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.

Interested to join alpha-testing?

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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

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

Claire O'Donovan

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 Daltoniks
    Rohan Thakur
  • 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 Biomedical Research
    Markus Stoeckli
  • Pfizer
    Stacey Oppenheimer
  • Sanofi
    Jens Riedel
  • Boeringer Ingelheim
    Michael Becker
  • Servier
    Georges Da Violante

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


Three dimensional cartography of microbiome and metabolome data onto radiological images of the human lung
  • Garg N,
  • Wang M,
  • Hyde E,
  • da Silva RR,
  • Melnik AV,
  • Protsyuk I,
  • Bouslimani A,
  • Lim YW,
  • Wong R,
  • Humphrey G,
  • Ackermann G,
  • Spivey T,
  • Brouha SS,
  • Bandeira N,
  • Lin GY,
  • Rohwer F,
  • Conrad DJ,
  • Alexandrov T,
  • Knight R,
  • Dorrestein P,

Cell Host & Microbe 22, 705–716

N-acyl Taurines and Acylcarnitines Cause an Imbalance in Insulin Synthesis and Secretion Provoking β Cell Dysfunction in Type 2 Diabetes
  • Aichler M,
  • Borgmann D,
  • Krumsiek J,
  • Buck A,
  • MacDonald PE,
  • Manning Fox JE,
  • Lyon J,
  • Light PE,
  • Keipert S,
  • Jastroch M,
  • Feuchtinger A,
  • Mueller NS,
  • Sun N,
  • Palmer A,
  • Alexandrov T,
  • Hrabe de Angelis M,
  • Neschen S,
  • Tschöp MH,
  • Walch A

Cell Metabolism. Volume 25, Issue 6, 6 June 2017, Pages 1334-1347.e4

Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae
  • Luzzatto-Knaan T,
  • Garg N,
  • Wang M,
  • Glukhov E,
  • Peng Y,
  • Ackermann G,
  • Amir A,
  • Duggan BM,
  • Ryazanov S,
  • Gerwick L,
  • Knight R,
  • Alexandrov T,
  • Bandeira N,
  • Gerwick WH,
  • Dorrestein P.

eLife 2017;6:e24214

From single cells to our planet—recent advances in using mass spectrometry for spatially resolved metabolomics
  • Petras D,
  • Jarmusch A,
  • Dorrestein P.

Current Opinion in Chemical Biology 2017 vol: 36 pp: 24-31

Imaging of Esophageal Lymph Node Metastases by Desorption Electrospray Ionization Mass Spectrometry
  • Abbassi-Ghadi N,
  • Golf O,
  • Kumar S,
  • Antonowicz S,
  • McKenzie JS,
  • Huang J,
  • Strittmatter N,
  • Kudo H,
  • Jones EA,
  • Veselkov K,
  • Goldin R,
  • Takats Z,
  • Hanna GB.

Cancer Research (2016) vol: 76, pp: 5647-5656

Integration of 3D multimodal imaging data of a head and neck cancer and advanced feature recognition
  • Lotz JM,
  • Hoffmann F,
  • Lotz J,
  • Heldmann S,
  • Trede D,
  • Oetjen J,
  • Becker M,
  • Ernst G,
  • Maass P,
  • Alexandrov T,
  • Guntinas-Lichius O,
  • Thiele H,
  • von Eggeling F.

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, In Press (Available online 1 September 2016).

Lifestyle chemistries from phones for individual profiling
  • Bouslimani A,
  • Melnik AV,
  • Xu Z,
  • Amir A,
  • da Silva RR,
  • Wang M,
  • Bandeira N,
  • Alexandrov T,
  • Knight R,
  • Dorrestein PC

Proc Natl Acad Sci U S A 2016 Nov 29 13(48):E7645-E7654

Investigating the spatial distribution of growth anomalies affecting Montipora capitata corals in a 3-dimensional framework
  • Burns JHR,
  • Alexandrov T,
  • Ovchinnikova E,
  • Gates RD,
  • Takabayashi M

Journal of Invertebrate Pathology October 2016 vol: 140, pp: 51–57

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats
  • Petras D, et al.

Anal. Chem. 2016 88 (22), pp 10775–10784

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen
  • Garg N et al.

mSystems 1(6):e00139-16.

Data for spatial analysis of growth anomaly lesions on Montipora capitata coral colonies using 3D reconstruction techniques
  • Burns JHR,
  • Alexandrov T,
  • Ovchinnikova K,
  • Gates RD,
  • Takabayashi M

Data in Brief December 2016 vol: 9, pp: 460–462

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.


Past events

Recent tweets



RT @thalexandrov: @KPMProject is the biggest-funded #kidney project by @NIH. Check out the approach developed collaboratively by 15 institu…



RT @Lachlan_EMBL: I'm getting great feedback from our users (and future users) at @OurCon. Really looking forward to implementing these ide…

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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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