DIA-NN_EasyFilter with KNIME (DEF)

DIA-NN_EasyFilter (DEF) is a KNIME-based workflow for filtering and qualitative/quantitative evaluation of DIA-NN (≥1.8) main reports. DEF enables identification validation, protein group inference, contaminant filtering, and run-level quantification assessment without requiring programming expertise.

Key Features

Two protein group inference strategies (2-unique peptide or proteotypic rule) Optional XIC-based peptide quality filtering Contaminant library filtering (MaxQuant, cRAP, Hao-Group, or custom FASTA) Interactive visualizations and grouped comparisons Rapid processing of large-scale DIA-NN reports

Installation

Download KNIME: https://www.knime.com/download Download DEF from: https://hub.knime.com/24mabuse Install required KNIME extensions (automatic prompt) Detailed instructions are provided in the step-by-step guide, or Data S2 of the associated manuscript.

Citation

If you use DEF, please cite: [bioXiv...](https://doi.org/10.64898/2026.03.07.710308)