glaDIAtor-nf

glaDIAtor-nf is a workflow for analyzing mass spectrometry data acquired using data independent acquisition (DIA) mode.

The package is designed to run both on workstations and HPC clusters, built with scaling in mind.

Dependencies

• NextFlow 25.10.4 (>= 22.10 should work)
• Java 25 (>= 17 should work)
• Working installation of Apptainer, Singularity, Podman, Docker or Guix.

Get the glaDIAtor-nf

git clone https://github.com/elolab/gladiator-nf.git

Input data

1. Raw experimental DIA data in proprietary format needs to be converted to mzML before it can be used by glaDIAtor-nf.
2. Determine instrument-specific parameters that were used during experiment:
   • precursor (MS1 spectrum) mass tolerance in ppm
   • fragment (MS2 spectrum) mass tolerance in Dalton

Example run

git clone --depth 1 https://github.com/elolab/gladiator-nf.git

mkdir example-run
cd example-run

mkdir dia-spectra
wget --no-directories --directory-prefix=dia-spectra 'ftp://massive-ftp.ucsd.edu/v05/MSV000090837/raw/Exp03_repeat_90minGradient_from_Exp02_same_Mastermix/210820_Grad090_LFQ_'{A,B}'_01.mzML'

mkdir protein-sequences
wget --directory-prefix=protein-sequences 'ftp://massive-ftp.ucsd.edu:/v05/MSV000090837/sequence/fasta/*.fasta'

gladiator_location="../gladiator-nf"
gladiator_container_type="singularity"  # singularity, podman, docker or guix

nextflow -config "${gladiator_location}/config/containers/${gladiator_container_type}.config" \
    run "${gladiator_location}/workflow/gladiator.nf" \
        --diafiles='dia-spectra/*.mzML' --fastafiles='protein-sequences/*.fasta' \
        --precursor_mass_tolerance=10 --fragment_mass_tolerance=0.02 --max_missed_cleavages=1

head results/*.{csv,tsv}

Documentation

• Getting started
• User guide
  • Input and output
  • Configuration

License

The glaDIAtor-nf workflow is licensed under GPL-3.0 license.

Licenses of the components:

• Apache 2.0
• Artistic 1.0
• BSD 3-Clause
• GPL-2.0
• GPL-3.0
• LGPL

Comprehensive list can be found at glaDIAtor-nf # Licenses.