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

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.

This press release features multimedia. View the full release here: https://www.businesswire.com/news/home/20250224096888/en/

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.

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

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