Tools & Libraries
Explore the ecosystem of tools and libraries that power the quantms workflow
Nextflow Pipelines
quantms
A cloud-ready Nextflow pipeline for DDA quantitative proteomics: label-free (LFQ) and isobaric labeling (TMT/iTRAQ) workflows.
- DDA-LFQ and DDA-ISO (TMT/iTRAQ) workflows in one pipeline
- ML-based PSM rescoring with MS2PIP and DeepLC
- Cloud-ready: AWS, GCP, Azure, HPC, and local execution
- Published in Nature Methods 2024
quantmsdiann
DIA proteomics Nextflow pipeline powered by DIA-NN, supporting both library-free and spectral library modes with standardized output.
- DIA proteomics powered by DIA-NN engine
- Library-free and spectral library acquisition modes
- Integrated with qpx for standardized Parquet output
- Scalable from laptop to cloud infrastructure
Python Libraries
mokume (successor to ibaqpy)
A unified protein quantification library that extends and replaces ibaqpy. Beyond iBAQ, mokume adds MaxLFQ, TopN, ratio quantification, normalization, batch correction, and differential expression — all from any search engine output.
- All ibaqpy functionality included (iBAQ absolute quantification)
- Additional methods: MaxLFQ, TopN, median, ratio (TMT/iTRAQ)
- Normalization, batch correction (ComBat), IRS, and differential expression
- Works with quantms, quantmsdiann, DIA-NN, MaxQuant, FragPipe outputs
qpx
Quantitative proteomics exchange format. A unified Parquet-based data standard for cross-tool and cross-dataset proteomics analysis.
- Convert from DIA-NN, MaxQuant, FragPipe, and Spectronaut
- Unified Parquet format with DuckDB query support
- Collection indexes for cross-dataset search
- Export to AnnData (.h5ad) for scverse compatibility
sdrf-pipelines
A set of tools to validate and convert SDRF files to workflow configuration formats for proteomics analysis pipelines.
- SDRF metadata validation and annotation
- Convert to workflow configs: MaxQuant, OpenMS, DIA-NN
- Standardized sample metadata for proteomics
- Community-maintained SDRF templates
Quality Control & Utilities
pmultiqc
A MultiQC plugin for visualizing and aggregating quality control metrics from proteomics data analysis workflows.
- MultiQC plugin for proteomics QC reporting
- Interactive HTML reports: PCA, heatmaps, CVs
- Supports LFQ, TMT, and DIA experiments
- Integrates with quantms and mokume outputs
ibaqpy → now part of mokume
The original iBAQ quantification library. Its functionality is now fully integrated into mokume, which extends it with MaxLFQ, TopN, normalization, batch correction, and differential expression. New projects should use mokume directly.
- iBAQ absolute protein quantification (original implementation)
- SDRF-driven metadata handling
- All features preserved and extended in mokume
- ibaqpy remains available for legacy compatibility
quantms-rescoring
PSM rescoring tool that adds deep-learning features to peptide-spectrum matches using MS2PIP, DeepLC, and AlphaPeptDeep to boost identification rates.
- PSM rescoring with MS2PIP and DeepLC
- AlphaPeptDeep integration for retention time prediction
- Percolator-based FDR control
- Boosts identification rates by 10–30%