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Bruker Launches Ultimate Sensitivity timsTOF Ultra 2 To Enable New Research Paradigms in Single-Cell and Subcellular Proteomics

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At the 72nd ASMS meeting, Bruker Corporation (Nasdaq: BRKR) launches the new top-of-the-line timsTOF Ultra 2 system with significantly further enhanced sensitivity for deep profiling of small cells, subcellular organelles, as well as increased sample loading flexibility. Together with new Spectronaut 19 software and the novel PreOmics ENRICHplus kit, Bruker is setting new 4D-Proteomics standards from highest sensitivity to large-scale, deep plasma proteomics. Bruker is also introducing OmniScape software for top-down sequence confirmation and de novo sequencing for intact, undigested proteoforms, dissociated in the mass spectrometer.

*Bruker Advances Ultimate Sensitivity with new timsTOF Ultra 2*

The new timsTOF Ultra 2 delivers ultimate sensitivity of up to 50% more protein groups and up to 100% more peptides on just 25 pg of protein digest, i.e. only 1/10th the protein mass of a HeLa cell. This makes timsTOF Ultra 2 the best choice to investigate immune homeostasis surveying low abundance proteins from small peripheral blood mononuclear cells (PBMCs), or from bacterial cells comprising the microbiome, or for immunopeptidomics to discover cancer neoantigens from fine needle biopsies.

New ion charge control (ICC2.0) software provides sample loading flexibility from low picogram amounts to about a microgram of protein digest.

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Bruker ProteoScape™ software now integrates Spectronaut 19 (SN19) software from Biognosys, the gold-standard for data-independent analysis (DIA). The new SN19 offers significantly improved search engine AI , advanced quantification, and allows precise predictions of timsTOF’s unique collision cross sections (DeepCCS), retention time (DeepiRT) and fragment ion intensity (DeepFrag), resulting in a 13% average increase in protein group identifications and improvements in quantification precision. See Biognosys Press Release

Bruker once again intends to offer field upgrades to the timsTOF Ultra 2 for timsTOF Ultra/SCP customers.

*PreOmics launches Reproducible, Affordable ENRICHplus Deep Plasma 4D-Proteomics Solution, Leveraging the Proven Robustness of the timsTOF HT*

The new single particle PreOmics ENRICHplus kit and the timsTOF HT now deliver up to 7-fold improvement in protein identification and quantification versus neat plasma. The increased depth of coverage, together with field-proven throughput and robustness of the timsTOF HT enables deep plasma proteomics at scale. See PreOmics Press Release

Dr. Roman Fischer, Associate Professor and Head of Discovery, Proteomics Facility, University of Oxford, UK, stated: "timsTOF technology, together with ENRICHplus, is changing the way we do plasma proteomics. On our timsTOF Pro we achieve on average 3800 protein identifications per sample with a throughput of 60 samples per day, while only using 20 µl of plasma. We never before achieved such depth with a single run of plasma, now enabling us to detect tissue leakage proteins and other low abundant potential biomarkers for cancer and neurodegenerative diseases. Together with the robust timsTOF system, ENRICHplus is game-changing for deep, affordable plasma proteomics at scale."

*Bruker Launches OmniScape Top-Down Software for Analysis of Intact Proteins*

Bruker is introducing OmniScape, the first top-down protein sequence software that covers protein de novo sequencing and lead sequence identification through homology searches for detailed proteoform analysis.

Dr. Boris Krichel, University of Wisconsin-Madison, summarized: “I am excited about the de novo sequencing to discover and annotate proteins in untargeted top-down proteomics. The most impressive function of OmniScape is the automatic suggestion of matching proteoforms based on multiple variable modifications.”

OmniScape supports different data types from LC-CCS-MS/MS, enabling for example the analysis of multiply phosphorylated proteins. Its ability to integrate different datasets yields very high sequence coverages, providing reliable sequence calls and PTMs. OmniScape can also process MALDI-ISD top-down spectra from the timsTOF fleX and axial MALDI instruments including the new neofleX, as well as data from non-Bruker instruments as a one-for-all top-down protein sequencing and isoform determination software solution.

Dr. Christian Isak Jørgensen, Senior Science Manager, Novonesis, Denmark, added: “OmniScape addresses a real need in the biotech industry producing recombinant proteins.”

*Novel Acquisition and Computational Capabilities for 4D-Glycoproteomics*

Bruker is introducing GlycoScape , the first real-time glycoproteomic software. GlycoScape has been developed in collaboration with the Radboud University Medical Center in the public-private partnership project EnFORCE led by Dr. Hans Wessels [1]. The software can identify glycopeptides on-the-fly as data are acquired and without the need to rely on glycan libraries, not only enabling identification of previously unreported glycans, but significantly minimizing false negative results. The unbiased read-out of glycoproteomic data by GlycoScape is critical for the advancement of glycobiology in translational and clinical research as these important research fields become accessible in the post-genomic era.

Dr. Hans Wessels, Senior Researcher at Radboud University in Nijmegen highlighted key advantages: “GlycoScape opens up the analysis of glycoproteomic mass spectrometry data from the timsTOF platform for on-the-fly processing without glycan database restrictions.”

GlycoScape leverages the glyco-PASEF method for ultra-sensitive and rapid glycoprotein data acquisition, using stepped energy CID and oxonium-ion-gated polygon-filtering, that was developed in collaboration with Prof. Albert Heck’s group at Utrecht University.

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.”