Molecular annotation engine

High-perfomance algorithms for high-resolution imaging mass spectrometry. Supporting open formats, molecular databases. Delivering molecular annotations, images, biological interpretation.
Free, open for everyone.

Contact us
DatasetCurrent analysisEngine analysisMolecule AMolecule B

will be able to process up to 100 datasets per day, each of 10 GB

How it works

A high-resolution imaging mass spectrometry dataset for one tissue section has 10.000.000 individual ion images. With 3 seconds for visual analysis of each image, looking
through all images would take 1 year.

No algorithms exist
for automated molecular annotation

Manual interpretation covers
up to 0.01% data only.

  • Slowing down the field progress
  • Hampering applications

Lack of global understanding of data is a bottleneck

The METASPACE engine is based on
efficient algorithms and big data technologies
to translate millions of ion images to hundreds of molecular images.

The modus operandi of METASPACE
is “data in, molecules out”. We aim at making
it deployable onto a workstation, cluster, or cloud, with the main instance to be freely available online.

Unified solution for everyone


The main instance of METASPACE will be freely available online to upload a dataset, browse through images of annotated molecules, and compare them between datasets.


A version for personal use will be provided that can be installed on a workstation or laptop without internet connection.


For high-capacity processing, we will make possible deployment of METASPACE onto a private cluster or into enterprise environment.


METASPACE is an open-source platform enabling creation of new products or services for spatial metabolomics. With a permissive license, it is free both for commerical and academic use or re-use.

Contributing to reproducible research

High-throughput molecular annotation with a controlled level of confidence makes possible to extract molecular knowledge from different datasets in a reproducible way enabling comparisons between replicates, users, and labs.

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Uniting expertise to achieve the goal


The new wave of ‘omics

Imaging mass spectrometry

Enabling untargeted metabolic imaging

Software development

Turning algorithms into user-friendly tools

Mass spectrometry

Workhorse of untargeted metabolomics


Key to interpretation of big imaging data


The project is funded by European Commission as a part
of Horizon 2020 program and unites 8 partners from 6 countries.

Theodore Alexandrov's team and header in 2 lines

We coordinate the project, participate in most of interactions, write part of algorythms and response for outreach.

Christoph Steinbeck

EBI leads outreach activities.

Zoltan Takats, Kirill Veselkov

ICL leads efforts on integrating LC-MS data, analysis of DESI-imaging data, and a case study on esophageal cancer.

Dennis Trede

SCiLS contributes with expertise in software development.

Pieter Dorrestein

UCSD leads a case study on cystic fibrosis.

Charles Pineau

UR1 contributes by profiding high-resolution imaging mass spectrometry infrastructure.

Lennart Martens

VIB contributes with the expertise in computational mass spectrometry and machine learning.

Oliver Panzer

ERS performs non-scientific management.

Advisory Board

To facilitate the impact of METASPACE from the project start, we composed the Advisory Board of experts from both academia and industry.

Mass spectrometry vendors

  • Bruker Daltonics
    Michael Becker
  • Thermo Fisher Scientific
    Alexander Makarov
  • Waters
    James Langridge
  • Shimadzu
    Ann-Christin Niehoff

Pharmaceutical industry

  • AstraZeneca
    Richard Goodwin
  • GSK
    Steve Castellino
  • Genentech
    Sheerin K. Shahidi-Latham
  • Novartis
    Markus Stoeckli
  • Pfizer
    Stacey Oppenheimer
  • Servier & Boeringer Ingelheim joining soon!

Scientific journals

  • Anal Chem
    Jonathan Sweedler, Ed.-in-Chief
    Joseph A. Loo, Associate Ed.
  • J Mass Spectrom
    Richard Caprioli, Ed.-in-Chief
  • Metabolomics
    Roy Goodacre, Ed.-in-Chief
  • Rapid Commun Mass Spec
    Dietrich Volmer, Ed

General and clinical metabolomics

  • TU Munich
    Kristina Schwamborn
  • U Notre Dame
    Amanda Hummon

Imaging mass spectrometry

  • Bayreuth U
    Andreas Roempp
  • Helmholtz Center München
    Axel Walch
  • Maastricht U
    Ron Heeren

High-resolution mass spectrometry

  • PNNL
    Ljiljana Pasa-Tolic
  • SpectroSwiss
    Yuri Tsybin


  • U of Jena
    Sebastian Boecker
  • U Washington
    Michael MacCoss

Open access

  • U of Cambridge
    Peter Murray-Rust

From now on METASPACE needs your attention

Please email us if interested to use METASPACE or would like to contribute


FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry
  • Palmer A,
  • Phapale P,
  • Chernyavsky I.
  • Lavigne R,
  • Fay D,
  • Tarasov A.
  • Kovalev V,
  • Fuchser J,
  • Nikolenko S.
  • Pineau C,
  • Becker M,
  • Alexandrov T.

Nature Methods (2016) doi:10.1038/nmeth.4072

Where imaging mass spectrometry stands: here are the numbers
  • Palmer A,
  • Trede D,
  • Alexandrov T.

Metabolomics (2016) 12: 107.

Serial 3D imaging mass spectrometry at its tipping point.
  • Palmer A,
  • Alexandrov T.

Bioinformatics, 2015, 31 (12): i375-i384.

Molecular cartography of the human skin surface in 3D.
  • Boulimani A,
  • Porto C,
  • Rath CM,
  • Wang M,
  • Guo Y,
  • Gonzalez A,
  • Berg-Lyon D,
  • Ackermann G,
  • Moeller Christensen GJ,
  • Nakatsuji T,
  • Zhang L,
  • Borkowski AW,
  • Meehan MJ,
  • Dorrestein K,
  • Gallo RL,
  • Bandeira N,
  • Knight R,
  • Alexandrov T,
  • Dorrestein P.

PNAS, approved March 6, 2015.

The challenge of on-tissue digestion for MALDI MSI — a comparison of different protocols to improve imaging experiments.
  • Hanna C. Diehl,
  • Birte Beine,
  • Julian Elm,
  • Dennis Trede,
  • Maike Ahrens,
  • Martin Eisenacher,
  • Katrin Marcus,
  • Helmut E. Meyer,
  • Corinna Henkel

Anal Bioanal Chem. 2015 Mar; 407(8):2223-43.


Past events

Recent tweets



RT @alexandrovteam: After attending #fosdem2017 by @metaspace2020 dev team the project configuration code will never smell again https://t.…



Milestone! 1st publication where METASPACE was used: Boughton, Hamilton, Adv Exp Med Biol



Have experience with imaging MS? Please complete our 2016 survey & spread word: Thank you!



Today we study how the field of imaging MS changed since 2015

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Feel free to contact us

Dr. Theodore Alexandrov, coordinatorEuropean Molecular Biology Laboratory Meyerhofstr. 1, 69117 Heidelberg, Germany
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