Quick Start Examples

Example 1: Convert MaxQuant Data

Convert MaxQuant output files to QPX format.

# Convert PSM data
qpxc convert maxquant-psm \
    --msms-file tests/examples/maxquant/maxquant_simple/msms.txt \
    --output-folder ./output

# Convert feature data
qpxc convert maxquant-feature \
    --evidence-file tests/examples/maxquant/maxquant_full/evidence.txt.gz \
    --sdrf-file tests/examples/maxquant/maxquant_full/PXD001819.sdrf.tsv \
    --protein-groups-file tests/examples/maxquant/maxquant_full/proteinGroups.txt \
    --output-folder ./output

# Convert protein groups
qpxc convert maxquant-pg \
    --protein-groups-file tests/examples/maxquant/maxquant_full/proteinGroups.txt \
    --sdrf-file tests/examples/maxquant/maxquant_full/PXD001819.sdrf.tsv \
    --output-folder ./output

Expected Output:

• output/psm-{uuid}.psm.parquet
• output/feature-{uuid}.feature.parquet
• output/pg-{uuid}.pg.parquet

Example 2: Convert DIA-NN Data

Process DIA-NN report files for Data-Independent Acquisition (DIA) data.

# Convert to feature format
qpxc convert diann \
    --report-path tests/examples/diann/small/diann_report.tsv \
    --qvalue-threshold 0.05 \
    --mzml-info-folder tests/examples/diann/small/mzml \
    --sdrf-path tests/examples/diann/small/PXD019909-DIA.sdrf.tsv \
    --output-folder ./output

# Convert to protein group format
qpxc convert diann-pg \
    --report-path tests/examples/diann/full/diann_report.tsv.gz \
    --pg-matrix-path tests/examples/diann/full/diann_report.pg_matrix.tsv \
    --sdrf-path tests/examples/diann/full/PXD036609.sdrf.tsv \
    --output-folder ./output

Expected Output:

• output/feature-{uuid}.feature.parquet
• output/pg-{uuid}.pg.parquet

Example 3: Absolute Expression Analysis

Calculate absolute protein expression from iBAQ data.

qpxc transform ae \
    --ibaq-file tests/examples/AE/PXD016999.1-ibaq.tsv \
    --sdrf-file tests/examples/AE/PXD016999-first-instrument.sdrf.tsv \
    --project-file tests/examples/AE/project.json \
    --output-folder ./output \
    --output-prefix ae_analysis

Expected Output:

• output/ae_analysis-{uuid}.absolute.parquet

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