Bruker Advances Functional Proteomics with Novel timsUltra AIP and timsOmni Workflows for Drug Discovery & Development and Disease Biology Research

SINGAPORE--(BUSINESS WIRE)--Sep 28, 2026--

At the Human Proteome Organization World Congress 2026, Bruker Corporation (Nasdaq: BRKR) today announced unique new timsUltra AIP and timsOmni workflows for deeper protein-sequence coverage, targeted validation, mobility-resolved glycopeptide characterization, structural proteomics, and oligonucleotide analysis. Multi-enzyme dia-PASEF provides additional peptide information for investigations of isoforms and proteoforms, while ProteoScape workflows connect PASEF discovery with prm-PASEF target validation on the same timsTOF platform. Novel timsOmni and integrated HDX-MS workflows extend structural analysis to glycopeptides, proteins, and nucleic acids.

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“ We are combining proteome depth, PTMs, proteoforms, protein interactions, and conformational and spatial context to enable richer multimodal training data for next-generation biological AI models,” said Frank H. Laukien, President and CEO of Bruker. “These complementary molecular dimensions can extend existing models for drug discovery and mechanisms of action with information closely linked to biological function, helping advance molecular medicine more rapidly in the post-genomic era.”

A. MultiDIA-PASEF workflow further increases sequence coverage for deeper proteoform characterization

A novel multi-enzyme method combines complementary protease digests with dia-PASEF on the timsUltra AIP ultra-high sensitivity mass spectrometer. In Parkinson’s brain samples, this yielded ~350,000 peptides per sample. Analysis across complementary digests provided ~14,500 protein isoforms corresponding to over 10,000 canonical proteins. By increasing protein sequence coverage, the workflow reveals peptide evidence for isoforms, sequence variants, and protein regions that are missed in single-enzyme MS-based proteomics or by affinity methods.

Prof. Nikolai Slavov, Founding Director, Parallel Squared Technology Institute and Distinguished Professor of Biological Engineering at Northeastern University, said: “ Deep sequence coverage is central to understanding proteoform biology. By combining complementary protease digests with sensitive dia-PASEF, we can improve peptide coverage and gain a more confident and detailed view of isoforms and proteoforms that otherwise remain hidden. ”

B. Discovery-to-Validation connects dia-PASEF discovery with prm-PASEF validation

A direct path from dda-PASEF, diagonal-PASEF, and dia-PASEF discovery to prm-PASEF target validation is now available within Bruker ProteoScape. Researchers can convert discovery into prm-PASEF target lists and move from discovery studies to targeted analysis of proteins, pathways, and biomarkers.

Prof. Stanley Stevens Jr. at the University of South Florida explained: “ Together with Bruker, we have developed automated workflows that bridge discovery proteomics and targeted assays. By simplifying and accelerating method development, this enables more precise quantitation, helping translate complex proteomics data into actionable biological insights. ”

C. AI transfer learning accelerates Spectronaut® adaptation to MS capabilities

Spectronaut v21 provides an AI analysis environment that can dynamically adapt to new mass spectrometry capabilities and acquisition methods. Modern 4D proteomics is represented by multi-dimensional feature maps, including precursor, fragment, retention time and ion-mobility. Through advanced transfer learning, Spectronaut dynamically tailors its AI models to new acquisition modes and instrument capabilities without requiring model redevelopment.

“ New acquisition modes and instrument configurations now become available before large training datasets can be generated, ” said Dr. Tejas Gandhi of Biognosys. “ Spectronaut’s transfer-learning accelerates AI model adaptation quickly as new MS technologies and methods become available.”

D. Guided PASEF EXciD for high-speed, mobility-resolved glycopeptide characterization

Bruker is advancing glycoproteomics with Guided PASEF EXciD, a timsOmni workflow for fast, selective electron-based fragmentation. Operating at more than 30 Hz, the method recognizes diagnostic glycan oxonium ions during acquisition and directs EXD or EXciD fragmentation to selected glycopeptide precursors. The workflow retains TIMS separation for ion mobility-resolved glycopeptide characterization.

Daniel Polasky, Assistant Professor in Pathology at the University of Michigan stated: “ A major challenge in glycoproteomics is translating complementary peptide and glycan fragment information into confident, biologically meaningful insights. By combining intelligent trapped eXd with automated analysis in FragPipe, researchers can readily characterize site-specific glycosylation and glycan structural diversity in complex biological samples. ”

E. Bruker and Affipro Analytics integrate HDX-MS workflows for structural proteomics

Bruker and Affipro Analytics announce a co-marketing and development agreement for integrated hydrogen-deuterium exchange MS workflows. The solution combines Affipro HDX-MS automation, Bruker HyStar control, and Affipro DeutEx analysis software to connect experimental setup, LC-MS control to molecular interactions, conformation dynamics and protein structure insights.

Dr. Petr Novak, co-founder of Affipro Analytics and Group Leader Structural Biology and Cell Signaling at the Institute of Microbiology of the Czech Academy of Sciences, commented: “By combining Affipro’s workflow expertise with TIMS separation, we provide more structural information at higher throughput to accelerate AI-assisted drug discovery and structural biology.”

