Bruker Introduces MetaboScape® 2.0 Solution for Metabolomics

TORONTO, Canada, August 22, 2016 – At the International Mass Spectrometry Conference (IMSC 2016), Bruker today announced the next-generation version 2.0 of its advanced MetaboScape® solution for metabolomics research and routine analysis.  This integrated solution for non-targeted metabolomics links impact II LC-QTOF-MS/MS data to the underlying biology based on metabolic pathway mapping.  MetaboScape 2.0 enables the annotation of unknown compounds and provides scientists with a higher degree of confidence in the identification of known metabolites through the use of high-resolution, accurate mass MS/MS fragment information.

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The chemical diversity of the metabolome and the almost infinite number of ways to perturb its balance presents a significant challenge to metabolomics researchers, who therefore require powerful, robust instruments to generate highest-quality data.  Due to its dynamic range of 5 orders of magnitude achieved at UHPLC speeds, combined with >50,000 Full-Sensitivity Resolution (FSR), and unique True Isotopic PatternTM high-fidelity isotopic ratio analysis of both precursor and product ions, the class-leading impact II mass spectrometer provides UHR-QTOF data at a superior quality level for the most challenging metabolomics samples.

For further productivity enhancements, flexible and powerful analysis software to process data and glean insights is a prerequisite for advanced metabolomics research solutions. The next-generation MetaboScape 2.0 solution offers the following benefits:

Automatic and confident identification of known compounds

The higher level of confidence in the identification of known compounds that MetaboScape 2.0 provides is derived from the user-definable levels for matching retention time, accurate mass, isotopic pattern information, and MS/MS spectral library spectra. A graphical Annotation Quality “AQ” representation (see Figure 1) provides confidence levels for each annotation.

Seamless annotation of unknown compounds

The integrated SmartFormula™ 3D feature provides highly specific molecular formula generation followed by structural assignment through CompoundCrawlerTM based public database queries and in silico fragmentation of structure candidates (see Figure 2).
A complementary MS/MS library query workflow, e.g. using the Bruker MetaboBASE Personal Library, allows for the assignment of compounds based on spectral similarity.

Assessing relevance and connecting data to biology

Using supervised and non-supervised statistics including PCA, t-Test, ANOVA, PLS and bucket correlation analysis combined with dedicated views quickly focus on the relevant information in complex metabolomics data sets. The mapping of identified metabolites on metabolic pathway maps using MetaboScape connects experimental data to biology.

Professor Pim Leonards at the Institute for Environmental Studies, VU University Amsterdam, The Netherlands, explains: “MetaboScape 2.0 will allow my team to mine complex data originating from environmental, non-targeted metabolomics studies. The confident identification of known compounds, in combination with the capability to automatically pinpoint and readily identify unknowns, is a powerful tool for assessing possible new metabolic pathways of neuro-active biocides.”

About MetaboScape 2.0

MetaboScape 2.0 software is part of the fully integrated Compass® Metabolomics Suite and provides non-targeted workflow capabilities. With the Compass PathwayScreener™ also being part of the Compass Metabolomics Suite, researchers can now get two sets of results for enhanced profiling from the same data set.  This is achieved by performing pathway-driven, targeted metabolomics analysis on the same data set used for non-targeted data mining.

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About the Bruker Corporation (NASDAQ: BRKR)

For more than 50 years, Bruker has enabled scientists to make breakthrough discoveries and develop new applications that improve the quality of human life.  Bruker’s high-performance scientific research instruments and high-value analytical solutions enable scientists to explore life and materials at molecular, cellular and microscopic levels.

In close cooperation with our customers, Bruker is enabling innovation, productivity and customer success in life science molecular research, in applied and pharma applications, in microscopy, nano-analysis and industrial applications, as well as in cell biology, preclinical imaging, clinical research, microbiology and molecular diagnostics.  For more information, please visit:

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Tony Lewtas
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Bruker Daltonics Division
T: +1 (978) 663 3660

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Bruker Corporation
T: +1 (978)-663-3660

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Automatic and confident identification of known compounds
(click to enlarge)

Figure 1: Automatic and confident identification of known compounds

Identification of known compounds, called de-replication, is essential to fully understand the biological context of metabolomics data. Confidence in ID is provided by matching retention time, accurate mass, isotopic pattern information, and MS/MS spectral library spectra according to user definable threshold levels and graphical representation of the achieved Annotation Quality.

Seamless annotation of unknown compounds
(click to enlarge)

Figure 2: Seamless annotation of unknown compounds

MetaboScape 2.0 simplifies identification of unknowns. The fully integrated, proprietary and unique SmartFormula™ 3D isotopic ratio routine for precursor and product ions automatically and confidently generates precise molecular formulae.  CompoundCrawlerTM provides hits for possible structures by accessing online databases. Subsequent in silico fragmentation of structure candidates provides the compound with the best score by matching measured fragemnt ions to generated fragment structures.


"metabolomics", "HRAM QTOF", "unknown ID", and "metabolic pathways"


  1. Bruker Poster Note PN-33: “Boosting compound identification confidence”
  2. Application Note LCMS-116: “What are we eating? MetaboScape Software; Enabling the De-replication and Identification of Unknowns in Food Metabolomics”
  3. MetaboScape 2.0 Brochure: Quickly Discover Metabolite Biomarkers and Use Pathway Mapping to Set them in a Biological Context