Workflow Overview

These documents describe a standardized Nextflow workflow for performing an open modification discovery DDA search. The source code for the workflow can be found at: https://github.com/mriffle/nf-openmod-dda.

Workflow Components

The workflow is made up of the following software components, each may be run multiple times for different tasks.

  • PanoramaWeb (https://panoramaweb.org/home/project-begin.view)

    Users may optionally use WebDAV URLs as locations for input data files in PanoramaWeb. The workflow will automatically download files as necessary.

  • msconvert (https://proteowizard.sourceforge.io/)

    If users supply RAW files as input, they will be converted to mzML using msconvert. If a local input directory already contains mzML files, those are used directly and any RAW files are ignored.

  • Magnum (https://magnum-ms.org/)

    Magnum is the primary search program that identifies peptides and finds modifications present in the raw mass spectrometry data.

  • Percolator (https://github.com/percolator/percolator)

    Percolator is a widely-used program for post processing of proteomics search results that uses machine learning to apply false discovery rates associated with peptide identifications.

  • Limelight XML Conversion (https://github.com/yeastrc/limelight-import-magnum-percolator)

    The Limelight XML converter converts the native output of Magnum and Percolator to Limelight XML, suitable for import into Limelight. This step will only run if uploading to Limelight is enabled.

  • Limelight (https://limelight-ms.org/)

    Limelight is a web application for visualization, analysis, and sharing of proteomics results generated from mass spectrometry data. If uploading to Limelight is enabled, the results will be uploaded automatically to the specified Limelight instance.

How to Run

This workflow uses the Nextflow standardized workflow platform. The Nextflow platform emphasizes ease of use, workflow portability, and containerization of the individual steps. To run this workflow, you do not need to install any of the software components of the workflow. There is no need to worry about installing necessary software libararies, version incompatibilities, or compiling or installing complex and fickle software.

To run the workflow you need only install Nextflow, which is relatively simple. To run the individual steps of the workflow on your own computer, you will need to install Docker. After these are installed, you will need to edit the pipeline configuration file to supply the locations of your data and execute a simple Nextflow command, such as:

nextflow run -resume -r main mriffle/nf-openmod-dda -c pipeline.config

The entire workflow will be run automatically, downloading Docker images as necessary, and the results output to the results/nf-openmod-dda directory. See How to Install the Workflow for more details on how to install Nextflow and Docker. See How to Run the Workflow for more details on how to run the workflow. And see Output & Results for more details on how to retrieve the results.