Proteomics MultiQC Report

Version: 1.0.0

Commit Hash: cfd859a66f60cd137691d32cb0a80efde6ffa194

Author: CauldronGO Team

Category: utilities

Subcategory: quality-control

Generate comprehensive quality control reports for mass spectrometry proteomics data using pmultiqc. Based on: Yue et al. (2025) bioRxiv 10.1101/2025.11.02.685980. Repository: https://github.com/bigbio/pmultiqc

Install with Cauldron get_app
README

Proteomics MultiQC Report

ID: pmultiqc-qc
Version: 1.0.0
Category: utilities
Author: CauldronGO Team

Description

Generate comprehensive quality control reports for mass spectrometry proteomics data using pmultiqc. Based on: Yue et al. (2025) bioRxiv 10.1101/2025.11.02.685980. Repository: https://github.com/bigbio/pmultiqc

Runtime

  • Environments: python

  • Entrypoint: pmultiqc_runner.py

Inputs

Name Label Type Required Default Visibility
input_directory Input Directory directory Yes - Always visible
platform Analysis Platform select (quantms, maxquant, diann, proteobench, mzid, generic) Yes generic Always visible
sdrf_file SDRF File (Optional) file No - Always visible
remove_decoy Remove Decoy Peptides boolean No true Always visible
decoy_affix Decoy Identifier text No DECOY_ Always visible
contaminant_affix Contaminant Identifier text No CONT_ Always visible
affix_type Affix Type select (prefix, suffix) No prefix Always visible
condition_column Condition Column (Optional) text No - Always visible
disable_table Disable Large Tables boolean No false Always visible

Input Details

Input Directory (input_directory)

Directory containing proteomics analysis results. For DIA-NN: must contain report.tsv or report.parquet. For MaxQuant: must contain txt/ folder with results files.

Analysis Platform (platform)

Select the proteomics analysis platform used to generate the data

  • Options: quantms, maxquant, diann, proteobench, mzid, generic

SDRF File (Optional) (sdrf_file)

Optional SDRF (Sample and Data Relationship Format) file to include in analysis

Remove Decoy Peptides (remove_decoy)

Exclude decoy peptides from identification counts

Decoy Identifier (decoy_affix)

Prefix or suffix used to identify decoy proteins

Contaminant Identifier (contaminant_affix)

Prefix or suffix used to identify contaminant proteins

Affix Type (affix_type)

Whether decoy/contaminant identifiers are prefixes or suffixes

  • Options: prefix, suffix

Condition Column (Optional) (condition_column)

Column name in SDRF file to use for grouping samples into conditions

  • Placeholder: condition

Disable Large Tables (disable_table)

Skip protein/peptide tables for very large datasets to reduce report size

Outputs

Name File Type Format Description
qc_report multiqc_report.html file html Interactive HTML quality control report
qc_data multiqc_data file directory Directory containing raw QC metrics data

Requirements

  • Python Version: >=3.10

Package Dependencies (Inline)

Packages are defined inline in the plugin configuration:

  • pmultiqc>=0.0.39
  • multiqc>=1.15
  • pandas>=2.0.0
  • click>=8.0.0

Note: When you create a custom environment for this plugin, these dependencies will be automatically installed.

Usage

Via UI

  1. Navigate to utilities → Proteomics MultiQC Report
  2. Fill in the required inputs
  3. Click Run Analysis

Via Plugin System

const jobId = await pluginService.executePlugin('pmultiqc-qc', {
  // Add parameters here
});