A Quantitative MS proteomics analysis pipeline
This workflow identifies peptides in mzML input data using MSGF+, and Percolator, quantifies isobarically labeled samples with OpenMS, and precursor peptides with Hardklor/Kronik, and processes that output to formatted peptide and protein/gene tables using Msstitch.
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.
How to run
nextflow run lehtiolab/ddamsproteomics --mzmls '/path/to/*.mzML' --tdb /path/to/proteins.fa --mods /path/to/mods.txt
The lehtiolab/ddamsproteomics pipeline comes with documentation about the pipeline, found in the
The pipeline takes multiple mzML files as input and performs identification and quantification to output results and a QC report (an example can be found here)
lehtiolab/ddamsproteomics was originally written by Jorrit Boekel and tries to follow the nf-core best practices and templates.