nf-core pipeline · archived · proteomics, shotgun-ms
nf-core/ddamsproteomics
A Nextflow pipeline for quantitative shotgun mass spectrometry proteomics based on Lehtiö lab protocols.
What nf-core/ddamsproteomics is
nf-core/ddamsproteomics is a bioinformatics analysis pipeline designed for quantitative shotgun mass spectrometry (MS) proteomics. It was developed to execute the analytical approaches established in the Lehtiö lab for characterising complex protein mixtures.
The project is currently archived and is no longer actively maintained. Researchers seeking comparable, up-to-date functionality are advised to use the nf-core/quantms pipeline instead.
What the pipeline does
The pipeline is implemented in Nextflow, orchestrating proteomics processing tasks across varied computing infrastructures. It packages software dependencies inside Docker and Singularity containers to ensure environment consistency and reproducible analytical results.
Key facts
- Pipeline engine
- Nextflow
- Domain
- Quantitative shotgun MS proteomics
- Originating laboratory
- Lehtiö lab
- Container support
- Docker, Singularity
- Project status
- Archived (no longer maintained)
- Successor pipeline
- nf-core/quantms
What you can use it for
- Quantitative shotgun proteomics
- Analysing quantitative shotgun mass spectrometry data according to Lehtiö lab workflows.
- Historical workflow reproduction
- Rerunning or verifying legacy quantitative MS experiments that originally relied on this specific pipeline configuration.
Strengths and limits
Good at
- Provides portable execution across multiple computing infrastructures through Nextflow.
- Uses Docker and Singularity containerisation for software dependency management and reproducible outputs.
Watch out for
- The pipeline is officially archived and receives no further updates, bug fixes, or maintenance.
- Modern feature development and broader community support have moved to the nf-core/quantms pipeline.
Questions
Can I run nf-core/ddamsproteomics without my own cluster?
The research agent runs nf-core/ddamsproteomics with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/ddamsproteomics under?
MIT, like every nf-core pipeline.
Is nf-core/ddamsproteomics currently maintained?
No. The pipeline has been archived and is no longer being developed or maintained.
Which pipeline replaces nf-core/ddamsproteomics?
nf-core/quantms provides more up-to-date functionality covering much of the same quantitative proteomics scope.
What container technologies are compatible with this workflow?
The pipeline includes support for both Docker and Singularity containers.
Written from nf-core/ddamsproteomics's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.