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:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- 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.
Version History
Version 1 (earliest) Created 25th Feb 2020 at 11:05 by Finn Bacall
Added/updated 26 files
Open
master
04626c3
Creators
Not specifiedAdditional credit
Leon Bichmann
Submitter
Views: 2770 Downloads: 360
Created: 25th Feb 2020 at 11:05
Last updated: 25th Feb 2020 at 15:19
None