Spectronaut-nf is a Nextflow pipeline that enables parallel processing of DIA proteomics data on HPC systems, reducing analysis time compared to single workstation execution.

bioRxiv · Jul 30, 2026 · PreprintBioinformatics

Stringent proteogenomic discovery of novel small proteins in Mycobacterium tuberculosis clinical reference strains

Benjamin Heiniger, Christian Schori, Mohammad Arefian, Amir Banaei‐Esfahani, Martin Schuler, Sònia Borrell, Chloé Loiseau, Daniela Brites, Iñaki Comas, Ruedi H. Aebersold, Sébastien Gagneux, Ben C. Collins, Christian H. Ahrens

The paper uses long-read assemblies and proteogenomic analysis to discover novel small proteins in Mycobacterium tuberculosis strains.

bioRxiv · Jul 17, 2026 · PreprintMicrobiology

Induced pluripotent stem cell-derived macrophages as a model for human inflammasome signaling

Chloe M. McKee, Melanie Cranston, Emma C. McKay, Mohammad Arefian, Thea J. Mawhinney, Ben C. Collins, Rebecca C. Coll

This study generates and benchmarks iPSC-derived macrophages (iMacs) as a model for human inflammasome signaling, showing they respond to multiple inflammasome stimuli and activate unique pathways.

bioRxiv · Sep 5, 2025 · PreprintImmunology

A gas phase fractionation acquisition scheme integrating ion mobility for rapid diaPASEF library generation

Jack Penny, Mohammad Arefian, Gunnar N. Schroeder, José Antonio Bengoechea, Ben C. Collins

The paper introduces an ion mobility-integrated gas phase fractionation (IM-GPF) method for rapid diaPASEF library generation, outperforming direct deconvolution and approaching offline fractionation performance.

PROTEOMICS · Mar 6, 2023Peer-reviewedSystems Biology