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CLI Reference

The qpx command-line tool provides a comprehensive set of commands for converting, transforming, visualizing, and analyzing mass spectrometry proteomics data.

Overview

The qpx CLI is organized into five main command groups:

Convert Commands

Convert various mass spectrometry data formats to the QPX standard format:

  • DIA-NN Conversion: Convert DIA-NN reports to feature and protein group formats
  • MaxQuant Conversion: Convert MaxQuant PSM, feature, and protein group data
  • FragPipe Conversion: Convert FragPipe PSM data to QPX format
  • QuantMS Conversion: Create QPX data files from mzTab format
  • idXML Conversion: Convert OpenMS idXML format PSM data

View detailed documentation →

Transform Commands

Transform and process data within the QPX ecosystem:

  • Absolute Expression (AE): Convert iBAQ absolute expression data to QPX format (format specification)
  • Differential Expression (DE): Convert MSstats differential expression analysis results
  • Gene Mapping: Map gene information to protein data
  • iBAQ Transformation: Process iBAQ quantification files
  • Spectra Mapping: Map spectra information
  • UniProt Mapping: Update UniProt annotation information
  • AnnData Merging: Merge multiple AE files into AnnData format

View detailed documentation →

Visualization Commands

Create various data visualization plots:

  • PSM/Peptide distribution plots
  • iBAQ distribution plots
  • Intensity distribution plots (KDE, box plots)
  • Peptide-protein distribution plots

View detailed documentation →

Statistics Commands

Perform statistical analysis on QPX data:

  • Project AE data statistics
  • PSM data statistics
  • Generate comprehensive statistical reports

View detailed documentation →

Project Management Commands

Manage project metadata and files:

  • Create project.json from PRIDE projects
  • Attach files to project metadata

View detailed documentation →

Quick Start

Installation

pip install qpx

Basic Usage

View all available commands:

qpxc --help

View help for a specific command group:

qpxc convert --help

View detailed help for a specific command:

qpxc convert diann --help

Common Options

Most commands support the following common options:

  • --verbose: Enable verbose logging for debugging
  • --output-folder: Specify the output directory
  • --output-prefix: Specify the output file prefix

Example Data Processing Workflow

A typical data processing workflow:

# 1. Convert raw data
qpxc convert maxquant-psm \
    --msms-file msms.txt \
    --output-folder ./output

# 2. Transform to absolute expression data
qpxc transform ae \
    --ibaq-file ibaq.tsv \
    --sdrf-file metadata.sdrf.tsv \
    --output-folder ./output

# 3. Generate visualization
qpxc visualize plot ibaq-distribution \
    --ibaq-path ./output/ae.parquet \
    --save-path ./plots/distribution.svg

# 4. Generate statistical report
qpxc stats analyze psm \
    --parquet-path ./output/psm.parquet \
    --save-path ./stats/report.txt

Getting Help