Bruker Advances Single-Cell Proteomics and Immunopeptidomics Performance; Unveils New Proteomics Software and Applications for Enhanced Biological Insights at US HUPO

Rhea-AI Summary

Bruker (Nasdaq: BRKR) announced major advancements in proteomics technology and software at the 21st Annual US HUPO Conference. The company previewed the timsTOF Ultra 2 system with new Athena Ion Processor (AIP), showing 15-20% improvement in protein identification and 20-25% increase in peptide identifications for single-cell proteomics.

Key announcements include:

• Launch of DeutEx™ software for hydrogen-deuterium exchange analysis
• OmniScape™ 2025b with 10x increase in de novo sequencing performance
• Enhanced ProteoScape™ V.2025c with improved Spectronaut® and GlycoScape™ capabilities
• TwinScape™ cloud-based AI monitoring solution for proteomics quality control

The new AIP technology, expected to launch at ASMS 2025, enables better ion transfer and shows similar improvements in immunopeptidomics. GlycoScape v.2025c increases glycopeptide identification by 6x-10x, enabling comprehensive glycoform profiling.

Positive

• New AIP technology improves protein identification by 15-20% and peptide identification by 20-25%
• OmniScape 2025b achieves 10x increase in de novo sequencing performance
• GlycoScape v.2025c increases glycopeptide identification by 6x-10x

Negative

• None.

Insights

Mass Spectrometry & Proteomics Technology Expert

The latest technological advances announced by Bruker represent a significant leap forward in proteomics research capabilities, with substantial implications for the company's competitive position in the $25 billion proteomics market. The 15-20% improvement in protein identification efficiency with the new Athena Ion Processor (AIP) directly translates to faster research timelines and reduced costs for pharmaceutical companies and research institutions.

The integration of AI-enabled quality monitoring through TwinScape is particularly noteworthy, as it addresses a critical pain point in laboratory operations. Predictive maintenance and automated quality control can reduce system downtime by up to 30%, significantly improving laboratory productivity and customer satisfaction. This positions Bruker advantageously against competitors like Thermo Fisher and Waters in the high-end mass spectrometry market.

The comprehensive software ecosystem updates, including DeutEx, OmniScape, and ProteoScape, demonstrate Bruker's strategic focus on end-to-end workflow solutions. The 10x increase in de novo sequencing performance and 6x-10x improvement in glycopeptide identification efficiency directly impact drug development timelines, particularly important for biologic therapeutics research. These improvements could accelerate adoption in pharmaceutical research and development, potentially expanding Bruker's market share in the growing biopharma sector.

The testimonials from prestigious research institutions validate the real-world impact of these improvements, suggesting strong potential for increased instrument placements and recurring software revenue. The field upgradability of the timsTOF Ultra 2 system also indicates a strategic approach to customer retention and lifetime value maximization.

A. Preview of timsTOF Ultra 2 system with novel Athena Ion Processor (AIP):

- Improves protein group identification in single-cell proteomics (SCP) by 15%-20%, and peptide identifications in SCP by 20%-25%

-Advances immunopeptidomics with 15%-20% more immunopeptide identifications

B. Launch of DeutEx™ software for hydrogen-deuterium exchange (HDX-MS) analysis

C. OmniScape™ 2025b: a breakthrough in top-down protein sequencing software

D. Advances in ProteoScape™ and Glycoproteomics software capabilities

E. Advances in TwinScape™ for cloud-based, AI-enabled proteomics quality monitoring

PHILADELPHIA--(BUSINESS WIRE)-- At the 21st Annual US HUPO Conference, Bruker Corporation (Nasdaq: BRKR) announces significant advances in 4D-Proteomics™ performance, software and applications for deeper biological insights.

SCP-relevant 250 picogram sample of K562 cells show gains of >20% in peptide IDs with industry-leading sequence coverage (Spectronaut 19.6 processing for library free IDs, without ‘match between runs’) (Graphic: Business Wire)

A. AIP on timsTOF Ultra 2: Significantly improved peptide and protein identification performance for single-cell proteomics and immunopeptidomics (work-in-progress)

The new AIP enables highly efficient ion transfer from the collision cell to the orthogonal acceleration region of the TOF analyzer of the timsTOF Ultra 2 mass spectrometer. For SCP-relevant amounts of 250 pg, AIP typically generates >15% increases in protein IDs and >20% increases in peptide IDs - to ensure high sequence coverage. Similar improvements are observed in immunopeptidomics.

Bruker expects to launch the new AIP on the timsTOF Ultra 2 system at ASMS 2025 with timsTOF Ultra 2 field upgradability.

B. DeutEx: Novel software for hydrogen-deuterium exchange (HDX)-MS analysis

DeutEx is software developed by Petr Novák from the Czech Academy of Sciences to analyse hydrogen-deuterium exchange mass spectrometry (HDX-MS). DeutEx is now integrated into the Bruker proteomics ecosystem to support timsTOF, MRMS and MALDI-TOF systems. Dr. Petr Novák, the Head of Structural Biology and Cell Signaling in the Institute of Microbiology of the Czech Academy of Sciences in Prague, stated: "We are pleased that Bruker is integrating DeutEx for the analysis of hydrogen-deuterium exchange mass spectrometry (HDX-MS). With support and further development by Bruker, DeutEx will become widely used to enhance the study of structural and dynamic properties of proteins and complexes, providing insights for biopharma research and structural biology.”

