Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

Introduction

nfcore/diaproteomics is a bioinformatics analysis pipeline used for quantitative processing of data independant (DIA) proteomics data.

The workflow is based on the OpenSwathWorkflow for SWATH-MS proteomic data. DIA RAW files (mzML) serve as inputs and library search is performed based on a given input spectral library. If specified internal retention time standarts (irts) will be used to align library and DIA measurements into the same retention time space. FDR rescoring is applied using Pyprophet based on a competitive target-decoy approach on peakgroup or global peptide and protein level. Finally, exctracted chromatograms are realigned and quantified using the TRIC algorithm.

Run

bash nextflow run nf-core/diaproteomics --dia_mzmls '*.mzML' --spectral_lib '*.pqp' --irts '*.pqp' --swath_windows '*.txt' -profile test,docker

See usage docs for all of the available options when running the pipeline.

Documentation

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

1. Installation
2. Pipeline configuration
   • Local installation
   • Adding your own system config
   • Reference genomes
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

Credits

nf-core/diaproteomics was originally written by Leon Bichmann.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on Slack (you can join with this invite).

Citation

You can cite the nf-core pre-print as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.