At the 23rd Human Proteome Organization (HUPO) World Congress, Bruker Corporation presented new advancements in its 4D-Proteomics technology. These updates aim to improve the accuracy and depth of large-scale proteomics research, addressing some of the limitations found in traditional high-plex methods.
Bruker’s timsTOF platform has already been widely used for proteomics and lipidomics, and its latest integration with the company’s ProteoScape and MetaboScape software has garnered positive reactions. Dr. Roman Fischer from the University of Oxford praised the system’s ability to process data in real time, saying, “It’s fantastic that Bruker now integrates both worlds with interactive multiomics visualization and statistical analysis.”
One of the key innovations Bruker announced was the diagonal-PASEF (Parallel Accumulation Serial Fragmentation) technology. This approach was developed in collaboration with researchers Dr. Matthias Mann from the Max Planck Institute and Dr. Stefan Tenzer from the University of Mainz. Diagonal-PASEF builds on Bruker’s existing ion mobility technology to increase both the specificity and coverage of proteomics analysis.
Two variations, synchro-PASEF and midia-PASEF, were introduced, offering high-throughput capabilities with improved sampling and signal strength. Dr. Jarrod Marto from Dana-Farber Cancer Institute shared his early experience with midia-PASEF, stating that his lab has had promising results in using the technique to study immune-related peptides and post-translational modifications. “We’re optimistic about its potential for expanding our understanding of these processes,” he said.
Another notable announcement was Bruker’s progress in making plasma proteomics more accessible and cost-effective. The company claims it has reduced the cost of large-scale plasma proteome profiling to around $100 per sample. Using the timsTOF HT platform combined with PreOmics ENRICH-iST methods, researchers can now identify up to 9,000 proteins in a sample, making it a practical option for larger studies, such as those in drug development or personalized medicine.
Bruker also introduced a more sensitive approach to analyzing glycopeptides, particularly in human plasma samples. Their timsTOF Ultra 2 platform, combined with the newly optimized glyco-PASEF technology, has shown promising results, doubling the number of identified glycopeptides. This innovation could open new doors in the study of glycoproteins, which play a key role in many biological processes.
A major development in peptide identification is the launch of TIMSrescore, a machine learning-based tool developed with Dr. Lennart Martens from the University of Ghent. This tool uses data like ion mobility and retention time to improve the accuracy of peptide identifications. It’s particularly useful in research on post-translational modifications and in distinguishing proteins in complex microbial samples.
Finally, Bruker announced updates to its ProteoScape software, which now integrates with MetaboScape for advanced multiomics analysis. This allows researchers to visualize and analyze both proteomics and metabolomics data side by side, using techniques like PCA and t-SNE for dimensionality reduction. Dr. Fischer from the University of Oxford noted that this integration could help translate complex data into meaningful biological insights.