MetaboScape

MetaboScape^® is a fully integrated SW solution which can be used across application areas, including discovery metabolomics, lipidomics, phenomics, foodomics, environmental, pharma and imaging.

The MetaboScape all-in-one software provides users with the flexibility to support semi-targeted discovery and non-targeted screening workflows ranging from processing, metabolite identification, statistics to pathway mapping. MetaboScape supports data acquired from both LC and high-throughput flow injection (FIA) MRMS aXelerate^® workflows. Furthermore, MS/MS data acquired on Bruker's QTOF and timsTOF systems and high-speed PASEF^® data from the timsTOF Pro and timsTOF fleX are supported. Finally, SpatialOMx^® MALDI imaging workflows from Bruker’s MRMS & timsTOF fleX are also supported in this solution.

Product configuration and licenses: The software product must be installed on a dedicated Windows 10 64-bit processing workstation which is not part of this product configuration. The minimal hardware requirements correspond to a HP Z4 workstation with 16GB RAM (64GB RAM or more recommended for timsTOF data), a CPU with at least 4 Cores and a 2TB HDD.

Included: Three floating licenses for MetaboScape. With the order, a valid customer email address must be specified. The software license ticket will be sent to this email address.

Libraries must be purchased separately. Bruker recommends using MetaboScape in combination with the MetaboBASE^® Personal Library comprised of accurate mass and MS/MS spectra from >100,000 reference standards.

WORKFLOWS

Metabolomics / Phenomics: MetaboScape is Bruker's all-in-one software for discovery metabolomics and phenomics. Its main purpose is to pinpoint and identify compounds that change as a result of perturbation or disease. The initial processing by the T-ReX^® algorithm comprises parameter-free retention time alignment and region-complete feature extraction to ensure robust data for confidence in statistical results. Different filtering, normalization, scaling and within batch-correction options complete the set of data preprocessing tools - a prerequisite for large phenomics studies. For ion-mobility enhanced TIMS and PASEF® 4D-Metabolomics™ data, T-ReX 4D automatically extracts CCS values that are used as additional criterion complementing the Annotation Quality Scoring. This intuitive tool gives visual feedback on the matching of all quality factors at a glance (exact mass, retention time, isotopic pattern quality, MS/MS spectrum and CCS value). To simplify the identification of knowns, MetaboScape supports the Bruker MetaboBASE^® Personal Library, Bruker HMDB Metabolite Library, the Bruker Sumner MetaboBASE Plant Library (including CCS values for >130 compounds), as well as custom libraries. Annotated data sets can be seamlessly mapped on metabolic pathways within MetaboScape and the generated data can be exported in various spreadsheet formats for further analysis.

Customized data export to a file format suitable for import at GNPS (https://gnps.ucsd.edu) is also supported. This helps to turn complementary data from Bruker's LC-(TIMS)-QTOF-MS/MS, GC-APCI-QTOF-MS and MRMS into useful knowledge.

Lipidomics: In lipidomics research, the confident identification of lipids is crucial. The 4D-Lipidomics™ workflows integrated in MetaboScape simplify these tasks tremendously. Rule based annotation routines enable the identification of lipid species taking into consideration the Lipidomics Standards Initiative guidelines. For timsTOF and timsTOF Pro / fleX PASEF data, MetaboScape offers the CCSPredict lipid confirmation tool. Based on machine learning, it predicts CCS values for lipid structures, which further increases the confidence in annotations. CCS and retention time aware Kendrick Mass Defect (KMD) plots offer an intuitive 4D visualization tool for the manual investigation of lipid assignments and the detection of novel lipid species.

Pharma: For the assignment of drug and xenobiotic metabolites MetaboScape supports a local BioTransformer (http://biotransformer.ca/) based metabolite prediction. Additionally, changes in time of these metabolites can be tracked and semi-quantified by using integrated time series plots.

Imaging / SpatialOMx: The SpatialOMx workflow combining MetaboScape and SCiLS^TM Lab softwares, now also offers a unique CCS-Aware annotation of features (drug metabolites, lipids, glycans) for MALDI molecular tissue images.