Functional proteomics workflows incorporating timsUltra AIP and timsOmni have been developed by Bruker. These have been launched at Human Proteome Organization World Congress 2026. These workflows help to achieve better sequence coverage of proteins and also validation of proteins. They also contribute to glycopeptide characterization, structural proteomics, and oligonucleotide sequencing. Moreover, dia-PASEF with multiple enzymes helps to achieve more peptide data for studying isoforms and proteoforms. ProteoScape combines PASEF discovery and prm-PASEF validation on the timsTOF platform.
“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.”
MultiDIA-PASEF Expands Proteoform Characterization
The MultiDIA-PASEF method of Bruker uses the complementary protease digests along with the dia-PASEF technique. The method is perform using the timsUltra AIP ultra-high sensitivity mass spectrometer. In the samples from brains of people suffering from Parkinson’s disease, the method resulted in around 350,000 peptides per sample. Analysis of the complementary digest method provided approximately 14,500 protein isoforms. These protein isoforms were related to more than 10,000 canonical proteins. This method allows better sequence coverage of the proteins.
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.”
The method can detect peptide evidence of the isoforms and sequence variants. It can also find missed protein sequences in the single enzyme proteomics analysis.
ProteoScape Connects Discovery and Validation
ProteoScape by Bruker now allows for the linking of dda-PASEF, diagonal-PASEF, and dia-PASEF discovery with PASEF prm validation. Target lists for Pm PASEF analysis can be generate from the results of discovery studies. Such an approach facilitates the 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.”
AI Transfer Learning Supports MS Analysis
The Spectronaut v21 has an adaptive AI analysis system, which is design for the development of the latest mass spectrometry approaches. It enables 4D proteomics by using multidimensional feature maps, which comprise information about precursors, fragments, retention time, and ion-mobility. Transfer learning is utilize to train AI models for novel acquisitions.
“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.”
timsOmni Advances Glycopeptide Research
Glycoproteomics is being developed by Bruker using Guided PASEF EXciD. The timsOmni procedure allows for rapid and selective fragmentation of ions via electrons. The technique functions at greater than 30 Hz when acquiring spectra. It detects diagnostications from glycans, and then fragmentation by EXD or EXciD is directed to targeted precursor ions.
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.”
HDX-MS Supports Structural Proteomics
Bruker and Affipro Analytics have entered into an agreement for marketing and development. This agreement involves the integrated H-D exchange MS workflows. This solution includes the integration of Affipro HDX-MS automation and Bruker HyStar control system. It also features the Affipro DeutEx analysis software. The workflow links up the experimental set up to LC-MS control and analysis of molecular interaction, conformational dynamics and protein structures.
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.”
timsOmni Expands Oligonucleotide Analysis
Valérie Gabelica of the University of Geneva was successful with advanced nucleic acid analysis by timsOmni. It provided complete coverage of the sequence of RNA and DNA oligonucleotides. It involved electron detachment dissociation and Omnitrap MS³ workflows. The combination of EDD with vibrational activation resonance CID can provide full sequence coverage, which helps in RNA and DNA oligonucleotide analysis. The same can be done for antisense medicines like Fomivirsen. Moreover, the native top-down analysis can be done on folded RNA structures.
The researchers can identify both protected and exposed regions within one experiment. The Omnitrap also provides softer activation with structurally informative radical fragments. All these features increase timsOmni application in oligonucleotide characterization and native RNA structural biology. In general, Bruker is increasing the application of functional proteomics to many areas of research. They include drug discovery, disease biology, structural research, and biological AI development.
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News Source: Businesswire.com
