QC-espresso: Brewing quality in proteomics

QC-espresso provides an automated, report-centered QC workflow for DIA-NN proteomics, generating structured HTML diagnostics that reveal issues like reduced identification depth and mass-error bias.

• Why it matters: DIA-NN output contains rich QC information, but researchers often lack a streamlined, reproducible way to assess acquisition quality, identification consistency, and quantitative reliability across experiments.
• What they did: QC-espresso ingests a DIA-NN report.parquet plus the matching FASTA database, then produces an HTML report with plots, run-level statistics, and exportable summary tables using R and Quarto.
• The result: Applied to three experimental datasets, it visualized lower identification depth linked to high contaminant content, altered retention-time/peak-width behavior, and systematic mass-error bias aligned with changes in precursor- and protein-level quantitative-quality metrics.

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