F. EDD-MS³ on timsOmni for complete oligonucleotide coverage and native RNA analysis

Valérie Gabelica at the University of Geneva achieved breakthrough nucleic acid analysis on the timsOmni™ with complete sequence coverage of RNA and DNA oligonucleotides through electron detachment dissociation (EDD) and Omnitrap MS³ workflows unique capabilities. Combining EDD with vibrational activation resonance CID, can achieve complete sequence coverage for RNA and DNA oligonucleotides, e.g., on the antisense drug Fomivirsen.

Native top-down analysis of folded RNA structures enabled localization of protected domains and of accessible regions in a single experiment. The Omnitrap can provide softer activation and retention of structurally informative radical fragments. Together, these capabilities extend timsOmni workflows to oligonucleotide characterization and native RNA structural biology.

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.

Bruker and Affipro Analytics integrate HDX-MS workflows for structural proteomics

Discovery-to-Validation target workflow

SEOUL, South Korea (AP) — Seoul has called for an official apology from Ukraine after President Volodymyr Zelenskyy revealed what it says was supposed to be a secret transfer of two North Korean prisoners of war to South Korea.

Zelenskyy told the U.N. General Assembly last week that Ukraine had recently sent the men to South Korea, after capturing them on a Ukraine-Russia battlefield in early 2025. The two are among thousands of North Korean soldiers sent to support Russia’s war against Ukraine.

South Korean President Lee Jae Myung quickly accused Ukraine of violating a nondisclosure agreement about the transfer. Ukraine denied making such a deal.

Late Sunday, Seong Ghi-hong, a senior presidential adviser for Lee on public relations, expressed “strong regret” over Ukraine’s latest actions and demanded an official apology and explanation.

The South Korean Foreign Ministry on Monday summoned Ukraine’s ambassador to Seoul, Andrii Vieshkin, to protest what it described as Kyiv’s “unilateral disclosure” of the prisoners’ transfer and its false denial that the two countries had agreed to keep the matter confidential.

Vieshkin said he would convey Seoul’s position to his government, the ministry said in a statement. Repeated calls to Ukraine’s Embassy in Seoul seeking comment were unanswered.

Seong said that Ukraine’s “false” denial of the nondisclosure agreement was “an act that seriously undermines trust between the two governments and causes significant damage to friendly relations between the two countries.”

Seong said the agreement was reached because Seoul was concerned about the safety of the North Korean soldiers and their relatives in the North while Kyiv worried about possible domestic criticism for forfeiting an opportunity to exchange them for Ukrainian soldiers held in Russia.

While still in Ukraine, the two soldiers said in media interviews that they wanted to resettle in South Korea.

Seoul had called on Ukraine not to send them back to North Korea, where they could face persecution. The South legally regards the North as part of its territory and has a policy of accepting and financially supporting North Korean defectors.

More than 34,000 North Koreans have fled to South Korea since the end of the 1950-53 Korean War, mostly in the last three decades. Most were female civilians from the North’s poorer northern provinces. Defections by soldiers are uncommon.

In his U.N. speech, Zelenskyy didn't provide details about the transfer, but said that “one of them, when he realized he was going to ​be taken prisoner, tried to kill himself and he was shocked that ​fate didn’t let him die. This is how they raise people in the North.”

Some experts say Zelenskyy likely decided to expose the danger of North Korean involvement in the war as a way to attract bigger Western assistance.

Meanwhile, South Korea's liberal government worried that news of the transfer could trigger an angry response from the North and hurt efforts to resume diplomacy between Pyongyang and Washington.

A growing arms exporter with a well-equipped and U.S.-backed military, South Korea has provided humanitarian aid and other support to Ukraine while joining U.S.-led economic sanctions against Russia since its invasion in 2022.

However, Seoul has resisted calls by Kyiv and NATO to provide direct military support to Ukraine in line with a long-standing policy of not supplying weapons to countries actively engaged in conflict.

North Korea and Russia confirmed in April 2025 that their soldiers fought together to repel a Ukrainian incursion into Russia’s Kursk border region. South Korea, the United States and others say North Korea has also supplied artillery, ammunition and missiles to Russia in return for economic and military assistance.

South Korea’s intelligence service estimated last year that North Korea sent about 15,000 troops and 2,000 of them were killed.

Expanding cooperation with Russia has helped North Korea's leader, Kim Jong Un, push back against U.S.-led pressure and more assertively accelerate a nuclear weapons program. Last month, U.S. President Donald Trump scaled back a military drill with South Korea in an apparent bid to restart diplomacy with Kim, but North Korea has suggested the step wasn't enough to convince it to return to talks.

Associated Press writer Kim Tong-hyung contributed to this report.

Ukraine's President Volodymyr Zelenskyy speaks during the 81st session of the United Nations General Assembly at United Nations headquarters, Wednesday, Sept. 23, 2026. (AP Photo/Seth Wenig)