ImmunAID-ms-parameters

# ImmunAID-ms-parameters Normalization parameters used to generate the proteomics data for the paper: **Adult patients with autoinflammation of unknown origin partially phenocopy the immune presentation of Still’s disease** ## Content of FragPipe parameters folder This repository includes two key configuration files for the FragPipe/MSFragger pipeline. - The `fragger.params` file defines all database search settings (e.g. enzyme specificity, mass tolerances, allowed missed cleavages, and fixed/variable modifications), ensuring the MS/MS search is fully reproducible and its search space is clearly documented. - The `sdrf.tsv` file follows the Sample and Data Relationship Format and describes the experimental design and sample metadata for each LC-MS/MS run (such as biological conditions, replicates, and raw file paths), enabling correct sample grouping, downstream statistical analysis, and transparent linkage between raw data and biological context. ## How to cite: If you use these parameters, please cite it as follows: Poulet, C., & Baiwir, D. (2026). ImmunAID-ms-parameters (Version 1.0.0) [Dataset]. University of Liège - GIGA Institute. Zenodo. https://doi.org/10.5281/zenodo.18413673 License: CC BY-NC-ND 4.0 Repository: https://gitlab.uliege.be/giga-rheumatology/public/immunaid-ms-parameters