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Using pmultiqc with DIA-NN Output

The diann plugin processes results from DIA-NN for data-independent acquisition (DIA) proteomics experiments.

DIA analysis uses quantmsdiann, not quantms

DIA experiments are processed by the dedicated quantmsdiann pipeline — not quantms. The quantms pipeline handles DDA workflows only (LFQ, TMT/iTRAQ). If you ran DIA-NN through quantmsdiann, your results will contain report.tsv/report.parquet files — not mzTab.

Supported Input Files

DIA-NN output does not use mzTab format. The input files are DIA-NN native reports:

File Pattern Description Source
report.tsv or report.parquet DIA-NN main report with precursor-level results DIA-NN / quantmsdiann
report.log.txt or diannsummary.log DIA-NN log file with software version and parameters DIA-NN / quantmsdiann
*sdrf.tsv SDRF-Proteomics metadata file (optional) User-provided
*ms_info.parquet Precomputed mzML statistics (optional) quantms-utils

No mzTab for DIA

Unlike the quantms DDA pipeline which produces mzTab output, DIA-NN and quantmsdiann produce report.tsv / report.parquet as the primary output. pmultiqc reads these directly — there is no mzTab conversion step for DIA experiments.

Running the Report

From quantmsdiann pipeline output

# Point to the quantmsdiann results directory
multiqc --diann-plugin /path/to/quantmsdiann/results -o ./report

From standalone DIA-NN

# Point to the directory containing report.tsv
multiqc --diann-plugin /path/to/diann/output -o ./report

Common options

# Disable hover tooltips for static/publication-ready reports
multiqc --diann-plugin /path/to/results -o ./report --disable-hoverinfo

# Disable large peptide/protein tables (faster for large experiments)
multiqc --diann-plugin /path/to/results -o ./report --disable-table

# Custom contaminant prefix
multiqc --diann-plugin /path/to/results -o ./report --contaminant-affix CONT

DIA-Specific Metrics

DIA-NN report files contain precursor-level data with DIA-specific confidence metrics (Q.Value, PG.Q.Value). The following QC sections are generated:

DIA-NN Metadata Table

Software version, library type (in-silico predicted vs. empirical), and key search parameters extracted from the log file:

  • DIA-NN version
  • Spectral library source
  • Mass accuracy settings (MS1 and MS2)
  • Protein inference method (genes vs. protein groups)

Experimental Design

When an SDRF file is present, an experimental design table links DIA raw files to samples, conditions, biological replicates, and fractions.

Identification Statistics

  • Identification Summary Table — per-sample counts of precursors, peptides, and protein groups passing FDR
  • MS/MS Identification Rate — fraction of MS2 events matched to library entries, by run
  • Number of Peptides per Protein — unique peptide distribution per protein group

Precursor-Level Metrics

  • Charge State Distribution — precursor charge frequencies (+1 through +6+)
  • Peptide Length Distribution — sequence length histogram
  • Peak Intensity Distribution — precursor intensities (log scale)
  • Peaks per MS2 Spectrum — fragment ion peak count histogram

MS1 Information (when ms_info.parquet is available)

  • Total Ion Chromatograms (TIC) — full-gradient signal per sample
  • Base Peak Chromatograms (BPC) — most abundant ion at each RT point
  • MS1 Peak Count — number of survey scans per run

Long-Trend Analysis

Cumulative identification plots across the retention time gradient — useful for detecting chromatographic issues.

DIA vs DDA Output Comparison

Feature DIA (quantmsdiann) DDA (quantms)
Primary output report.tsv / report.parquet mzTab
pmultiqc plugin --diann-plugin --quantms-plugin
Quantification level Precursor (MS2) Feature (MS1)
FDR columns Q.Value, PG.Q.Value PSM-level PEP
Library In-silico or empirical Not applicable
Pipeline quantmsdiann quantms

File Format Notes

  • DIA-NN produces both .tsv and .parquet report formats. The .parquet format is preferred for large experiments (>50 samples) as it loads significantly faster.
  • When running through quantmsdiann, the report is typically named diann_report.tsv or diann_report.parquet.
  • Fragment-level filtering uses Q.Value and PG.Q.Value thresholds from the DIA-NN log.
  • Bruker .d raw formats are detected automatically; chromatographic metrics may differ slightly from Thermo .raw data.