Bruker Launches de novo Sequencing for Immunopeptidomics, Library-Free dia-PASEF, Mass Dynamics Knowledge Visualization

Rhea-AI Summary

Bruker Corporation (NASDAQ: BRKR) has unveiled significant advancements in bioinformatics at the 19th US HUPO conference. Key highlights include the launch of the PaSER™ Novor sequencing algorithm, enhancing immunopeptidomics with real-time results derived from over 1.7 million data points. The updated dia-PASEF data analysis features library-free TIMS DIA-NN software, improving quantification accuracy. Additionally, a partnership with Mass Dynamics introduces advanced visualization tools for 4D-Proteomics. These innovations aim to enhance proteomic workflows, particularly for small tumor biopsy samples, and are expected to facilitate faster clinical outcomes.

Positive

• Launch of the PaSER Novor algorithm enhances accuracy and speed for immunopeptidomics.
• Real-time sequencing capabilities derived from extensive data points improve efficiency.
• Collaboration with Mass Dynamics introduces advanced visualization for proteomics.
• Updates to dia-PASEF data analysis enhance quantification accuracy.

Negative

• None.

• PaSER™ Novor faster, real-time de novo sequencing for immunopeptidomics
• Library-free dia-PASEF® analysis with PaSER 2023b proteomics software
• Partnership with Mass Dynamics for 4D-Proteomics™ knowledge visualization

CHICAGO--(BUSINESS WIRE)-- At the 19th US HUPO, Bruker Corporation (Nasdaq: BRKR) announced important bioinformatics launches for 4D-Proteomics on the timsTOF platform: A novel de novo sequencing algorithm was developed in collaboration with Rapid Novor Inc., using over 1.7 million PASEF data-points to improve accuracy and speed for immunopeptidomics in real-time. The unmatched sensitivity of the timsTOF SCP system coupled to the new PaSER Novor algorithm delivers a significant performance boost for immunopeptidomics, especially for small tumor biopsy samples.

timsTOF SCP ultra-high sensitivity MS (Photo: Business Wire)

dia-PASEF data analysis using library-free TIMS DIA-NN software now features further improved quantification accuracy, while Mass Dynamics graphical visualization and statistical cloud software now seamlessly integrates with 4D-Proteomics dia-PASEF data.

A. PaSER Novor for Immunopeptide Sequencing

With PaSER Novor, Bruker launches advanced capabilities for immunopeptidomics, developed in collaboration with Rapid Novor Inc., a Canadian software and CRO services company for antibody sequencing.

Immunopeptidomics requires the sequencing of peptides that are not proteolytic in nature from small tumor biopsy samples on the timsTOF SCP ultra-high sensitivity platform. The search space for proteomics database algorithms can become too big for accurate searches, resulting in low reproducibility and long search times. PaSER Novor derives the peptide sequence from fragment ion spectra de novo after training with over 1.7 million timsTOF data points for real-time results using the GPU-enabled Bruker PaSER proteomics software platform.

Professor Tony Purcell, Head Immunoproteomics Laboratory at Monash University, said: “De novo searches have been a critical aspect in my lab’s research for many years. This novel algorithm delivers results with accuracy at the speed of data acquisition and enables immunopeptidomics at scale and in real time. This has major implications in how fast my group can translate research into actionable information, and it pushes this workflow even closer to delivering clinical patient impact on an unprecedented timescale.”

B. TIMS-DIA-NN 2.0 Enables Library-free dia-PASEF

TIMS DIA-NN is a CCS-centric version of DIA-NN [1] with significant enhancements. TIMS DIA-NN 2.0 can now process dia-PASEF data in a library free approach with further improved quantification accuracy through novel machine learning capabilities.

Dr. Brett Phinney, Director UC Davis Proteomics Core facility, commented: “Proteomics has come a long way, but chromatography and data analysis are just as important as the mass spectrometry instruments. Stable chromatography over large sample cohorts, coupled with real-time search for DDA and DIA have brought the efficiency of my lab to new levels, and this only gets better with library-free search capabilities of TIMS DIA-NN.”

C. Graphical Knowledge Visualization by Mass Dynamics for 4D-Proteomics

Through Bruker’s collaboration with Prof. Andrew Webb at WEHI, co-founder of Mass Dynamics Pty Ltd - a software company in Australia, timsTOF 4D-Proteomics can now leverage Mass Dynamics statistical analyses, interactive and intuitive visualizations for knowledge extraction in proteomics. Beyond lists of protein groups, volcano plots, protein-protein interactions, PCA plots and a myriad of other visualizations facilitate biological and disease insights.

Co-founder and CEO of Mass Dynamics Paula Burton stated: “The integration of PaSER’s real-time search and Mass Dynamics’ discovery service is a formidable alliance. Life scientists can now focus on biological questions and leverage proteomics for answers.”

Dr. Dennis Trede, Director of Informatics, Bruker Life Sciences Mass Spectrometry, commented: “We are pleased that our partnerships with Rapid Novor and Mass Dynamics are resulting in meaningful proteomics advances. The ultra-high sensitivity of the timsTOF SCP with Rapid Novor now enable at scale immunopeptidomics from small tumor biopsies.”

All Bruker software solutions announced at US HUPO can be used with all models of the timsTOF platform: timsTOF Pro 2, timsTOF HT, timsTOF SCP, and timsTOF fleX. The Biognosys Spectronaut® 17 software, with its novel Direct DIA+ capability, launched at the International HUPO Cancun meeting, and also fully supports dia-PASEF timsTOF data.

References:

1. Nat Commun. 2022 Jul 8;13(1):3944. https://doi.org/10.1038/s41467-022-31492-0.

About Bruker Corporation (Nasdaq: BRKR)

Bruker is enabling scientists to make breakthrough 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 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. Please visit www.bruker.com.

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Source: Bruker Corporation

FAQ

What is the PaSER Novor algorithm launched by Bruker (BRKR)?

The PaSER Novor algorithm is a novel sequencing algorithm that improves real-time accuracy and speed for immunopeptidomics using over 1.7 million data points.

How does the new dia-PASEF analysis improve results for Bruker (BRKR)?

The updated dia-PASEF analysis featuring library-free TIMS DIA-NN software enhances quantification accuracy and efficiency.

What partnership did Bruker (BRKR) announce for knowledge visualization?

Bruker announced a partnership with Mass Dynamics to provide advanced graphical visualizations for 4D-Proteomics.

What are the implications of the new technologies for clinical outcomes related to BRKR?

These technologies aim to expedite immunopeptidomics from small tumor biopsies, potentially leading to faster clinical results.