MetaboScape

MetaboScape is an all-in-one software suite from Bruker designed for discovery metabolomics, lipidomics, phenomics, foodomics, environmental analysis, and pharmaceutical research. It processes non-targeted analyses from Bruker's ESI and MALDI Imaging instruments within a unified workflow, enabling users to pinpoint and identify drugs, metabolites, lipids, and glycans and place them in a biological context.

The software supports workflows ranging from basic compound identification to advanced statistical analysis, and operates on a client-server architecture that allows multiple users to share methods and access shared datasets, making it suitable for core facilities and large sample cohorts.

Core Data Processing: T-ReX Algorithm Family

• T-ReX 4D performs retention time alignment, deisotoping, and feature extraction for LC-MS and PASEF-based data, incorporating collisional cross section (CCS) values from ion mobility separation for additional identification confidence.
• T-ReX² and T-ReX³ support MALDI Imaging workflows in conjunction with SCiLS Lab software, enabling spatial profiling and CCS-enabled annotation of metabolites, lipids, glycans, and drug metabolites on timsTOF fleX systems.
• T-ReX 2D processes flow injection analysis (FIA) MRMS data from the chromatography-free MRMS aXelerate workflow, supporting high-throughput phenomics with mass resolutions exceeding 1 million and mass accuracies below 0.2 ppm.

Compound Identification Capabilities

• Annotation Quality (AQ) scoring provides five indicators of data quality, including CCS values as an orthogonal identification parameter.
• SmartFormula3D determines molecular formulas by matching accurate mass and isotopic patterns of both precursor and fragment ions.
• CompoundCrawler queries local and public databases using candidate molecular formulas to return possible structure candidates.
• MetFrag performs in silico fragmentation, matching theoretical fragment structures to measured MS/MS peaks and scoring the most likely structure.
• MS/MS bucket matching identifies chemically related compounds by grouping features with similar MS/MS spectra.
• Target compounds can be automatically annotated using user-defined Analyte Lists.
• Supports the MetaboBASE Personal Library, HMDB Metabolite Library, Bruker Sumner MetaboBASE Plant Library (including CCS values for over 130 compounds), and custom libraries.
• Data export in a format compatible with GNPS (Global Natural Products Social Molecular Networking).

Interactive User Interface and MS/MS Annotation Modes

• Dynamic Feature Tables allow navigation and filtering of large datasets.
• The context-sensitive MS/MS spectrum viewer adapts automatically to the annotation type, offering four dedicated modes: SF (SmartFormula) for molecular formula annotation of fragment peaks and neutral losses; LS (Lipid Species) for identification of side chain neutral losses and head group fragments; SL (Spectral Library) for butterfly plot comparison of measured and reference spectra; and MF (MetFrag) for mapping MS/MS peaks to substructures of the annotated compound.

Statistical Analysis and Biological Context

• Supervised and non-supervised statistical tools include PCA, t-test, ANOVA, PLS, and bucket correlation analyses.
• Pathway mapping places identified metabolites in a biological context.
• Time series plots track and semi-quantify changes in metabolites over time.
• Batch correction offsets sample effects in large cohorts.

Lipidomics Workflow

• Rule-based lipid class annotation follows Lipidomics Standards Initiative (LSI) guidelines to reduce over-annotation.
• Kendrick Mass Defect (KMD) plots visualise lipid compositional maps using homologous repeating units such as CH2.
• The customisable 4D Kendrick mass defect plot supports visualisation across four dimensions: x-axis, y-axis, colour scale, and bubble size, enabling validation of lipid class identifications and detection of false positives.
• CCS trends across lipid classes can be used to confirm annotations and assist in identifying unknowns.
• CCS-Predict Pro, a fully integrated tool, provides CCS prediction for small molecules and lipids.

Pharma and Drug Metabolite Workflows

• Local BioTransformer-based metabolite prediction supports annotation of drug metabolites and xenobiotics such as pesticides, toxins, and narcotics.
• Applicable to liquid samples and directly to tissue via the SpatialOMx workflow.
• Compatible with LC-MS/MS, LC-PASEF, FIA-MRMS, and MALDI Imaging acquisition modes.
• Time series plots enable tracking and semi-quantification of drug metabolite changes over time.

In Silico Derivatization

• Automatically generates derivatized structures for target compounds based on customisable reaction definitions.
• Predicts product fragmentation and CCS values for derivatized structures.
• Retains reference to original underivatized structures throughout the workflow.

SpatialOMx Imaging Workflow

• Combines MetaboScape with SCiLS Lab to annotate MALDI Imaging data with compound information.
• Supports detection of additional compound classes using the MALDI-2 source on the timsTOF fleX.
• Enables CCS-enabled spatial annotation of metabolites, lipids, and glycans in tissue images.

MetaboScape integrates with complementary Bruker tools including TASQ for targeted quantification, SCiLS Lab for mass spectrometry imaging, and CCS-Predict Pro for CCS prediction. Semi-targeted workflows in MetaboScape are designed to work alongside TASQ for absolute quantification. The software supports data from Bruker timsTOF and MRMS instrument platforms and is compatible with the scimaX MRMS system for ultra-high resolution phenomics applications.