Biognosys unveils next-generation proteomics software with breakthrough immunopeptidomics capabilities
Swiss proteomics leader Biognosys has launched two major software updates that promise to revolutionise mass spectrometry-based protein analysis, with particular advances in immunopeptidomics research critical for therapeutic development.
The company announced Spectronaut 20 and SpectroMine™ 5 at the ASMS 2025 Annual Conference in Baltimore, introducing breakthrough technologies that deliver unprecedented peptide identification rates and enhanced analytical capabilities for clinical researchers.
Revolutionary search engine powers identification breakthroughs
At the heart of both software releases lies Kuiper, Biognosys’ novel search engine powered by proprietary prediction models specifically optimised for unspecific searches. This technological innovation represents a significant leap forward in proteomics data analysis, particularly for immunopeptidomics applications where comprehensive peptide identification remains challenging.
Spectronaut 20 delivers remarkable performance improvements, achieving up to 80% more peptide identifications in immunopeptidomics HLA class I workflows compared to previous versions. The software also features accelerated processing through directDIA runtime improvements and enhanced quantitative accuracy for timsTOF data via ion-mobility sensitive algorithms.
“Immunopeptidomics is key to understanding how our therapeutics are making a difference for patients,” said Daniel Green, Ph.D., Head of Bioinformatics at Greywolf Therapeutics. “Spectronaut 20 empowers us to leverage complex datasets with greater speed and depth, delivering critical insights into MHC-I antigen modulation and its effects on immune recognition.”
Enhanced cloud compatibility enables scalable research
Both software packages now offer Linux support and cloud compatibility, enabling high-throughput proteomics data analysis in cloud and high-performance computing environments. This advancement facilitates scalable, next-generation research workflows essential for large-scale clinical studies.
SpectroMine 5, designed for DDA-based proteomics, incorporates the same Kuiper engine technology to deliver significantly enhanced identification performance. The addition of Linux support extends the software’s utility
in diverse computational environments.
Clinical applications demonstrate real-world impact
The practical applications of these technological advances extend beyond laboratory efficiency. Biognosys will present research showcasing their P2 Enrichment System, a nanoparticle-based plasma workflow that offers unprece-dented depth, reproducibility, and throughput in plasma proteomics analysis.
Collaborators from Johns Hopkins School of Medicine will demonstrate the P2 system’s real-world application in clinical studies focusing on circulating biomarker discovery for early detection of neurodegenerative diseases – a critical area where enhanced sensitivity and precision can significantly impact patient outcomes. “The P2 Enrichment System from Biognosys was seamlessly transferred to our lab at the Broad Institute,” said Steven A. Carr, Ph.D., Senior Director of Proteomics and Institute Scientist at the Broad Institute of MIT and Harvard. “We were impressed by the clarity and robustness of the protocols, as well as the exceptional performance of the technology across our sample sets.”
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