Bruker Advances CCS-Enabled 4D-Proteomics timsTOF Solutions for Immunopeptidomes and Glycoproteomics at US HUPO

Rhea-AI Summary

Bruker Corporation (BRKR) announces advancements in immunopeptidomics, glycoproteomics, and other 4D-proteomics workflows at the 20th US Human Proteome Organization Congress 2024. The company introduces innovative software, methods, and tools to enhance post-genomic research, disease biology insights, and biomarker discovery.

Positive

• Bruker collaborates with Rapid Novor Inc. to develop Novor v2.0 software for de novo immunopeptidomic profiling, trained on over 1.4 million spectra mapping to more than 150,000 HLA peptides.
• TwinScape, a digital-twin performance monitoring engine, uses iRT peptide standards to ensure sustained peak performance in LC-MS and sample prep, facilitating multi-omics studies.
• Bruker introduces the glyco-PASEF method for ultra-high sensitivity 4D-glycopeptide analysis, offering novel software solutions like GlycoScape and MSFragger-Glyco for glycoproteomics research.
• Spectronaut 18 software is now accessible for Bruker ProteoScape users, enabling real-time 4D proteomics analysis with library-free searches using Biognosys directDIA technology.
• Biognosys launches a high-throughput ENRICHMENT plasma proteomics service for large-scale protein quantification, expanding research capabilities with over 4.5k proteins and 55k peptides at 1% FDR specificity.
• PreOmics introduces sample prep tools for proteomics with over 50 BeatBox placements for efficient cell lysis and high-performance FFPE/FF tissue homogenization.

Negative

• None.

Insights

Biotechnology Analyst

The recent announcement by Bruker Corporation regarding the advancement in proteomics technology is a significant stride in the field of biotechnology, particularly in the context of cancer immunotherapy research and glycoproteomics. The Novor V2.0 software, which enhances the timsTOF systems for immunopeptidomic profiling, represents a critical tool for identifying tumor-associated antigens. This development is poised to expedite the discovery and validation of new targets for cancer immunotherapy, which could lead to more personalized and effective treatment options.

Moreover, the introduction of the glyco-PASEF method for ultra-high sensitivity glycopeptide analysis is a noteworthy advancement. Glycoproteins play a pivotal role in numerous biological processes and diseases and their analysis is crucial for understanding disease mechanisms and developing biomarkers. The ability to analyze glycoproteins with increased sensitivity and specificity could lead to breakthroughs in the diagnosis and treatment of diseases with a glycoprotein component, such as autoimmune disorders and certain types of cancer.

Healthcare Technology Analyst

The integration of machine learning and advanced software tools like TwinScape and Spectronaut 18 into Bruker's proteomics technology suite signifies a leap in analytical capabilities. TwinScape's digital-twin technology, which leverages iRT peptide standards, is designed to ensure sustained peak performance and quality control in laboratories. This is particularly relevant for large-scale studies where data consistency and instrument reliability are paramount. Enhanced quality control will likely contribute to more robust multi-omics data, facilitating better cross-lab comparability and potentially accelerating the pace of scientific discovery.

Furthermore, the accessibility of Spectronaut 18 for Bruker ProteoScape users introduces a new dimension of flexibility and efficiency in proteomics research. The ability to perform library-free searches with directDIA could democratize high-throughput proteomics, making it more accessible to a broader range of research institutions and pharmaceutical companies. This, in turn, could stimulate innovation in drug discovery and development pipelines, ultimately benefiting patients.

Pharmaceutical Industry Analyst

From an industry perspective, the advancements announced by Bruker Corporation could have a considerable impact on the pharmaceutical sector, particularly in the areas of drug discovery and molecular diagnostics. The ENRICHMENT plasma proteomics service launched by Biognosys, which allows for the large-scale quantification of proteins, is a prime example of how high-throughput technologies are transforming the landscape of biomarker discovery and validation. The ability to quantify approximately 4,500 proteins with high specificity is a substantial enhancement over previous capabilities and could significantly shorten the timeline for identifying potential drug targets and biomarkers.

