This document describes the output produced by the pipeline.

The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

For detailed information about file formats and how they are in the various steps visit the detailed documentation of the OpenSwathWorkflow.


Several csv tables are generated summarizing peptide or protein quantities (if protein level msstats was applied). In addition PDF reports are created.

  • Output visualizations:
    • the number of peptide / protein identifications
    • the peptide charge distribution
    • the library and DIA measurement RT deviation
    • the comparative quantities across samples as heatmap
    • (+ if protein level MSstat was applied additional comparative volcano plots)


Several files summarizing the used spectral library are generated, depending on whether the library and iRTs were generated from provided matched DDA data.

  • Library files:
    • a tsv table listing all peptide precursors and their transitions used for the library
    • a pqp file storing the library in sqlite format including generated decoy transitions
    • a pqp file storing the iRT library in sqlite format
    • if merging of multiple libraries and RT alignment was specified, the pairwise alignment graph is exported as pdf.


For each provided DIA MS run the OpenSwathWorkflow output is reported.

  • OpenSwathWorkflow output:
    • osw files storing the scoring output in sqlite format
    • chrom.mzML file storing the extracted ion chromatogram for each peptide transition


Several files summarizing the pyprophet local or global scoring results for each DIA MS run separately, aggregated in sqlite format and visualized as report.

  • PyprophetOutput
    • osw files storing the aggregated scoring output per sample
    • tsv files storing the scoring output as table for each MS run
    • pdf reports visualizing the aggregated target decoy score distributions

Pipeline information

Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.

Output files:

  • pipeline_info/
    • Reports generated by Nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and
    • Reports generated by the pipeline: pipeline_report.html, pipeline_report.txt and software_versions.csv.
    • Documentation for interpretation of results in HTML format: results_description.html.