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lehtiolab/nf-labelcheck

A proteomics pipeline for running labelchecks.

Nextflow

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

nextflow run lehtiolab/nf-labelcheck --input '/path/to/inputdef.txt' --tdb /path/to/proteins.fa --isobaric tmt10plex

Where inputdef.txt is a tab-separated file containing a header for one-channel-per-file runs:

mzmlfile    instrument    setname    channel
/path/to/fn.mzML    qe    setA    126
...

or pooled channels in a file:

mzmlfile    instrument    setname
/path/to/fn.mzML    qe    setA
...

Each of these inputs leads to a slightly different report, see examples for pooled, and non-pooled results. The pipeline performs identification and quantification, and the output contains graphs to display the amount of incorporated isobaric label per sample on both peptide and PSM level. For the non-pooled runs, a PSM/peptide is considered to be not labeled if any of its K residues or its N-term have not been labeled. For pooled reports there is information on the amount of PSMs with missing values per channel. The report also shows the amount of labeling in the different channels per sample, as well as missed cleavages.

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

Credits

lehtiolab/nf-labelcheck was originally written by Jorrit Boekel and took inspiration and boilerplate from the nf-core best practices and templates.

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Proteomics nextflow labelcheck pipeline with report

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