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Bruker is Ushering in the Age of Spatial Single-Cell Metabolomics

  • Novel unbiased, in situ Spatial Single-Cell Metabolomics (SSCM) enables high-throughput metabolic tissue characterization with single-cell resolution
  • New 5 µm microGRID™ technology for timsTOF® fleX MALDI mode provides virtually artifact-free small-molecule images across large field of view
  • Novel 4D-Metabolomics methods use CCS-Predict Pro AI/DL to enrich lipids, metabolite, and glycan libraries with molecular collision cross sections (CCS)

At the 18th International Conference of the Metabolomics Society, Bruker Corporation (Nasdaq: BRKR) announced key innovations for spatial multiomics with a focus on unbiased Spatial Single-Cell Metabolomics (SSCM) for probing differential cellular phenotypes based on the metabolic signature of tissues and single cells.

Combining SSCM with the recently announced MALDI HiPLEX-IHC workflow enables in situ single cell immunometabolomics studies that integrate metabolomics-based immune reprogramming with targeted proteomics. This single-cell multiomics workflow is enabled by the new microGRIDsmartbeam™ 3D MALDI source for timsTOF® fleX systems for sub-micron positioning for spatial resolution down to five micrometers (5 µm), virtually eliminating any artifacts in the co-registration of MALDI molecular images with optical microscopy.

Single-cell technologies have revolutionized the understanding of heterogeneous biological processes underlying cancer, regenerative medicine, aging, and liver diseases. Studying cell-to-cell tissue variation enhances translational research, for example, in the development of better cancer research methods for the development of therapeutics targeting rare tumor cells.

Professor Theodore Alexandrov, Head of the Metabolomics Core Facility and Molecular Medicine Partnership Unit at the EMBL in Heidelberg, Germany, will lead a new project called SpaceM in the BioStudio Faculty of the BioInnovation Institute in Copenhagen, Denmark, focusing on single-cell metabolomics for drug discovery and precision medicine.

Dr. Alexandrov commented: “We are in the process of developing the SpaceM technology for spatial single-cell metabolomics, developed at EMBL Heidelberg, into a platform for rapid drug discovery. As part of the BioStudio program at the BioInnovation Institute in Copenhagen, we will use a timsTOF fleX MALDI-2 imaging system for fast, sensitive, and specific in situ analyses of single cells to determine their metabolic states. In addition, the latest microGRID technology will provide us with the high spatial resolution needed to precisely interrogate single cells.”

Bruker today also announced the next-generation of its advanced MetaboScape® and TASQ® software for metabolomic profiling and quantitation. MetaboScape 2022b now features integration of CCS-Predict Pro machine learning. Accurate and reproducible CCS values measured on the timsTOF platform can be matched to CCS values predicted from compound libraries or biotransformation algorithms, adding an orthogonal dimension for confident compound annotation.

TASQ 2022b complements the established target screening and quantitation functionality by a CCS-enabled isotope tracing workflow module. Data processing for large scale stable isotope tracer experiments is simplified as key algorithms such as the correction for naturally occurring isotopes and fractional contribution of isotopic labels are provided.

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


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