Quantitative shotgun MS proteomics as done in Lehtio lab
Please see nf-core/quantms for a more up to date pipeline that covers much of the same functionality.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
The nf-core/ddamsproteomics pipeline comes with documentation about the pipeline, found in the docs/
directory: