Head of Bioinformatics Group, Center for Proteomics and Metabolomics, Leiden University Medical Center Interested in workflows and automated workflow composition for analysis of mass spectrometry data, in particular within proteomics or metabolomics, integration with genomics data and the scientific literature
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 ...
nf-core/ddamsproteomics
Quantitative shotgun MS proteomics as done in Lehtio lab
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 / singularity containers making installation trivial and results highly reproducible.
Documentation
The nf-core/ddamsproteomics pipeline comes with documentation about the pipeline, found in the docs/ directory:
Installation Pipeline configuration
Local ...
Type: Nextflow
Creator: Project author name (use a comma to separate multiple names).
Submitter: Finn Bacall