Additionally, the improvements in sample preparation tools, such as the BeatBox system for cell lysis and tissue homogenization, underscore the importance of efficiency and affordability in proteomic research. Streamlining these processes is critical for the scalability of proteomic studies, which can have a direct impact on the cost and speed of bringing new therapies to market. As the pharmaceutical industry continues to focus on personalized medicine, tools that enable the rapid and cost-effective analysis of biological samples will be increasingly valuable.

• Novor V2.0 software with novel ML algorithm trained on HLA peptides yields immunopeptidome from de novo peptide sequencing with further improved IDs
• TwinScape™ digital-twin technology with iRT™ standards supports highest timsTOF performance with intelligent feedback – well beyond ‘just up-time’
• New glyco-PASEF^® method for ultra-high sensitivity 4D glycopeptide analysis
• Spectronaut^® 18 software now available for Bruker ProteoScape™ users
• Biognosys launches high-throughput ENRICHMENT plasma proteomics service for large-scale quantification of ~4.5k proteins with ~55k peptides at 1% FDR specificity
• PreOmics^® sample prep tools for proteomics now with >50 BeatBox^® placements for fast cell lysis and affordable, high-performance FFPE/FF tissue homogenization

PORTLAND, Ore.--(BUSINESS WIRE)-- At the 20^th US Human Proteome Organization Congress 2024, Bruker Corporation (Nasdaq: BRKR) announced progress in immunopeptidomics, glycoproteomics and other CCS-enabled 4D-proteomics workflows. The rapid advances in deep, at-scale proteomics, glycomics and peptidomics research solutions complement other performance-leading life-science tools for the post-genomic era by Bruker. Together they enable post-genomic molecular and cell biology research, with key insights into disease biology and biomarkers for next-gen molecular diagnostics and drug discovery.

Bruker's Immunopeptidomics Workflow (Graphic: Business Wire)

The advances featured at US HUPO include improved machine-learning de novo sequencing (Novor V2.0), a novel high-performance monitoring digital-twin software (TwinScape), the new glyco-PASEF method for high-sensitivity glycopeptide analysis, and access to Spectronaut 18 for users of Bruker ProteoScape, a GPU-powered software for real-time 4D proteomics, now with access to library-free searches by Biognosys directDIA^®.

A. Advancing Cancer Immunotherapy Research

Bruker enhances its timsTOF HT and timsTOF Ultra systems with the new software Novor v2.0 for de novo immunopeptidomic profiling. Novor v2.0, developed in collaboration with Rapid Novor Inc., was trained on >1,400,000 spectra mapping to >150,000 HLA peptides for research on small amounts of patient material derived from fine needle biopsies.

Dr. Juliane Walz, Professor of Peptide-based Immunotherapy and Medical Director for Translational Immunology at Universitätsklinikum Tübingen in Germany commented: “Our research focuses on the field of immunology and the development of novel peptide-based immunotherapy concepts for tumor and infectious diseases. Bruker’s trapped ion mobility separation combination with time-of-flight mass spectrometry enables immunopeptidomics with high speed and sensitive detection of HLA-presented peptides. Applying this technology, we have expanded the benign reference immunopeptidome databases with >150,000 HLA peptides. This allows us to confidently define tumor-associated antigens to fast-track immunotherapy development.”

B. Peak timsTOF Performance using TwinScape

TwinScape is a new digital-twin performance monitoring and quality control engine, leveraging iRT peptide standards to support sustained peak performance in sample prep and LC-MS. For synergistic multi-omics studies in the post-genomic era, a combination of depth of coverage, robustness, and scalable quantitation is required. TwinScape enables larger controlled studies and valid cross-lab comparability.

Dr. Anne-Claude Gingras, VP of Research at Sinai Health, Director at Lunenfeld-Tanenbaum Research Institute, and Professor in Molecular Genetics in Toronto, Canada said: “We support a variety of projects in our proteomics facility. It is critical that our instruments are at peak performance and that we always have a pulse on them. The combination of Bruker ProteoScape, TwinScape and the Biognosys iRT kit have become integral for monitoring our instruments to ensure everything is operating up to highest standards. TwinScape is great for an over-time view of QC and system performance. It has been especially useful in pinpointing if there ever is a sample, LC or MS problem.”

