lehtiolab/nf-labelcheck repository overview

⁠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 --isobaric tmt10plex --sampletable samples.txt

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.