At the 23rd Human Proteome Organization World Congress, Bruker Corporation (Nasdaq: BRKR) announced significant advancements in deep, unbiased, and high-sensitivity 4D-Proteomics. These developments enable robust, high-fidelity, large-scale studies while minimizing the inherent cross-talk issues associated with affinity high-plex technologies.
A. Enhanced Specificity and Proteome Coverage with Diagonal-PASEF
Bruker, in collaboration with Dr. Matthias Mann (Max Planck Institute) and Dr. Stefan Tenzer (University of Mainz), introduced diagonal-PASEF in 2023, which builds on scanning quadrupole and trapped ion mobility spectrometry (TIMS). This advancement supports synchro-PASEF and midia-PASEF, now compatible with Spectronaut 19, DIA-NN 1.9, MaxQuant 2.6.3, and midiaID.
Synchro-PASEF enables high-throughput acquisitions while enhancing quantitative precision through better ion sampling, shorter cycle times, and up to three times improved signal strength.
Midia-PASEF enhances immunopeptidomics and post-translational modifications (PTMs) by extracting DDA-like spectra for de novo sequencing and searching large databases.
Dr. Jarrod Marto from Dana-Farber Cancer Institute noted the positive impact of midia-PASEF on their research into genomic alterations and small molecule probes, particularly for quantitative analysis of PTMs and MHC-associated peptides.
B. Achievement of One-Hundred Dollar Deep, High-Accuracy Plasma Proteome
Bruker leads in deep, unbiased plasma proteome profiling, delivering high peptide fidelity and cost-effective large-scale studies. Using PreOmics ENRICH-iST or ENRICHplus methods, timsTOF HT with Spectronaut 19 achieves robust protein identification with 99% specificity and 1% FDR, allowing deep, high-fidelity plasma proteomics for as low as $100 per sample.
Biopharma can explore ultra-deep plasma proteome discovery, identifying up to 7,000 proteins (or 9,000 at lower throughput) through research services from Biognosys or by licensing the proprietary P2 ultra-deep plasma enrichment technology for in-house use.
C. Introducing High-Sensitivity Plasma Glycopeptide Analysis on timsTOF Ultra 2
Bruker’s glyco-PASEF® has been optimized for ultra-high sensitivity on the timsTOF Ultra 2 with human plasma samples. This new method, combined with ENRICHplus, doubles the number of glycopeptides identified and utilizes GlycoScape® software for comprehensive glycobiology analysis.
D. Increased Peptide and Protein Identifications with ML-Enhanced TIMSrescore
The timsTOF platform now routinely identifies over 100,000 peptides from human cell line proteomics with less than 1 µg loading in just 20 minutes. This high sequence coverage (typically over 10 peptides per protein) is essential for confident identification and quantification, as well as for detecting PTMs in immunopeptidomics and metaproteomics.
Bruker also introduces TIMSrescore, developed with Dr. Lennart Martens’ team at the University of Ghent. By applying machine learning to timsTOF data, TIMSrescore enhances high-confidence peptide identification for dda-PASEF, crucial for distinguishing highly similar proteins among diverse microbial species with high stringency (99.9% specificity at 0.1% FDR).
Dr. Martens remarked on the enthusiastic adoption of TIMS2Rescore in the proteomics community, highlighting its integration into Bruker ProteoScape software to maximize the value of 4D-Proteomics.
E. Multiomics Visualization and Insights for Proteomics and Metabolomics
Bruker ProteoScape™ now enables visualization and statistical analysis of 4D-Multiomics data from MetaboScape® for metabolomics and lipidomics. This includes dimensional reduction techniques (PCA, LDA, t-SNE) and intuitive visualizations like interactive multiomics Volcano plots.
Dr. Roman Fischer from the University of Oxford praised the capabilities of ProteoScape and MetaboScape for real-time analysis, expressing excitement over Bruker’s integration of proteomics and lipidomics with interactive visualization and statistical tools.
