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

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.

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.