What does MetaboScape do?

It is data-processing software for metabolomics and mass spectrometry imaging, automatically extracting molecular features, performing spatial visualization and statistical modeling, covering the full chain from spectrum to molecular map.

Which imaging-source data does it support?

It can import imaging data generated by sources such as MALDI, DESI, and LDPI, extracting and annotating by m/z features, supporting standard-format exchange.

What is the relationship between MetaboScape and SCiLS Lab?

Both are mass spectrometry imaging analysis software with overlapping functions (feature extraction, visualization, statistics); MetaboScape is often bundled with specific vendor high-resolution platforms, while SCiLS Lab is also common in the MALDI ecosystem, selectable by platform and format compatibility.

What data format does MetaboScape require?

It supports vendor formats and standard exchange formats (such as imzML); specific import capability depends on version and platform, it is recommended to confirm the compatibility of the analyzer used.

Technology Primer · Mass Spectrometry Imaging

MetaboScape Metabolomics Imaging Software

MetaboScape is data-processing software for metabolomics and mass spectrometry imaging, providing molecular feature extraction, spatial visualization, and statistical modeling capabilities, often used for imaging data analysis paired with high-resolution mass spectrometers (such as Bruker timsTOF, MALDI-TOF).

Table of Contents
Core Function: From Spectrum to Molecular Map Connection with Mass Spectrometry Imaging Statistics and Biological Interpretation Selection and Ecosystem Positioning

MetaboScape Metabolomics Imaging Software — schematic diagram

Core Function: From Spectrum to Molecular Map

MetaboScape centers on molecular features, automatically clustering ions from massive imaging spectra, de-isotoping, aligning retention time and m/z, generating an annotation-ready feature list, and then mapping features back to spatial coordinates to form ion images.

Its workflow covers the full chain from raw spectrum import, feature extraction, database annotation to spatial visualization, reducing manual screening cost, suitable for large-field, many-pixel imaging datasets.

Connection with Mass Spectrometry Imaging

The software can import imaging data generated by sources such as MALDI, DESI, and LDPI, supporting standard-format exchange and presenting molecular spatial distribution as heat maps and overlay maps. Data from ambient matrix-free sources are also extracted and annotated by m/z features.

The annotation step relies on built-in or custom databases (such as metabolite and lipid libraries), combined with mass accuracy and fragment (MS/MS) information to improve assignment credibility; unknown peaks can be exported for subsequent standard verification.

Statistics and Biological Interpretation

MetaboScape provides region comparison, differential-feature screening, and basic statistical modeling, helping users advance from where is the signal to which molecules distinguish regions/groups, connecting to the biological questions of spatial metabolomics.

Its results can be registered with histological images (H&E, IHC) to achieve molecular-morphology joint interpretation; the export format is compatible with downstream tools and the imzML ecosystem.

Selection and Ecosystem Positioning

MetaboScape is often provided with specific vendor high-resolution platforms, suitable for users already within the corresponding ecosystem; if using other analyzers (such as Orbitrap, Q-TOF), data-import compatibility must be confirmed. Alternatives include SCiLS Lab, MSiReader, etc.

For matrix-free ambient imaging (LDPI/DPI) users, software selection prioritizes data-format compatibility to ensure imaging spectra can be correctly imported and annotated.

Frequently Asked Questions (FAQ)

What does MetaboScape do?: It is data-processing software for metabolomics and mass spectrometry imaging, automatically extracting molecular features, performing spatial visualization and statistical modeling, covering the full chain from spectrum to molecular map.
Which imaging-source data does it support?: It can import imaging data generated by sources such as MALDI, DESI, and LDPI, extracting and annotating by m/z features, supporting standard-format exchange.
What is the relationship between MetaboScape and SCiLS Lab?: Both are mass spectrometry imaging analysis software with overlapping functions (feature extraction, visualization, statistics); MetaboScape is often bundled with specific vendor high-resolution platforms, while SCiLS Lab is also common in the MALDI ecosystem, selectable by platform and format compatibility.
What data format does MetaboScape require?: It supports vendor formats and standard exchange formats (such as imzML); specific import capability depends on version and platform, it is recommended to confirm the compatibility of the analyzer used.

Get Specifications & Quotation

To obtain detailed specifications, compatible models, or a quotation for the MSI LDPI / DPI full series imaging ion sources, visit the Neo-Source official website, or contact the official team for compatibility advice tailored to your mass spectrometer (Agilent / SCIEX / Thermo and other mainstream MS).

SCiLS Lab Mass Spectrometry Imaging Analysis Software imzML Mass Spectrometry Imaging Data Standard Format MALDI Mass Spectrometry Imaging (MSI)DESI

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