C. New glyco-PASEF for Ultra-High Sensitivity 4D-Glycopeptide Analysis

Bruker presents the novel timsTOF glyco-PASEF method with polygon filtering developed with the Heck Group at Utrecht University, the GlycoScape software developed collaboratively with the Van Gool Group at Radboud University, and MSFragger-Glyco software developed by the Nesvizhskii Group at the University of Michigan.

Dr. Albert Heck, Professor of Chemistry and Pharmaceutical Sciences at Utrecht University and Scientific Director of the Netherlands Proteomics Center, noted: “I am pleased with our pioneering work in leveraging the unique strengths of the timsTOF platform for glycoproteomics, now translated to the glyco-PASEF method for research in glycobiology.”

Bruker is now offering GlycoScape™ real-time glycoproteomic software, developed with Alain van Gool’s team at Radboud University, for early access beta-testing.

Bruker also announces that the MSFragger-Glyco software now supports timsTOF data. Dr. Alexey Nesvizhskii, Professor of Computational Medicine, Bioinformatics and Pathology at University of Michigan, and creator of MSFragger, stated: “My team is gratified by the popularity of MSFragger for ultrafast searches, including the identification of post-translationally modified peptides. Our software suite supports the analysis of PASEF data, and we are delighted that Bruker now offers it with timsTOF instruments. This recognition acknowledges the broad applicability of our tools to timsTOF-generated proteomics data.”

D. Software Advances for dia-PASEF^®

The newest release of Bruker ProteoScape makes a Spectronaut 18 module available for dia-PASEF analysis, enabling real-time results using GPU computing, including directDIA for library-free searches. Bruker ProteoScape now also upgrades TIMS DIA-NN software to version 3.0 with improved quantitation accuracy.

About Bruker Corporation – the Emerging Leader of the Post-Genomic Era

Bruker (Nasdaq: BRKR) is enabling scientists 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 pharma applications, in microscopy and nanoanalysis, as well as in industrial applications. 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/20240311088724/en/

Media Contact

Petra Scheffer

Bruker Daltonics Marketing Communications

T: +49 (421) 2205-2843

E: petra.scheffer@bruker.com

Investor Relations Contact

Justin Ward

Sr. Director Investor Relations & Corp Development

T: +1 (978) 313-5800

E: Investor.Relations@bruker.com

Source: Bruker Corporation

FAQ

What software did Bruker Corporation develop for de novo immunopeptidomic profiling?

Bruker collaborated with Rapid Novor Inc. to develop Novor v2.0 software for de novo immunopeptidomic profiling, trained on over 1.4 million spectra mapping to more than 150,000 HLA peptides.

What is TwinScape and what is its purpose?

TwinScape is a digital-twin performance monitoring engine that uses iRT peptide standards to ensure sustained peak performance in LC-MS and sample prep, facilitating multi-omics studies.

What method did Bruker introduce for ultra-high sensitivity 4D-glycopeptide analysis?

Bruker introduced the glyco-PASEF method for ultra-high sensitivity 4D-glycopeptide analysis, offering novel software solutions like GlycoScape and MSFragger-Glyco for glycoproteomics research.

Which software is now accessible for Bruker ProteoScape users, enabling real-time 4D proteomics analysis with library-free searches?

Spectronaut 18 software is now accessible for Bruker ProteoScape users, enabling real-time 4D proteomics analysis with library-free searches using Biognosys directDIA technology.

What service did Biognosys launch for large-scale protein quantification?

Biognosys launched a high-throughput ENRICHMENT plasma proteomics service for large-scale protein quantification, expanding research capabilities with over 4.5k proteins and 55k peptides at 1% FDR specificity.

What tools did PreOmics introduce for proteomics?

PreOmics introduced sample prep tools for proteomics with over 50 BeatBox placements for efficient cell lysis and high-performance FFPE/FF tissue homogenization.