Version 1

Workflow Type: Nextflow


Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

Build Status Nextflow

install with bioconda Docker


nfcore/diaproteomics is a bioinformatics analysis pipeline used for quantitative processing of data independant (DIA) proteomics data.

The workflow is based on the OpenSwathWorkflow for SWATH-MS proteomic data. DIA RAW files (mzML) serve as inputs and library search is performed based on a given input spectral library. If specified internal retention time standarts (irts) will be used to align library and DIA measurements into the same retention time space. FDR rescoring is applied using Pyprophet based on a competitive target-decoy approach on peakgroup or global peptide and protein level. Finally, exctracted chromatograms are realigned and quantified using the TRIC algorithm.


bash nextflow run nf-core/diaproteomics --dia_mzmls '*.mzML' --spectral_lib '*.pqp' --irts '*.pqp' --swath_windows '*.txt' -profile test,docker

See usage docs for all of the available options when running the pipeline.


The nf-core/diaproteomics pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting


nf-core/diaproteomics was originally written by Leon Bichmann.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on Slack (you can join with this invite).


You can cite the nf-core pre-print as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.

Version History

Version 1 (earliest) Created 25th Feb 2020 at 11:05 by Finn Bacall

Added/updated 26 files

Open master 04626c3
help Creators and Submitter
Not specified
Additional credit

Leon Bichmann


Views: 1709   Downloads: 30

Created: 25th Feb 2020 at 11:05

Last updated: 25th Feb 2020 at 15:19

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