Proteomics label-free quantification (LFQ) analysis pipeline
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.
Download the pipeline and test it on a minimal dataset with a single command:
Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use
-profile <institute>in your command. This will enable either
singularityand set the appropriate execution settings for your local compute environment.
Start running your own analysis!
By default, the pipeline currently performs the following:
- Conversion to indexed mzML
- Peptide database search (with multiple search engines)
- Re-scoring (with e.g. Percolator)
- Merging with ConsensusID
- FDR filtering
- Modification localization with Luciphor2 (e.g. phospho-sites)
- Protein inference and grouping
- Label-free relative quantification by either spectral counting or feature-based alignment and integration
- Downstream processing includes statistical post-processing with MSstats and quality control with PTXQC
It performs conversion to indexed mzML, database search (with multiple search engines), re-scoring (with e.g. Percolator), merging, FDR filtering, modification localization with Luciphor2 (e.g. phospho-sites), protein inference and grouping as well as label-free quantification by either spectral counting or feature-based alignment and integration. Downstream processing includes statistical post-processing with MSstats and quality control with PTXQC. For more info, see the output docs.
nf-core/proteomicslfq was originally written by Julianus Pfeuffer, Lukas Heumos, Leon Bichmann, Timo Sachsenberg, Yasset Perez-Riverol.
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
If you use nf-core/proteomicslfq for your analysis, please cite it using the following doi: 10.5281/zenodo.4106005
You can cite the
nf-core publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
In addition, references of tools and data used in this pipeline
can be found in the