METASPACE docs

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What's new ​

August 2026 ​

Cross-dataset statistical analysis (Pro) ​

A new Pro feature for comparing molecular abundance across datasets is now documented, alongside a reorganized sidebar section for it.

Features

  • Cross-Dataset Statistical Analysis — builds an Experiment from regions (ROIs, segmentation clusters, or whole datasets) across multiple datasets, tagged with sample metadata, and tests differential ion abundance between conditions using a limma-based moderated statistical model — robust even with as few as 3 replicates per condition
  • Existing Multi-Dataset Comparison page moved from Visualization into a new Cross-Dataset Comparison category, alongside the new feature

Interpretation guide

  • Understanding Cross-Dataset Statistical Results — explains why limma is used instead of a plain t-test or Wilcoxon test, how empirical Bayes moderation and replicate correlation work conceptually, how to read omnibus vs. pairwise results, and what each design warning means

RMS and median normalization ​

The TIC normalization checkbox in the ion image viewer has been replaced by a Normalization dropdown offering three per-pixel methods. TIC remains the most commonly used option and the recommended starting point.

Features

  • RMS and median normalization added alongside TIC, selectable from the normalization dropdown on the annotation page
  • Normalization is also available on the multi-dataset comparison page
  • Datasets processed before this release need to be reprocessed for RMS and median to become available

Documentation

June 2026 ​

Spatial pattern analysis (Pro) ​

Two new Pro features for spatial pattern analysis are now documented.

Features

  • Spatial Segmentation — automatically partitions dataset pixels into chemically coherent tissue regions without manual ROI drawing; includes cluster markers panel, heatmap, and diagnostics
  • ROI Differential Analysis — identifies metabolites enriched or depleted in a selected ROI vs. all other regions, using log₂ fold change and AUC as effect-size metrics

Interpretation guides

May 2026 ​

Stable-isotope labeling in custom databases ​

Features

  • Custom Databases — custom databases now support stable-isotope labeled compounds; encode labeled atoms with pseudo-element symbols (Cx, Nx, Hx, Ox, Sx) directly in the formula column for ¹³C, ¹⁵N, ²H, ¹⁸O, and ³⁴S tracing experiments

April 2026 ​

Documentation site launch ​

This is the first release of the METASPACE documentation site. It covers the core platform features, interpretation guides, and submission workflows.

Getting started

  • Overview of the platform and a typical METASPACE workflow
  • Dataset organization with groups, members, and projects

Features

  • Ion image visualization, multi-channel viewer, and optical image overlay
  • Multi-dataset comparison
  • ROI selection for spatial pattern analysis
  • Sharing and publishing datasets and projects
  • Custom databases, METASPACE Converter, Detectability App, and Python Client
  • imzML Browser: spectral visualization and reference peak normalization

Interpretation guides

  • Understanding the annotation page, MSM scoring, and FDR
  • Off-sample filtering
  • Colocalization

Submission guides

  • Exporting data to imzML format
  • The upload page walkthrough
  • Metadata recommendations