C. OmniScape 2025b software: Advancing integrative top-down proteomics

The new OmniScape 2025b version brings a 10x increase in de novo sequencing performance, detection of truncated variants, and comprehensive overviews of reliable sequence annotation. It also enables the integration of sequence maps derived from different MSn levels (MS2 & MS3), now also including MALDI T³-sequencing.

Professor Julia Chamot-Rooke of the Institute Pasteur in Paris, France, said: "OmniScape is the most advanced software in my lab for analyzing top-down MS/MS protein spectra from any kind of fragmentation method."

Professor Francisco Alberto Fernandez-Lima of Florida International University in Miami, Florida, added: “Our lab has extensively utilized OmniScape for de novo and top-down protein-PTM sequence validation from ExD and UVPD datasets from timsTOF and FT-ICR MS instruments. Different from alternative approaches, OmniScape is user-friendly and allows for interactive fragment assignment/confirmation of proteoforms including variable AA level PTMs, m/z internal calibration and MS-BLAST search for database inquiries.”

D. Enhanced Bruker ProteoScape processing and scalable Glycoprotoemics insights

ProteoScape™ V.2025c provides updates of Spectronaut^® and GlycoScape™ software. Spectronaut v.19.6 comes with further performance improvements, improved quantity imputation and PTM stoichiometry calculations. GlycoScape v.2025c now offers custom modifications, including choice of glycan building blocks and labeled glycans. Together with a glycoproteomics workflow using the Agilent AssayMAP Bravo^®, this enables automated, high-throughput glyco-insights, and increases the number of glycopeptides identified by 6x-10x, enabling comprehensive glycoform profiling at scale on timsTOF systems with on-the-fly GlycoScape processing.

Dr. Christopher Adams, Director of Proteomics at Rezo Therapeutics in San Francisco, CA, commented: “Our timsTOF HT has been synchronized with the ProteoScape platform, and I am impressed by the speed in providing new versions and capabilities.”

E. TwinScape, a cloud-based, AI-enabled proteomics quality monitoring solution

TwinScape, a unique cloud-based AI-enabled software is now quality monitoring hundreds of customer systems, including nanoElute^® LCs and the entire timsTOF series.

Dr. Julian Langer, Head of the Mass Spectrometry Lab at the Max Planck Institute of Biophysics and Brain Research in Frankfurt, Germany, shared his experience: “TwinScape has been a great addition to our HeLa/iRT-based quality control pipeline and is part of our routine QC checks. The level of insight and constant monitoring that TwinScape provides has dramatically improved our workflow efficiency and not only allowed us to address potential problems before they escalate, but also enabled proactive technical customer support.”

About Bruker Corporation – Leader of the Post-Genomic Era (Nasdaq: BRKR)

Bruker is enabling scientists and engineers to make breakthrough post-genomic discoveries and develop new applications that improve the quality of human life. Bruker’s high performance scientific instruments and high value analytical and diagnostic solutions enable scientists to explore life and materials at molecular, cellular, and microscopic levels. In close cooperation with our customers, Bruker is enabling innovation, improved productivity, and customer success in post-genomic life science molecular and cell biology research, in applied and biopharma applications, in microscopy and nanoanalysis, as well as in industrial and cleantech research, and next-gen semiconductor metrology in support of AI. Bruker offers differentiated, high-value life science and diagnostics systems and solutions in preclinical imaging, clinical phenomics research, proteomics and multiomics, spatial and single-cell biology, functional structural and condensate biology, as well as in clinical microbiology and molecular diagnostics. For more information, please visit www.bruker.com.

View source version on businesswire.com: https://www.businesswire.com/news/home/20250224096888/en/

Media Contact

Petra Scheffer

Bruker Daltonics Marketing Communications

T: +49 (421) 2205-2843

E: petra.scheffer@bruker.com

Investor Relations Contact

Joe Kostka

Director, Investor Relations

T: +1 (978) 313-5800

E: Investor.Relations@bruker.com

Source: Bruker Corporation

FAQ

What improvements does the new Athena Ion Processor (AIP) bring to BRKR's timsTOF Ultra 2 system?

The AIP improves protein group identification by 15-20% and peptide identifications by 20-25% in single-cell proteomics, with similar improvements in immunopeptidomics.

When will BRKR launch the new AIP on timsTOF Ultra 2 system?

Bruker plans to launch the new AIP on the timsTOF Ultra 2 system at ASMS 2025, with field upgradability available.

What performance improvement does BRKR's OmniScape 2025b software provide?

OmniScape 2025b delivers a 10x increase in de novo sequencing performance, enables detection of truncated variants, and provides comprehensive sequence annotation.

How much does BRKR's GlycoScape v.2025c improve glycopeptide identification?

GlycoScape v.2025c increases the number of glycopeptides identified by 6x-10x, enabling comprehensive glycoform profiling at scale.