quantms

Cloud-ready Nextflow pipeline for DDA quantitative proteomics.

quantms orchestrates end-to-end proteomics analysis — from raw mass spectrometry data to protein quantification, quality control, and differential expression. It supports DDA label-free (LFQ) and isobaric labeling (TMT/iTRAQ) workflows.

DIA users: DIA proteomics is handled by the dedicated quantmsdiann pipeline.

Key Features

• Two DDA workflows: LFQ and TMT/iTRAQ (isobaric labeling) in a single pipeline
• ML-powered rescoring: MS2PIP, DeepLC, and Percolator boost identification rates by 10-30%
• Cloud-ready: Runs on AWS, GCP, Azure, HPC clusters, or your laptop via Nextflow
• Standardized metadata: SDRF-driven experiment annotation ensures reproducibility
• Quality control: Integrated pmultiqc reports with interactive HTML dashboards
• Ecosystem integration: Output compatible with mokume, qpx, and the quantms data portal

Quick Start

# Install Nextflow
curl -s https://get.nextflow.io | bash

# Run the test profile
nextflow run bigbio/quantms \
    -profile test,docker \
    --outdir results/

# Run with your data
nextflow run bigbio/quantms \
    -profile docker \
    --input samplesheet.csv \
    --database uniprot_human.fasta \
    --outdir results/

Workflows

Workflow	Flag	Description
DDA-LFQ	--workflow lfq	Label-free quantification using OpenMS + search engines
DDA-ISO	--workflow iso	Isobaric labeling (TMT, iTRAQ) with channel-level quantification

See Workflows for detailed descriptions.

Citation

Dai C, Pfeuffer J, Wang H, et al. quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data. Nature Methods. 2024;21:1603-1607. DOI: 10.1038/s41592-024-02343-1

Ecosystem

Tool	Description
quantmsdiann	DIA proteomics pipeline powered by DIA-NN
mokume	Protein quantification library (successor to ibaqpy)
qpx	Data format conversion and QPX format tools
pmultiqc	Interactive QC reporting for proteomics
portal.quantms.org	Browse reanalyzed proteomics datasets