README.md

lehtiolab/nf-labelcheck

A proteomics pipeline for running labelchecks.

Introduction

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 containers making installation trivial and results highly reproducible.

How to run

• install Nextflow
• install Docker, Singularity, or Conda
• run pipeline:

nextflow run lehtiolab/nf-labelcheck --mzmls '/path/to/*.mzML' --tdb /path/to/proteins.fa

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

• Running the pipeline
• Output and how to interpret the results
• Troubleshooting

The labelcheck pipeline takes multiple mzML files as input and performs identification and quantification to output an HTML report (an example can be found here) containing graphs to display the amount of incorporated isobaric label per sample on both peptide and PSM level. A PSM/peptide is considered to be not labeled if any of its K residues or its N-term have not been labeled. The report also shows the amount of labeling in the different channels per sample.

Credits

lehtiolab/nf-labelcheck was originally written by Jorrit Boekel and tries to follow the nf-core best practices and templates.