prideQC documentation#

Quality control from raw mass-spectrometry data, with evidence-based SDRF refinement
prideQC computes QC metrics directly from mass-spectrometry data, produces structured and visual reports, and then uses supported study-level evidence to improve technical SDRF metadata while preserving provenance.
A raw mass-spectrometry input enters per-file QC, which creates structured evidence used independently by reporting and gated SDRF refinement.

prideQC analyzes raw data into per-file QC evidence. The resulting mzQC files can be summarized with pmultiqc, while structured run summaries feed cohort-level SDRF refinement. Uncertain proposals can abstain.#

Getting started

Install prideQC, analyze raw data, inspect outputs, and refine an SDRF.

Getting started
QC workflow

See what prideQC measures from spectra and how the evidence is represented.

QC workflow
Measurement precision & mass shifts

Understand mass-error estimation and recurrent neutral-mass-shift scouting with synthetic examples.

Measurement precision & mass-shift evidence
Reporting

Generate interactive study-level QC reports with pmultiqc / MultiQC.

Reporting with pmultiqc / MultiQC
SDRF refinement

Learn how run-level QC evidence is synthesized into conservative, auditable metadata proposals.

SDRF refinement
CLI reference

Reference the main prideQC commands and options.

CLI reference

What prideQC is designed to do#

prideQC connects two tasks that are usually handled separately:

  1. Compute reproducible QC evidence from raw mass-spectrometry data.

  2. Use sufficiently supported evidence to refine technical SDRF metadata.

The first task is always primary. Metadata refinement is downstream of the measured QC evidence and can abstain when the evidence is incomplete, ambiguous, or inconsistent.

Core capabilities#

Run-level QC

  • scan and chromatogram metrics

  • acquisition characteristics

  • peak-type and diagnostic-ion evidence

  • structured per-file summaries

Measurement precision

  • precursor mass-error precision

  • fragment mass-error precision

  • conservative tolerance suggestions

  • explicit support and diagnostics

Mass-shift evidence

  • recurrent related-spectrum neutral-mass shifts

  • OpenMS / UniMod mass-compatible candidates

  • ambiguity and support retained explicitly

Study-level refinement

  • cohort synthesis across files

  • confidence-gated SDRF proposals

  • validation, provenance, and audit artifacts

  • optional adjudication for unresolved cases

Documentation map#

External resources#