Explore the ecosystem of tools and libraries that power the quantms workflow
A cloud-ready Nextflow pipeline for DDA quantitative proteomics: label-free (LFQ) and isobaric labeling (TMT/iTRAQ) workflows.
DIA proteomics Nextflow pipeline powered by DIA-NN, supporting both library-free and spectral library modes with standardized output.
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.
Quantitative proteomics exchange format. A unified Parquet-based data standard for cross-tool and cross-dataset proteomics analysis.
A set of tools to validate and convert SDRF files to workflow configuration formats for proteomics analysis pipelines.
A MultiQC plugin for visualizing and aggregating quality control metrics from proteomics data analysis workflows.
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.
PSM rescoring tool that adds deep-learning features to peptide-spectrum matches using MS2PIP, DeepLC, and AlphaPeptDeep to boost identification rates.