Example Workflow

Complete Workflow Overview

The complete qpx workflow includes data conversion, statistical analysis, transformation, and visualization - from raw data to publication-ready plots.

Detailed Example

A complete example of processing proteomics data with qpx:

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

qpxc convert maxquant-feature \
    --evidence-file data/evidence.txt.gz \
    --sdrf-file data/experiment.sdrf.tsv \
    --protein-groups-file data/proteinGroups.txt \
    --output-folder ./output

# 2. Calculate absolute expression
qpxc transform ae \
    --ibaq-file data/ibaq.tsv \
    --sdrf-file data/experiment.sdrf.tsv \
    --output-folder ./output

# 3. Generate statistics
qpxc stats analyze psm \
    --parquet-path ./output/psm.parquet \
    --save-path ./reports/statistics.txt

# 4. Create visualizations
qpxc visualize plot box-intensity \
    --feature-path ./output/feature.parquet \
    --save-path ./plots/intensity_distribution.svg

# 5. Create project metadata
qpxc project create \
    --project-accession PXD001234 \
    --sdrf-file data/experiment.sdrf.tsv \
    --output-folder ./project

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