.11
    • Upgrade Crystal-C to 1.5.10
    • Upgrade MSBooster to 1.4.14
    • Upgrade Philosopher to 5.1.3-RC9
    • Upgrade PTM-Shepherd to 3.0.11
    • Upgrade TMT-Integrator to 6.1.3
    • Upgrade FragPipe-PDV to 1.5.6
    • Upgrade FragPipe-SpecLib to 0.1.58
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