Bruker Corporation announced progress in immunopeptidomics, glycoproteomics and other CCS-enabled 4D-proteomics workflows. The rapid advances in deep, at-scale proteomics, glycomics and peptidomics research solutions complement other performance-leading life-science tools for the post-genomic era by Bruker. Together they enable post-genomic molecular and cell biology research, with key insights into disease biology and biomarkers for next-gen molecular diagnostics and drug discovery.

The advances featured at US HUPO include improved machine-learning de novo sequencing (Novor V2.0), a novel high-performance monitoring digital-twin software (TwinScape), the new glyco-PASEF method for high-sensitivity glycopeptide analysis, and access to Spectronaut 18 for users of BrukerProteoScape, a GPU-powered software for real-time 4D proteomics, now with access to library-free searches by Biognosys directDIA. A. Advancing Cancer Immunotherapy Research: Bruker enhances its timsTOF HT and timsTOF Ultra systems with the new software Novor v2.0 for de novo immunopeptidomic profiling. Novor v2.0, developed in collaboration with Rapid Novor Inc., was trained on >1,400,000 spectra mapping to >150,000 HLA peptides for research on small amounts of patient material derived from fine needle biopsies.

B. Peak timsTOF Performance using TwinScape: TwinScape is a new digital-twin performance monitoring and quality control engine, leveraging iRT peptide standards to support sustained peak performance in sample prep and LC-MS. For synergistic multi-omics studies in the post-genomic era, a combination of depth of coverage, robustness, and scalable quantitation is required. TwinScape enables larger controlled studies and valid cross-lab comparability. C. New glyco-PASEF for Ultra-High Sensitivity 4D-Glycopeptide Analysis: Bruker presents the novel timsTOF glyco-PASEF method with polygon filtering developed with the Heck Group at Utrecht University, the GlycoScape software developed collaboratively with the Van Gool Group at Radboud University, and MSFragger-Glyco software developed by the Nesvizhskii Group at the University of Michigan.

D. Software Advances for dia-PASEF: The newest release of Bruker ProteoScape makes a Spectronaut 18 module available for dia-PASEF analysis, enabling real-time results using GPU computing, including directDIA for library-free searches. Bruker ProteoScape now also upgrades TIMS DIA-NN software to version 3.0 with improved quantitation accuracy.